x What's hot today: Current papers in developmental biology and gene function

What's hot today:
Current papers in developmental biology and gene function


Friday, December 15th

November 2017
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Brown, E. B., Patterson, C., Pancoast, R. and Rollmann, S. M. (2017). Artificial selection for odor-guided behavior in Drosophila reveals changes in food consumption. BMC Genomics 18(1): 867. PubMed ID: 29132294
Appropriate behavioral responses to the chemical cues of predators are important for organismal survival and can influence traits such as organismal life span and food consumption. However, understanding the genetic mechanisms underlying odor-guided behavior, correlated responses in other traits, and how these constrain or promote their evolution, remain an important challenge. This study performed artificial selection for attractive and aversive behavioral responses to four chemical compounds, two aromatics (4-ethylguaiacol and 4-methylphenol) and two esters (methyl hexanoate and ethyl acetate), for thirty generations. Artificial selection for odor-guided behavior revealed symmetrical responses to selection for each of the four chemical compounds. Next, whether selection for odor-guided behavior resulted in correlated responses in life history traits and/or food consumption. We found changes in food consumption upon selection for behavioral responses to aromatics was tested. In many cases, lines selected for increased attraction to aromatics showed an increase in food consumption. RNA sequencing of lines selected for responses to 4-ethylguaiacol was performed to identify candidate genes associated with odor-guided behavior and its impact on food consumption. The study detected 91 genes that were differentially expressed among lines, many of which were associated with metabolic processes. RNAi-mediated knockdown of select candidate genes further supports their role in odor-guided behavior and/or food consumption. This study identifies novel genes underlying variation in odor-guided behavior and further elucidates the genetic mechanisms underlying the interrelationship between olfaction and feeding.
Chen, D., Kolomenskiy, D., Nakata, T. and Liu, H. (2017). Forewings match the formation of leading-edge vortices and dominate aerodynamic force production in revolving insect wings. Bioinspir Biomim [Epub ahead of print]. PubMed ID: 29052556
In many flying insects, forewings and hindwings are coupled mechanically to achieve flapping flight synchronously while being driven by action of the forewings. How the forewings and hindwings as well as their morphologies contribute to aerodynamic force production and flight control remains unclear. This study demonstrates that the forewings can produce most of the aerodynamic forces even with the hindwings removed through a computational fluid dynamic study of three revolving insect wing models, which are identical to the wing morphologies and Reynolds numbers of hawkmoth (Manduca sexta), bumblebee (Bombus ignitus) and fruitfly (Drosophila melanogaster). The forewing morphologies match the formation of leading-edge vortices (LEV) and are responsible for generating sufficient lift forces at the mean angles of attack and the Reynolds numbers where the three representative insects fly. The LEV formation and pressure loading keep almost unchanged with the hindwing removed, and even lead to some improvement in power factor and aerodynamic efficiency. Moreover, the results indicate that the size and strength of the LEVs can be well quantified with introduction of a conical LEV angle, which varies remarkably with angles of attack and Reynolds numbers but within the forewing region while showing less sensitivity to the wing morphologies. This implies that the forewing morphology very likely plays a dominant role in achieving low-Reynolds number aerodynamic performance in natural flyers as well as in revolving and/or flapping micro air vehicles.
Anreiter, I., Kramer, J. M. and Sokolowski, M. B. (2017). Epigenetic mechanisms modulate differences in Drosophila foraging behavior. Proc Natl Acad Sci U S A 114(47): 12518-12523. PubMed ID: 29078350
Little is known about how genetic variation and epigenetic marks interact to shape differences in behavior. The foraging (for) gene regulates behavioral differences between the rover and sitter Drosophila melanogaster strains, but the molecular mechanisms through which it does so have remained elusive. This study shows that the epigenetic regulator G9a interacts with for to regulate strain-specific adult foraging behavior through allele-specific histone methylation of a for promoter (pr4). Rovers have higher pr4 H3K9me dimethylation, lower pr4 RNA expression, and higher foraging scores than sitters. The rover-sitter differences disappear in the presence of G9a null mutant alleles, showing that G9a is necessary for these differences. Furthermore, rover foraging scores can be phenocopied by transgenically reducing pr4 expression in sitters. This compelling evidence shows that genetic variation can interact with an epigenetic modifier to produce differences in gene expression, establishing a behavioral polymorphism in Drosophila.
Bretman, A., Rouse, J., Westmancoat, J. D. and Chapman, T. (2017). The role of species-specific sensory cues in male responses to mating rivals in Drosophila melanogaster fruitflies. Ecol Evol 7(22): 9247-9256. PubMed ID: 29187965
Complex sets of cues can be important in recognizing and responding to conspecific mating competitors and avoiding potentially costly heterospecific competitive interactions. Drosophila males can detect sensory inputs from conspecifics to assess the level of competition. They respond to rivals by significantly extending mating duration and gain significant fitness benefits from doing so. This study tested the idea that the multiple sensory cues used by D. melanogaster males to detect conspecifics also function to minimize "off-target" responses to heterospecific males that they might encounter (Drosophila simulans, Drosophila yakuba, Drosophila pseudoobscura, or Drosophila virilis). Focal D. melanogaster males exposed to D. simulans or D. pseudoobscura subsequently increased mating duration, but to a lesser extent than following exposure to conspecific rivals. The magnitude of rivals' responses expressed by D. melanogaster males did not align with genetic distance between species, and none of the sensory manipulations caused D. melanogaster to respond to males of all other species tested. However, when "false" sensory cues were removed or provided, D. melanogaster males became more likely to show increased mating duration responses to heterospecific males. It is suggested that benefits of avoiding inaccurate assessment of the competitive environment may shape the evolution of recognition cues.

Thursday, December 14th

Kohzaki, H., Asano, M. and Murakami, Y. (2018). DNA replication machinery is required for development in Drosophila. Front Biosci (Landmark Ed) 23: 493-505. PubMed ID: 28930557
In Drosophila, some factors involved in chromosome replication seem to be involved in gene amplification and endoreplication, which are actively utilized in particular tissue development, but direct evidence has not been shown. Therefore, this study examined the effect of depletion of replication factors on these processes. First, it was confirmed that RNAi knockdown can be used for the depletion of replication factors by comparing the phenotypes of RNAi knockdown and deletion or point mutants of the components of DNA licensing factor, MCM2, MCM4 and Cdt1. Next, it was found that tissue-specific RNAi knockdown of replication factors caused tissue-specific defects, probably due to defects in DNA replication. In particular, depletion inhibited gene amplification of the chorion gene in follicle cells and endoreplication in salivary glands, showing that chromosomal DNA replication factors are required for these processes. Finally, using RNAi, the genes for chromosomal DNA replication that affected tissue development. Interestingly, wing specific knockdown of Mcm10 induced wing formation defects. These results suggest that some components of chromosomal replication machinery are directly involved in tissue development.
Hinnant, T. D., Alvarez, A. A. and Ables, E. T. (2017). Temporal remodeling of the cell cycle accompanies differentiation in the Drosophila germline. Dev Biol 429(1): 118-131. PubMed ID: 28711427
To describe how the cell cycle is remodeled in germ cells as they differentiate in situ, the Drosophila Fluorescence Ubiquitin-based Cell Cycle Indicator (Fly-FUCCI) system, in which degradable versions of GFP::E2f1 and RFP::CycB fluorescently label cells in each phase of the cell cycle was used. The lengths of the G1, S, and G2 phases of the cell cycle during oogenesis were found to change dramatically over the course of differentiation, and the 4/8-cell cyst was identified as a key developmental transition state in which cells prepare for specialized cell cycles. The data suggest that the transcriptional activator E2f1, which controls the transition from G1 to S phase, is a key regulator of mitotic divisions in the early germline. The data support the model that E2f1 is necessary for proper GSC proliferation, self-renewal, and daughter cell development. In contrast, while E2f1 degradation by the Cullin 4 (Cul4)-containing ubiquitin E3 ligase (CRL4) is essential for developmental transitions in the early germline, the data do not support a role for E2f1 degradation as a mechanism to limit GSC proliferation or self-renewal. Taken together, these findings provide further insight into the regulation of cell proliferation and the acquisition of differentiated cell fate, with broad implications across developing tissues.
Kim, T., Lara-Gonzalez, P., Prevo, B., Meitinger, F., Cheerambathur, D. K., Oegema, K. and Desai, A. (2017). Kinetochores accelerate or delay APC/C activation by directing Cdc20 to opposing fates. Genes Dev 31(11): 1089-1094. PubMed ID: 28698300
Evolutionary Homolog Study
Mitotic duration is determined by activation of the anaphase-promoting complex/cyclosome (APC/C) bound to its coactivator, Cdc20 (see Drosophila Fizzy. Kinetochores, the microtubule-interacting machines on chromosomes, restrain mitotic exit when not attached to spindle microtubules by generating a Cdc20-containing complex that inhibits the APC/C. This study, shows that flux of Cdc20 through kinetochores also accelerates mitotic exit by promoting its dephosphorylation by kinetochore-localized protein phosphatase 1 (see Drosophila Flapwing), which allows Cdc20 to activate the APC/C. Both APC/C activation and inhibition depend on Cdc20 fluxing through the same binding site at kinetochores. The microtubule attachment status of kinetochores therefore optimizes mitotic duration by controlling the balance between opposing Cdc20 fates.
Cahoon, C. K., Yu, Z., Wang, Y., Guo, F., Unruh, J. R., Slaughter, B. D. and Hawley, R. S. (2017). Superresolution expansion microscopy reveals the three-dimensional organization of the Drosophila synaptonemal complex. Proc Natl Acad Sci U S A 114(33): E6857-e6866. PubMed ID: 28760978
The synaptonemal complex (SC) assembles between homologous chromosomes and is essential for accurate chromosome segregation at the first meiotic division. In Drosophila, many SC components within the complex have been dissected through a combination of genetic analyses and superresolution and electron microscopy. The inability to optically resolve the minute distances between proteins in the complex has precluded its 3D characterization. A recently described technology termed expansion microscopy (ExM) uniformly increases the size of a biological sample, thereby circumventing the limits of optical resolution. By adapting the ExM protocol to render it compatible with structured illumination microscopy, it is possible to examine the 3D organization of several known Drosophila SC components. These data provide evidence that two layers of SC are assembled. It is further speculated that each SC layer may connect two nonsister chromatids, and a 3D model of the Drosophila SC is presented based on these findings.
Lane, S. I. R., Morgan, S. L., Wu, T., Collins, J. K., Merriman, J. A., ElInati, E., Turner, J. M. and Jones, K. T. (2017). DNA damage induces a kinetochore-based ATM/ATR-independent SAC arrest unique to the first meiotic division in mouse oocytes. Development 144(19): 3475-3486. PubMed ID: 28851706
Evolutionary Homolog Study
Mouse oocytes carrying DNA damage arrest in meiosis I, thereby preventing creation of embryos with deleterious mutations. The arrest is dependent on activation of the spindle assembly checkpoint, which results in anaphase-promoting complex (APC) inhibition. However, little is understood about how this checkpoint is engaged following DNA damage. This study found that within minutes of DNA damage checkpoint proteins are assembled at the kinetochore, not at damage sites along chromosome arms, such that the APC is fully inhibited within 30 min. Despite this robust response, there is no measurable loss in k-fibres, or tension across the bivalent. Through pharmacological inhibition this study observed that the response is dependent on Mps1 kinase (see Drosophila Mps1), aurora kinase (see Drosophila Aurora B) and Haspin (see Drosophila Haspin). Using oocyte-specific knockouts this study found the response does not require the DNA damage response kinases ATM or ATR. Furthermore, checkpoint activation does not occur in response to DNA damage in fully mature eggs during meiosis II, despite the divisions being separated by just a few hours. Therefore, mouse oocytes have a unique ability to sense DNA damage rapidly by activating the checkpoint at their kinetochores.
Overlack, K., Bange, T., Weissmann, F., Faesen, A. C., Maffini, S., Primorac, I., Muller, F., Peters, J. M. and Musacchio, A. (2017). BubR1 promotes Bub3-dependent APC/C inhibition during spindle assembly checkpoint signaling. Curr Biol 27(19): 2915-2927 e2917. PubMed ID: 28943088
Evolutionary Homolog Study
The spindle assembly checkpoint (SAC) prevents premature sister chromatid separation during mitosis. Phosphorylation of unattached kinetochores by the Mps1 kinase (see Drosophila Mps1) promotes recruitment of SAC machinery that catalyzes assembly of the SAC effector mitotic checkpoint complex (MCC). The SAC protein Bub3 (see Drosophila Bub3) is a phospho-amino acid adaptor that forms structurally related stable complexes with functionally distinct paralogs named Bub1 (see Drosophila Bub1) and BubR1 (see Drosophila Bub1R). A short motif ("loop") of Bub1, but not the equivalent loop of BubR1, enhances binding of Bub3 to kinetochore phospho-targets. This study asked whether the BubR1 loop directs Bub3 to different phospho-targets. The BubR1 loop is essential for SAC function and cannot be removed or replaced with the Bub1 loop. BubR1 loop mutants bind Bub3 and are normally incorporated in MCC in vitro but have reduced ability to inhibit the MCC target anaphase-promoting complex (APC/C), suggesting that BubR1:Bub3 recognition and inhibition of APC/C requires phosphorylation. Thus, small sequence differences in Bub1 and BubR1 direct Bub3 to different phosphorylated targets in the SAC signaling cascade.

Wednesday, December 13th

Baker, R., Nakamura, N., Chandel, I., Howell, B., Lyalin, D. and Panin, V. M. (2017). Protein O-mannosyltransferases affect sensory axon wiring and dynamic chirality of body posture in the Drosophila embryo. J Neurosci. PubMed ID: 29167399
Genetic defects in protein O-mannosyltransferases, POMT1 and POMT2, underlie severe muscular dystrophies. POMT genes are evolutionarily conserved in metazoan organisms. In Drosophila, both male and female POMT mutants show a clockwise rotation of adult abdominal segments, suggesting a chirality of underlying pathogenic mechanisms. This study describes and analyzes a similar phenotype in POMT mutant embryos that show left-handed body torsion. The experiments demonstrated that coordinated muscle contraction waves are associated with asymmetric embryo rolling, unveiling a new chirality marker in Drosophila development. Using genetic and live imaging approaches, it was revealed that the torsion phenotype results from differential rolling and aberrant patterning of peristaltic waves of muscle contractions. The results demonstrated that peripheral sensory neurons are required for normal contractions that prevent accumulation of torsion. POMT mutants show abnormal axonal connections of sensory neurons. POMT transgenic expression limited to sensory neurons significantly rescued the torsion phenotype, axonal connectivity defects and abnormal contractions in POMT mutant embryos. Taken together, these data suggested that protein O-mannosylation is required for normal sensory feedback to control coordinated muscle contractions and body posture. This mechanism may shed light on analogous functions of POMT genes in mammals and help elucidate etiology of neurological defects in muscular dystrophies.
Bozler, J., Kacsoh, B. Z., Chen, H., Theurkauf, W. E., Weng, Z. and Bosco, G. (2017). A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long term memory genes. PLoS Genet 13(10): e1007054. PubMed ID: 29084214
The ability to integrate experiential information and recall it in the form of memory is observed in a wide range of taxa, and is a hallmark of highly derived nervous systems. Storage of past experiences is critical for adaptive behaviors that anticipate both adverse and positive environmental factors. The process of memory formation and consolidation involve many synchronized biological events including gene transcription, protein modification, and intracellular trafficking: However, many of these molecular mechanisms remain illusive. With Drosophila as a model system this study used a nonassociative memory paradigm and a systems level approach to uncover novel transcriptional patterns. RNA sequencing of Drosophila heads during and after memory formation identified a number of novel memory genes. Tracking the dynamic expression of these genes over time revealed complex gene networks involved in long term memory. In particular, this study focuses on two functional gene clusters of signal peptides and proteases. Bioinformatics network analysis and prediction in combination with high-throughput RNA sequencing identified previously unknown memory genes, which when genetically knocked down resulted in behaviorally validated memory defects.
Bahrampour, S., Gunnar, E., Jonsson, C., Ekman, H. and Thor, S. (2017). Neural lineage progression controlled by a temporal proliferation program. Dev Cell 43(3): 332-348.e334. PubMed ID: 29112852
Great progress has been made in identifying transcriptional programs that establish stem cell identity. In contrast, only limited insight has been gained into how these programs are down-graded in a timely manner to halt proliferation and allow for cellular differentiation. Drosophila embryonic neuroblasts undergo such a temporal progression, initially dividing to bud off daughters that divide once (type I), then switching to generating non-dividing daughters (type 0), and finally exiting the cell cycle. This study identifies six early transcription factors that drive neuroblast and type I daughter proliferation. Early factors are gradually replaced by three late factors, acting to trigger the type I-->0 daughter proliferation switch and eventually to stop neuroblasts. Early and late factors regulate each other and four key cell-cycle genes, providing a logical genetic pathway for these transitions. The identification of this extensive driver-stopper temporal program controlling neuroblast lineage progression may have implications for studies in many other systems.
Cao, L. H., Yang, D., Wu, W., Zeng, X., Jing, B. Y., Li, M. T., Qin, S., Tang, C., Tu, Y. and Luo, D. G. (2017). Odor-evoked inhibition of olfactory sensory neurons drives olfactory perception in Drosophila. Nat Commun 8(1): 1357. PubMed ID: 29116083
Inhibitory response occurs throughout the nervous system, including the peripheral olfactory system. While odor-evoked excitation in peripheral olfactory cells is known to encode odor information, the molecular mechanism and functional roles of odor-evoked inhibition remain largely unknown. This study examined Drosophila olfactory sensory neurons and found that inhibitory odors triggered outward receptor currents by reducing the constitutive activities of odorant receptors, inhibiting the basal spike firing in olfactory sensory neurons. Remarkably, this odor-evoked inhibition of olfactory sensory neurons elicited by itself a full range of olfactory behaviors from attraction to avoidance, as did odor-evoked olfactory sensory neuron excitation. These results indicated that peripheral inhibition is comparable to excitation in encoding sensory signals rather than merely regulating excitation. Furthermore, it was demonstrated that a bidirectional code with both odor-evoked inhibition and excitation in single olfactory sensory neurons increases the odor-coding capacity, providing a means of efficient sensory encoding.

Tuesday, December 12th

Bushnell, H. L., Feiler, C. E., Ketosugbo, K. F., Hellerman, M. B., Nazzaro, V. L. and Johnson, R. I. (2017). JNK is antagonized to ensure the correct number of interommatidial cells pattern the Drosophila retina. Dev Biol [Epub ahead of print]. PubMed ID: 29133184
Apoptosis is crucial during the morphogenesis of most organs and tissues, and is utilized for tissues to achieve their proper size, shape and patterning. Many signaling pathways contribute to the precise regulation of apoptosis. This study shows that Jun N-terminal Kinase (JNK) activity contributes to the coordinated removal of interommatidial cells via apoptosis in the Drosophila pupal retina. This is consistent with previous findings that JNK activity promotes apoptosis in other epithelia. However, JNK activity was found to be repressed by Cindr (the CIN85 and CD2AP ortholog) in order to promote cell survival. Reducing the amount of Cindr resulted in ectopic cell death. Increased expression of the Drosophila JNK basket in the setting of reduced cindr expression was found to result in even more severe apoptosis, whilst ectopic death was found to be reduced if retinas were heterozygous for basket. Hence Cindr is required to properly restrict JNK-mediated apoptosis in the pupal eye, resulting in the correct number of interommatidial cells. A lack of precise control over developmental apoptosis can lead to improper tissue morphogenesis.
Byrne, D. J., Harmon, M. J., Simpson, J. C., Blackstone, C. and O'Sullivan, N. C. (2017). Roles for the VCP co-factors Npl4 and Ufd1 in neuronal function in Drosophila melanogaster. J Genet Genomics 44(10): 493-501. PubMed ID: 29037990
The VCP-Ufd1-Npl4 complex regulates proteasomal processing within cells by delivering ubiquitinated proteins to the proteasome for degradation. Mutations in VCP are associated with two neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and inclusion body myopathy with Paget's disease of the bone and frontotemporal dementia (IBMPFD). Extensive study has revealed crucial functions of VCP within neurons. By contrast, little is known about the functions of Npl4 or Ufd1 in vivo. Using neuronal-specific knockdown of Npl4 or Ufd1 in Drosophila melanogaster, it is inferred that Npl4 contributes to microtubule organization within developing motor neurons. Moreover, Npl4 RNAi flies present with neurodegenerative phenotypes including progressive locomotor deficits, reduced lifespan and increased accumulation of TAR DNA-binding protein-43 homolog (TBPH). Knockdown, but not overexpression, of TBPH also exacerbates Npl4 RNAi-associated adult-onset neurodegenerative phenotypes. In contrast, this study finds that neuronal knockdown of Ufd1 has little effect on neuromuscular junction (NMJ) organization, TBPH accumulation or adult behaviour. These findings suggest the differing neuronal functions of Npl4 and Ufd1 in vivo.
Baumann, D. G., Dai, M. S., Lu, H. and Gilmour, D. S. (2017). GFZF, a glutathione S-transferase protein implicated in cell cycle regulation and hybrid inviability, is a transcriptional co-activator. Mol Cell Biol [Epub ahead of print]. PubMed ID: 29158293
The core promoter of protein-encoding genes plays a central role in regulating transcription. M1BP is a transcriptional activator that associates with a core promoter element known as Motif 1 that resides at thousand of genes in Drosophila. To gain insight into how M1BP functions, this study identified an interacting protein called GFZF. GFZF had been previously identified in genetic screens for factors involved in maintenance of hybrid inviability, the G2-M DNA damage checkpoint, and RAS/MAPK signaling but its contribution to these processes was unknown. This study shows that GFZF resides in the nucleus and functions as a transcriptional co-activator. In addition, GFZF is a glutathione S-transferase(GST). Thus, GFZF is the first transcriptional co-activator with intrinsic GST activity, and its identification as a transcriptional co-activator provides an explanation for its role in numerous biological processes.
Cao, J., Bollepalli, M. K., Hu, Y., Zhang, J., Li, Q., Li, H., Chang, H., Xiao, F., Hardie, R. C., Rong, Y. S. and Hu, W. (2017). A single residue mutation in the Galphaq subunit of the G protein complex causes blindness in Drosophila. G3 (Bethesda). PubMed ID: 29158337
Heterotrimeric G proteins play central roles in many signaling pathways, including the phototransduction cascade in animals. However, the degree of involvement of the G protein subunit Galphaq is not clear since animals with strong loss of function mutations previously reported remain responsive to light stimuli. This study recovered a new allele of Galphaq in Drosophila that abolishes light response in a conventional ERG assay, and reduces sensitivity in whole-cell recordings of dissociated cells by at least 5 orders of magnitude. In addition, mutant eyes demonstrate a rapid rate of degeneration in the presence of light. The new allele is likely the strongest hypomorph described to date. Interestingly, the mutant protein is produced in the eyes but carries a single amino acid change of a conserved hydrophobic residue that has been assigned to the interface of interaction between Galphaq and its downstream effector PLC. This study thus uncovered possibly the first point mutation that specifically affects this interaction in vivo.

Monday, December 11th

Krebs, A. R., Imanci, D., Hoerner, L., Gaidatzis, D., Burger, L. and Schubeler, D. (2017). Genome-wide single-molecule footprinting reveals high RNA Polymerase II turnover at paused promoters. Mol Cell 67(3): 411-422.e414. PubMed ID: 28735898
Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. This study harnessed single-molecule footprinting to quantify distinct steps of initiation in vivo throughout the Drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy. Additionally, perturbation of transcriptional initiation reveals an unexpectedly high turnover of polymerases at paused promoters-an observation confirmed at the level of nascent RNAs. These observations argue that absence of elongation is largely caused by premature termination rather than by stable polymerase stalling. In support of this non-processive model, it was observed that induction of the paused heat shock promoter depends on continuous initiation. This study provides a framework to quantify protein binding at single-molecule resolution and refines concepts of transcriptional pausing.
Bali, A. and Shravage, B. V. (2017). Characterization of the Autophagy related gene-8a (Atg8a) promoter in Drosophila melanogaster. Int J Dev Biol 61(8-9): 551-555. PubMed ID: 29139541
Autophagy is an evolutionarily conserved process which is upregulated under various stress conditions, including nutrient stress and oxidative stress. Amongst autophagy related genes (Atgs), Atg8a (LC3 in mammals) is induced several-fold during nutrient limitation in Drosophila. The minimal Atg8a cis-regulatory module (CRM) which mediates transcriptional upregulation under various stress conditions is not known. This study describes the generation and analyses of a series of Atg8a promoter deletions which drive the expression of an mCherry-Atg8a fusion cassette. Expression studies revealed that a 200 bp region of Atg8a is sufficient to drive expression of Atg8a in nutrient rich conditions in fat body and ovaries, as well as under nutrient deficient conditions in the fat body. Furthermore, this 200 bp region can mediate Atg8a upregulation during developmental histolysis of the larval fat body and under oxidative stress conditions induced by H2O2. Finally, the expression levels of Atg8a from this promoter are sufficient to rescue the lethality of the Atg8a mutant. The 200 bp promoter-fusion reporter provides a valuable tool which can be used in genetic screens to identify transcriptional and post-transcriptional regulators of Atg8a (Bali, 2017).
Barr, K. A., Martinez, C., Moran, J. R., Kim, A. R., Ramos, A. F. and Reinitz, J. (2017). Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation. BMC Syst Biol 11(1): 116. PubMed ID: 29187214
Models that incorporate specific chemical mechanisms have been successful in describing the activity of Drosophila developmental enhancers as a function of underlying transcription factor binding motifs. Despite this, the minimum set of mechanisms required to reconstruct an enhancer from its constituent parts is not known. Synthetic biology offers the potential to test the sufficiency of known mechanisms to describe the activity of enhancers, as well as to uncover constraints on the number, order, and spacing of motifs. Using a functional model and in silico compensatory evolution, putative synthetic even-skipped stripe 2 enhancers with varying degrees of similarity to the natural enhancer. These elements represent the evolutionary trajectories of the natural stripe 2 enhancer towards two synthetic enhancers designed ab initio. In the first trajectory, spatially regulated expression was maintained, even after more than a third of binding sites were lost. In the second, sequences with high similarity to the natural element did not drive expression, but a highly diverged sequence about half the length of the minimal stripe 2 enhancer drove ten times greater expression. Additionally, homotypic clusters of Zelda or Stat92E motifs, but not Bicoid, drove expression in developing embryos. The results show that the gene regulation model explains much of the function of the stripe 2 enhancer. Cases where expression deviated from prediction indicates that undescribed factors likely act to modulate expression. Activation driven Bicoid and Hunchback is highly sensitive to spatial organization of binding motifs. In contrast, Zelda and Stat92E drive expression from simple homotypic clusters, suggesting that activation driven by these factors is less constrained. Collectively, the 40 sequences generated in this work provides a powerful training set for building future models of gene regulation.
Baudouin-Gonzalez, L., Santos, M. A., Tempesta, C., Sucena, E., Roch, F. and Tanaka, K. (2017). Diverse cis-regulatory mechanisms contribute to expression evolution of tandem gene duplicates. Mol Biol Evol 34(12): 3132-3147. PubMed ID: 28961967
Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. This study directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 Ma. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, the study shows that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. This analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. It is argued that these findings will encourage studying cis-regulatory evolution at the whole-locus level to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression.

Friday, December 8th

Adewoye, A. B., Nuzhdin, S. V. and Tauber, E. (2017). Mapping quantitative trait loci underlying circadian light sensitivity in Drosophila. J Biol Rhythms 32(5): 394-405. PubMed ID: 28990443
Despite the significant advance in understanding of the molecular basis of light entrainment of the circadian clock in Drosophila, the underlying genetic architecture is still largely unknown. The aim of this study was to identify loci associated with variation in circadian photosensitivity, which are important for the evolution of this trait. Complementary approaches were used that combined quantitative trait loci (QTL) mapping, complementation testing, and transcriptome profiling to dissect this variation. A major QTL was identified on chromosome 2, which was subsequently fine mapped using deficiency complementation mapping into 2 smaller regions spanning 139 genes, some of which are known to be involved in functions that have been previously implicated in light entrainment. Two genes implicated with the clock and located within that interval, timeless and cycle, failed to complement the QTL, indicating that alleles of these genes contribute to the variation in light response. Specifically, the timeless s/ls polymorphism that has been previously shown to constitute a latitudinal cline in Europe is also segregating in the recombinant inbred lines and is contributing to the phenotypic variation in light sensitivity. This study also profiled gene expression in 2 recombinant inbred strains that differ significantly in their photosensitivity and a total of 368 transcripts were identified that showed differential expression (false discovery rate < 0.1). Of 131 transcripts that showed a significant recombinant inbred line by treatment interaction (i.e., putative expression QTL), 4 are located within QTL2.
Aw, W. C., Garvin, M. R., Melvin, R. G. and Ballard, J. W. O. (2017). Sex-specific influences of mtDNA mitotype and diet on mitochondrial functions and physiological traits in Drosophila melanogaster. PLoS One 12(11): e0187554. PubMed ID: 29166659
This study determined the sex-specific influence of mtDNA type (mitotype) and diet on mitochondrial functions and physiology in two Drosophila melanogaster lines. In many species, males and females differ in aspects of their energy production. These sex-specific influences may be caused by differences in evolutionary history and physiological functions. We predicted the influence of mtDNA mutations should be stronger in males than females as a result of the organelle's maternal mode of inheritance in the majority of metazoans. In contrast, it was predicted the influence of diet would be greater in females due to higher metabolic flexibility. Four diets were included that differed in their protein: carbohydrate (P:C) ratios as they are the two-major energy-yielding macronutrients in the fly diet. Four mitochondrial function traits (Complex I oxidative phosphorylation, reactive oxygen species production, superoxide dismutase activity, and mtDNA copy number) and four physiological traits (fecundity, longevity, lipid content, and starvation resistance) were examined. Traits were assayed at 11 d and 25 d of age. Consistent with predictions it was observe that the mitotype influenced males more than females supporting the hypothesis of a sex-specific selective sieve in the mitochondrial genome caused by the maternal inheritance of mitochondria. Also, consistent with predictions, it was found that the diet influenced females more than males.
Shilova, V. Y., Zatsepina, O. G., Garbuz, D. G., Funikov, S. Y., Zelentsova, E. S., Schostak, N. G., Kulikov, A. M. and Evgen'ev, M. B. (2017). Heat shock protein 70 from a thermotolerant Diptera species provides higher thermoresistance to Drosophila larvae than correspondent endogenous gene. Insect Mol Biol. PubMed ID: 28796386
Heat shock proteins (Hsp70s) from two Diptera species that drastically differ in their heat shock response and longevity were investigated. Drosophila melanogaster is characterized by the absence of Hsp70 and other hsps under normal conditions and the dramatic induction of hsp synthesis after temperature elevation. The other Diptera species examined belongs to the Stratiomyidae family (Stratiomys singularior) and exhibits high levels of inducible Hsp70 under normal conditions coupled with a thermotolerant phenotype and much longer lifespan. To evaluate the impact of hsp70 genes on thermotolerance and longevity, use was made of a D. melanogaster strain that lacks all hsp70 genes. Single copies of either S. singularior or D. melanogaster hsp70 were introduced into this strain and the transgenic flies wer examined in terms of thermotolerance and longevity. Transgenic strains were developed containing the S. singularior hsp70 gene under control of a D. melanogaster hsp70 promoter. Although these adult flies did synthesize the corresponding mRNA after heat shock, they were not superior to the flies containing a single copy of D. melanogaster hsp70 in thermotolerance and longevity. By contrast, Stratiomyidae Hsp70 provided significantly higher thermotolerance at the larval stage in comparison with endogenous Hsp70.
Abrat, O. B., Storey, J. M., Storey, K. B. and Lushchak, V. I. (2018). High amylose starch consumption induces obesity in Drosophila melanogaster and metformin partially prevents accumulation of storage lipids and shortens lifespan of the insects. Comp Biochem Physiol A Mol Integr Physiol 215: 55-62. PubMed ID: 29054808
There are very few studies that have directly analyzed the effects of dietary intake of slowly digestible starches on metabolic parameters of animals. The present study examined the effects of slowly digestible starch with high amylose content (referred also as amylose starch) either alone, or in combination with metformin on the development, lifespan, and levels of glucose and storage lipids in the fruit fly Drosophila melanogaster. Consumption of amylose starch in concentrations 0.25-10% did not affect D. melanogaster development, whereas 20% starch delayed pupation and reduced the number of larvae that reached the pupal stage. Starch levels in larval food, but not in adult food, determined levels of triacylglycerides in eight-day-old adult flies. Rearing on diet with 20% starch led to shorter lifespan and a higher content of triacylglycerides in the bodies of adult flies as compared with the same parameters in flies fed on 4% starch diet. Food supplementation with 10mM metformin partly attenuated the negative effects of high starch concentrations on larval pupation and decreased triacylglyceride levels in adult flies fed on 20% starch. Long-term consumption of diets supplemented with metformin and starch decreased lifespan of the insects, compared with the diet supplemented with starch only. The data show that in Drosophila high starch consumption may induce a fat fly phenotype and metformin may partially prevent it.

Thursday, December 7th

Molina-Mateo, D., Fuenzalida-Uribe, N., Hidalgo, S., Molina-Fernandez, C., Abarca, J., Zarate, R. V., Escandon, M., Figueroa, R., Tevy, M. F. and Campusano, J. M. (2017). Characterization of a presymptomatic stage in a Drosophila Parkinson's disease model: Unveiling dopaminergic compensatory mechanisms. Biochim Biophys Acta [Epub ahead of print]. PubMed ID: 28716706
Parkinson disease (PD) is a degenerative disorder characterized by several motor symptoms including shaking, rigidity, slow movement and difficult walking, which has been associated to the death of nigro-striatal dopaminergic neurons. >90% of PD patients also present olfactory dysfunction. Although the molecular mechanisms responsible for this disease are not clear, hereditary PD is linked to mutations in specific genes, including the PTEN-induced putative kinase 1 (PINK1). This work provides a thorough temporal description of the behavioral effects induced by a mutation in the PINK1 gene in adult Drosophila. The data suggests that the motor deficits associated to PD are fully revealed only by the third week of age. However, olfactory dysfunction is detected as early as the first week of age. Immunofluorescence and neurochemical data is provided that led to a proposal that compensatory changes occur in this Drosophila model for PD. These compensatory changes are associated to specific components of the dopaminergic system: the biosynthetic enzymes, Tyrosine hydroxylase and Dopa decarboxylase, and the Dopamine transporter, a plasma membrane protein involved in maintaining dopamine extracellular levels at physiologically relevant levels. Thus, these data help define presymptomatic and symptomatic phases in this PD animal model, and that compensatory changes occur in the dopaminergic neurons in the presymptomatic stage.
Lee, B. I., Suh, Y. S., Chung, Y. J., Yu, K. and Park, C. B. (2017). Shedding light on Alzheimer's beta-Amyloidosis: Photosensitized methylene blue inhibits self-assembly of beta-amyloid peptides and disintegrates their aggregates. Sci Rep 7(1): 7523. PubMed ID: 28790398
Abnormal aggregation of beta-amyloid (Abeta) peptides is a major hallmark of Alzheimer's disease (AD). In spite of numerous attempts to prevent the beta-amyloidosis, no effective drugs for treating AD have been developed to date. Among many candidate chemicals, methylene blue (MB) has proved its therapeutic potential for AD in a number of in vitro and in vivo studies; but the result of recent clinical trials performed with MB and its derivative was negative. In this study, with the aid of multiple photochemical analyses, it is reported that photoexcited MB molecules can block Abeta42 aggregation in vitro. Furthermore, an in vivo study using Drosophila AD model demonstrates that photoexcited MB is highly effective in suppressing synaptic toxicity, resulting in a reduced damage to the neuromuscular junction (NMJ), an enhanced locomotion, and decreased vacuole in the brain. The hindrance effect is attributed to Abeta42 oxidation by singlet oxygen (1O2) generated from photoexcited MB. Finally, it was shown that photoexcited MB possess a capability to disaggregate the pre-existing Abeta42 aggregates and reduce Abeta-induced cytotoxicity. This work suggests that light illumination can provide an opportunity to boost the efficacies of MB toward photodynamic therapy of AD in future.
Avery, A. W., Thomas, D. D. and Hays, T. S. (2017). beta-III-spectrin spinocerebellar ataxia type 5 mutation reveals a dominant cytoskeletal mechanism that underlies dendritic arborization. Proc Natl Acad Sci U S A 114(44): E9376-e9385. PubMed ID: 29078305
A spinocerebellar ataxia type 5 (SCA5) L253P mutation in the actin-binding domain (ABD) of beta-III-spectrin causes high-affinity actin binding and decreased thermal stability in vitro. This study shows in mammalian cells, at physiological temperature, that the mutant ABD retains high-affinity actin binding. Significantly, evidence is provided that the mutation alters the mobility and recruitment of beta-III-spectrin in mammalian cells, pointing to a potential disease mechanism. To explore this mechanism, a Drosophila SCA5 model was developed in which an equivalent mutant Drosophila beta-spectrin is expressed in neurons that extend complex dendritic arbors, such as Purkinje cells, targeted in SCA5 pathogenesis. The mutation causes a proximal shift in arborization coincident with decreased beta-spectrin localization in distal dendrites. SCA5 beta-spectrin dominantly mislocalizes alpha-spectrin and ankyrin-2, components of the endogenous spectrin cytoskeleton. These data suggest that high-affinity actin binding by SCA5 beta-spectrin interferes with spectrin-actin cytoskeleton dynamics, leading to a loss of a cytoskeletal mechanism in distal dendrites required for dendrite stabilization and arbor outgrowth.
Arnes, M., Casas-Tinto, S., Malmendal, A. and Ferrus, A. (2017). Amyloid beta42 peptide is toxic to non-neural cells in Drosophila yielding a characteristic metabolite profile and the effect can be suppressed by PI3K. Biol Open 6(11): 1664-1671. PubMed ID: 29141953
The human Abeta42 peptide is associated with Alzheimer's disease through its deleterious effects in neurons. Expressing the human peptide in adult Drosophila in a tissue- and time-controlled manner, this study shows that Abeta42 is also toxic in non-neural cells, neurosecretory and epithelial cell types in particular. This form of toxicity includes the aberrant signaling by Wingless morphogen leading to the eventual activation of Caspase 3. Preventing Caspase 3 activation by means of p53 keeps epithelial cells from elimination but maintains the Abeta42 toxicity yielding more severe deleterious effects to the organism. Metabolic profiling by nuclear magnetic resonance (NMR) of adult flies at selected ages post Abeta42 expression onset reveals characteristic changes in metabolites as early markers of the pathological process. All morphological and most metabolic features of Abeta42 toxicity can be suppressed by the joint overexpression of PI3K.

Wednesday, December 6th

Albert, E. A. and Bokel, C. (2017). A cell based, high throughput assay for quantitative analysis of Hedgehog pathway activation using a Smoothened activation sensor. Sci Rep 7(1): 14341. PubMed ID: 29085027
The Hedgehog (Hh) signalling cascade plays an important role in development and disease. In the absence of Hh ligand, activity of the key signal transducer Smoothened (Smo) is downregulated by the Hh receptor Patched (Ptc). However, the mechanisms underlying this inhibition, and especially its release upon ligand stimulation, are still poorly understood, in part because tools for following Smo activation at the subcellular level were long lacking. To address this deficit this study has developed a high throughput cell culture assay based on a fluorescent sensor for Drosophila Smo activation. A small molecule inhibitor library was screened, and increased Smo sensor fluorescence was observed with compounds aimed at two major target groups, the MAPK signalling cascade and Polo and Aurora kinases. Biochemical validation for selected inhibitors (dobrafenib, tak-733, volasertib) confirmed the screen results and revealed differences in the mode of Smo activation. Furthermore, monitoring Smo activation at the single cell level indicated that individual cells exhibit different threshold responses to Hh stimulation, which may be mechanistically relevant for the formation of graded Hh responses. Together, these results thus provide proof of principle that this assay may become a valuable tool for dissecting the cell biological basis of Hh pathway activation.
Narciso, C. E., Contento, N. M., Storey, T. J., Hoelzle, D. J. and Zartman, J. J. (2017). Release of applied mechanical loading stimulates intercellular calcium waves in Drosophila wing discs. Biophys J 113(2): 491-501. PubMed ID: 28746859
Mechanical forces are critical but poorly understood inputs for organogenesis and wound healing. Calcium ions (Ca2+) are critical second messengers in cells for integrating environmental and mechanical cues, but the regulation of Ca2+ signaling is poorly understood in developing epithelial tissues. This study reports a chip-based regulated environment for microorgans that enables systematic investigations of the crosstalk between an organ's mechanical stress environment and biochemical signaling under genetic and chemical perturbations. This method enabled definition of the essential conditions for generating organ-scale intercellular Ca2+ waves in Drosophila wing discs that are also observed in vivo during organ development. Mechanically induced intercellular Ca2+ waves are shown to require fly extract growth serum as a chemical stimulus. Using the chip-based regulated environment for microorgans, it was demonstrated that not the initial application but instead the release of mechanical loading is sufficient, but not necessary, to initiate intercellular Ca2+ waves. The Ca2+ response depends on the prestress intercellular Ca2+ activity and not on the magnitude or duration of the mechanical stimulation applied. Mechanically induced intercellular Ca2+ waves rely on IP3R-mediated Ca2+-induced Ca2+ release and propagation through gap junctions. Thus, intercellular Ca2+ waves in developing epithelia may be a consequence of stress dissipation during organ growth.
Matsushima, Y., Hirofuji, Y., Aihara, M., Yue, S., Uchiumi, T., Kaguni, L. S. and Kang, D. (2017). Drosophila protease ClpXP specifically degrades DmLRPPRC1 controlling mitochondrial mRNA and translation. Sci Rep 7(1): 8315. PubMed ID: 28814717
ClpXP is the major protease in the mitochondrial matrix in eukaryotes, and is well conserved among species. ClpXP is composed of a proteolytic subunit, ClpP, and a chaperone-like subunit, ClpX. Although it has been proposed that ClpXP is required for the mitochondrial unfolded protein response, additional roles for ClpXP in mitochondrial biogenesis are unclear. This study found that Drosophila leucine-rich pentatricopeptide repeat domain-containing protein 1 (DmLRPPRC1) is a specific substrate of ClpXP. Depletion or introduction of catalytically inactive mutation of ClpP increases DmLRPPRC1 and causes non-uniform increases of mitochondrial mRNAs, accumulation of some unprocessed mitochondrial transcripts, and modest repression of mitochondrial translation in Drosophila Schneider S2 cells. Moreover, DmLRPPRC1 over-expression induces the phenotypes similar to those observed when ClpP is depleted. Taken together, ClpXP regulates mitochondrial gene expression by changing the protein level of DmLRPPRC1 in Drosophila Schneider S2 cells.
Akhmetova, K., Balasov, M., Svitin, A., Chesnokova, E., Renfrow, M. and Chesnokov, I. (2017). Phosphorylation of Pnut at the early steps of Drosophila embryo development affects association of the Septin complex with membrane and is important for viability. G3 (Bethesda). PubMed ID: 29079679
Septin proteins are polymerizing GTPases that are found in most eukaryotic species. Septins are important for cytokinesis and participate in many processes involving spatial modifications of the cell cortex. In Drosophila, septin proteins Pnut, Sep1 and Sep2 form a hexameric septin complex. This study found that septin protein Pnut is phosphorylated during the first two hours of Drosophila embryo development. To study the effect of Pnut phosphorylation in a live organism, a new Drosophila pnut null mutant was created that allows for the analysis of Pnut mutations during embryogenesis. To understand the functional significance of Pnut phosphorylation, Drosophila strains carrying non-phosphorylatable and phospho-mimetic mutant pnut transgenes were established. The expression of the non-phosphorylatable Pnut protein resulted in semi-lethality and abnormal protein localization, whereas, the expression of the phospho-mimetic mutant form of Pnut disrupted the assembly of a functional septin complex and septin filament formation in vitro. Overall, these findings indicate that the controlled phosphorylation of Pnut plays an important role in regulating septin complex functions during organism development.

Tuesday, December 5th

Kaieda, Y., Masuda, R., Nishida, R., Shimell, M., O'Connor, M. B. and Ono, H. (2017). Glue protein production can be triggered by steroid hormone signaling independent of the developmental program in Drosophila melanogaster. Dev Biol 430(1): 166-176. PubMed ID: 28782527
Steroid hormones regulate life stage transitions, allowing animals to appropriately follow a developmental timeline. During insect development, the steroid hormone ecdysone is synthesized and released in a regulated manner by the prothoracic gland (PG) and then hydroxylated to the active molting hormone, 20-hydroxyecdysone (20E), in peripheral tissues. This study manipulated ecdysteroid titers, through temporally controlled over-expression of the ecdysteroid-inactivating enzyme, CYP18A1, in the PG using the GeneSwitch-GAL4 system in the fruit fly Drosophila melanogaster. Expression was monitored of a 20E-inducible glue protein gene, Salivary gland secretion 3 (Sgs3), using a Sgs3:GFP fusion transgene. In wild type larvae, Sgs3-GFP expression is activated at the midpoint of the third larval instar stage in response to the rising endogenous level of 20E. By first knocking down endogenous 20E levels during larval development and then feeding 20E to these larvae at various stages, it was found that Sgs3-GFP expression could be triggered at an inappropriate developmental stage after a certain time lag. This stage-precocious activation of Sgs3 required expression of the Broad-complex, similar to normal Sgs3 developmental regulation, and a small level of nutritional input. It is suggested that these studies provide evidence for a tissue-autonomic regulatory system for a metamorphic event independent from the primary 20E driven developmental progression.
Li, K., Zhang, X., Zuo, Y., Liu, W., Zhang, J. and Moussian, B. (2017). Timed Knickkopf function is essential for wing cuticle formation in Drosophila melanogaster. Insect Biochem Mol Biol 89: 1-10. PubMed ID: 28821399
The insect cuticle is an extracellular matrix that consists of the polysaccharide chitin, proteins, lipids and organic molecules that are arranged in distinct horizontal layers. In Drosophila melanogaster, these layers are not formed sequentially, but, at least partially, at the same time. Timing of the underlying molecular mechanisms is conceivably crucial for cuticle formation. To study this issue, the time period was determined during which the function of Knickkopf (Knk), a key factor of chitin organization, is required for wing cuticle differentiation in D. melanogaster. Although knk is expressed throughout metamorphosis, it was demonstrated that its expression 30 h prior and 48 h after pupariation is essential for correct wing cuticle formation. In other words, expression beyond this period is futile. Importantly, manipulation of Knk expression during this time causes wing bending suggesting an effect of Knk amounts on the physical properties of the wing cuticle. Manipulation of Knk expression also interferes with the structure and function of the cuticle surface. First, it was shown that the shape of surface nano-structures depends on the expression levels of knk. Second, it was found that cuticle impermeability is compromised in wings with reduced knk expression. In summary, despite the extended supply of Knk during metamorphosis, controlled amounts of Knk are important for correct wing cuticle differentiation and function in a concise period of time.
Abbasi, R. and Marcus, J. M. (2017). A new A-P compartment boundary and organizer in holometabolous insect wings. Sci Rep 7(1): 16337. PubMed ID: 29180689
Decades of research on the highly modified wings of Drosophila melanogaster has suggested that insect wings are divided into two Anterior-Posterior (A-P) compartments separated by an axis of symmetry. This axis of symmetry is created by a developmental organizer that establishes symmetrical patterns of gene expression that in turn pattern the A-P axis of the wing. Butterflies possess more typical insect wings and butterfly wing colour patterns provide many landmarks for studies of wing structure and development. Using eyespot colour pattern variation in Vanessa butterflies, this study shows an additional A-P axis of symmetry running between wing sectors 3 and 4. Boundaries of Drosophila mitotic clones suggest the existence of a previously undetected Far-Posterior (F-P) compartment boundary that coincides with this additional A-P axis. A similar compartment boundary is evident in butterfly mosaic gynandromorphs. It is suggested that this additional compartment boundary and its associated developmental organizer create an axis of wing colour pattern symmetry and a gene expression-based combinatorial code, permitting each insect wing compartment to acquire a unique identity and allowing for the individuation of butterfly eyespots.
Ma, M., Cao, X., Dai, J. and Pastor-Pareja, J. C. (2017). Basement membrane manipulation in Drosophila wing discs affects Dpp retention but not growth mechanoregulation. Dev Cell 42(1): 97-106.e104. PubMed ID: 28697337
Basement membranes (BMs) are extracellular matrix polymers basally underlying epithelia, where they regulate cell signaling and tissue mechanics. Constriction by the BM shapes Drosophila wing discs, a well-characterized model of tissue growth. Recently, the hypothesis that mechanical factors govern wing growth has received much attention, but it has not been definitively tested. This study manipulated BM composition to cause dramatic changes in tissue tension. Increased tissue compression when perlecan was knocked down did not affect adult wing size. BM elimination, decreasing compression, reduced wing size but did not visibly affect Hippo signaling, widely postulated to mediate growth mechanoregulation. BM elimination, in contrast, attenuated signaling by bone morphogenetic protein/transforming growth factor beta ligand Dpp, which was not efficiently retained within the tissue and escaped to the body cavity. The results challenge mechanoregulation of wing growth, while uncovering a function of BMs in preserving a growth-promoting tissue environment.

Monday, December 4th

Turissini, D. A. and Matute, D. R. (2017). Fine scale mapping of genomic introgressions within the Drosophila yakuba clade. PLoS Genet 13(9): e1006971. PubMed ID: 28873409
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of Sao Tome, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. This report quantifies the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). The genomes of 86 individuals were sequenced from all three species. A new statistical framework was developed and applied, using a hidden Markov approach, to identify introgression. Introgression was found to have occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, this study found that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). It was additionally shown that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, the results indicate that genetic exchange between these species is currently rare.
Siddiq, M. A., Loehlin, D. W., Montooth, K. L. and Thornton, J. W. (2017). Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nat Ecol Evol 1(2): 25. PubMed ID: 28812605
Identifying the genetic basis for adaptive differences between species requires explicit tests of historical hypotheses concerning the effects of past changes in gene sequence on molecular function, organismal phenotype and fitness. This challenge was addressed by combining ancestral protein reconstruction with biochemical experiments and physiological analysis of transgenic animals that carry ancestral genes. A widely held hypothesis of molecular adaptation was tested in this study-that changes in the alcohol dehydrogenase protein (ADH) along the lineage leading to Drosophila melanogaster increased the catalytic activity of the enzyme and thereby contributed to the ethanol tolerance and adaptation of the species to its ethanol-rich ecological niche. These experiments strongly refute the predictions of the adaptive ADH hypothesis and caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence. The experimental strategy employed can be used to decisively test other adaptive hypotheses and the claims they entail about past biological causality.
Schmidt, J. M., Battlay, P., Gledhill-Smith, R. S., Good, R. T., Lumb, C., Fournier-Level, A. and Robin, C. (2017). Insights into DDT Resistance from the Drosophila melanogaster Genetic Reference Panel. Genetics [Epub ahead of print]. PubMed ID: 28935691
Insecticide resistance is considered a classic model of microevolution, where a strong selective agent is applied to a large natural population, resulting in a change in frequency of alleles that confer resistance. While many insecticide resistance variants have been characterized at the gene level, they are typically single genes of large effect identified in highly resistant pest species. In contrast, multiple variants have been implicated in DDT resistance in Drosophila melanogaster, however only the Cyp6g1 locus has previously been shown to be relevant to field populations. This study used genome-wide association studies to identify DDT-associated polygenes and used selective sweep analyses to assess their adaptive significance. Two candidate DDT resistance loci were identified and verified. A largely uncharacterized gene, CG10737, has a function in muscles that ameliorates the effects of DDT, while a putative detoxifying P450, Cyp6w1, shows compelling evidence of positive selection.
Nourmohammad, A., Rambeau, J., Held, T., Kovacova, V., Berg, J. and Lassig, M. (2017). Adaptive evolution of gene expression in Drosophila. Cell Rep 20(6): 1385-1395. PubMed ID: 28793262
Gene expression levels are important quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies have revealed substantial adaptive evolution at the genomic level, but the evolutionary modes of gene expression remain controversial. This study presents evidence that adaptation dominates the evolution of gene expression levels in flies. 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection. The results are derived from time-resolved data of gene expression divergence across a family of related species, using a probabilistic inference method for gene-specific selection. Adaptive gene expression is stronger in specific functional classes, including regulation, sensory perception, sexual behavior, and morphology. Moreover, a large group of genes was identifed with sex-specific adaptation of expression, which predominantly occurs in males. This analysis opens an avenue to map system-wide selection on molecular quantitative traits independently of their genetic basis.

Friday, December 1st

Lynch, Z. R., Schlenke, T. A., Morran, L. T. and de Roode, J. C. (2017). Ethanol confers differential protection against generalist and specialist parasitoids of Drosophila melanogaster. PLoS One 12(7): e0180182. PubMed ID: 28700600
As parasites coevolve with their hosts, they can evolve counter-defenses that render host immune responses ineffective. These counter-defenses are more likely to evolve in specialist parasites than generalist parasites; the latter face variable selection pressures between the different hosts they infect. Natural populations of the fruit fly Drosophila melanogaster are commonly threatened by endoparasitoid wasps in the genus Leptopilina, including the specialist L. boulardi and the generalist L. heterotoma, and both wasp species can incapacitate the cellular immune response of D. melanogaster larvae. Given that ethanol tolerance is high in D. melanogaster and stronger in the specialist wasp than the generalist, this study tested whether fly larvae could use ethanol as an anti-parasite defense and whether its effectiveness would differ against the two wasp species. Fly larvae were found to benefit from eating ethanol-containing food during exposure to L. heterotoma; a two-fold decrease in parasitization intensity and a 24-fold increase in fly survival to adulthood were observed. Although host ethanol consumption did not affect L. boulardi parasitization rates or intensities, it led to a modest increase in fly survival. Thus, ethanol conferred stronger protection against the generalist wasp than the specialist. Test were made to see whether fly larvae can self-medicate by seeking ethanol-containing food after being attacked by wasps, but found no support for this hypothesis was found. Female flies were allowed to choose between control and ethanol-containing oviposition sites in the presence vs. absence of wasps and generally found significant preferences for ethanol regardless of wasp presence. Overall, these results suggest that D. melanogaster larvae obtain protection from certain parasitoid wasp species through their mothers' innate oviposition preferences for ethanol-containing food sources.
Noh, S., Everman, E. R., Berger, C. M. and Morgan, T. J. (2017). Seasonal variation in basal and plastic cold tolerance: Adaptation is influenced by both long- and short-term phenotypic plasticity. Ecol Evol 7(14): 5248-5257. PubMed ID: 28770063
Understanding how thermal selection affects phenotypic distributions across different time scales will allow prediction of the effect of climate change on the fitness of ectotherms. This study tested how seasonal temperature variation affects basal levels of cold tolerance and two types of phenotypic plasticity in Drosophila melanogaster. Developmental acclimation occurs as developmental stages of an organism are exposed to seasonal changes in temperature and its effect is irreversible, while reversible short-term acclimation occurs daily in response to diurnal changes in temperature. Wild flies were selected from a temperate population across seasons and two cold tolerance metrics (chill-coma recovery and cold stress survival) and their responses to developmental and short-term acclimation were measured. Chill-coma recovery responded to seasonal shifts in temperature, and phenotypic plasticity following both short-term and developmental acclimation improved cold tolerance. This improvement indicated that both types of plasticity are adaptive, and that plasticity can compensate for genetic variation in basal cold tolerance during warmer parts of the season when flies tend to be less cold tolerant. A significantly stronger trade-off was observed between basal cold tolerance and short-term acclimation during warmer months. For the longer-term developmental acclimation, a trade-off persisted regardless of season. A relationship between the two types of plasticity may provide additional insight into why some measures of thermal tolerance are more sensitive to seasonal variation than others.
Morimoto, J., Simpson, S. J. and Ponton, F. (2017). Direct and trans-generational effects of male and female gut microbiota in Drosophila melanogaster. Biol Lett 13(7). PubMed ID: 28724687
There is increasing evidence of the far-reaching effects of gut bacteria on physiological and behavioural traits, yet the fitness-related consequences of changes in the gut bacteria composition of sexually interacting individuals remain unknown. To address this question, the gut microbiota of fruit flies, Drosophila melanogaster, were manipulated by monoinfecting flies with either Acetobacter pomorum (AP) or Lactobacillus plantarum (LP). Re-inoculated individuals were paired in all treatment combinations. LP-infected males had longer mating duration and induced higher short-term offspring production in females compared with AP-infected males. Furthermore, females of either re-inoculation state mated with AP-infected males were more likely to have zero offspring after mating, suggesting a negative effect of AP on male fertility. Finally, the effects of male and female gut bacteria interacted to modulate their daughters', but not sons' body mass, revealing a new trans-generational effect of parental gut microbiota. In conclusion, this study shows direct and trans-generational effects of the gut microbiota on mating and reproduction.
Poudel, S., Kim, Y., Gwak, J. S., Jeong, S. and Lee, Y. (2017). Gustatory receptor 22e is essential for sensing chloroquine and strychnine in Drosophila melanogaster. Insect Biochem Mol Biol 88: 30-36. PubMed ID: 28751111
Chloroquine, an amino quinolone derivative commonly used as an anti-malarial drug, is known to impart an unpleasant taste. Little research has been done to study chloroquine taste in insects; therefore, this study examined both the deterrant properties and mechanisms underlying chloroquine perception in fruit flies. The antifeedant effect of chloroquine was identified by screening 21 gustatory receptor (Grs) mutants through behavioral feeding assays and electrophysiology experiments. Two molecular sensors, GR22e and GR33a, were found to act as chloroquine receptors, and chloroquine-mediated activation of GRNs was found to occur through S-type sensilla. At the same time, the chloroquine receptor was successfully recapitulated by expressing GR22e in ectopic gustatory receptor neurons. GR22e was found to form a part of the strychnine receptor. It is suggested that the Drosophila strychnine receptor might have a very complex structure since five different GRs are required for strychnine-induced action potentials.
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