Closely Related Fruit Fly Species Living at Different Latitudes Diverge in Their Circadian Clock Anatomy and Rhythmic Behavior

2018 ◽  
Vol 33 (6) ◽  
pp. 602-613 ◽  
Author(s):  
Marta Beauchamp ◽  
Enrico Bertolini ◽  
Peter Deppisch ◽  
Jonathan Steubing ◽  
Pamela Menegazzi ◽  
...  
Keyword(s):  
Circadian Clock ◽  
High Latitude ◽  
Expression Patterns ◽  
Fruit Fly ◽  
Adaptive Significance ◽  
High Latitudes ◽  
Pigment Dispersing Factor ◽  
Clock Network ◽  
Rhythmic Behavior ◽  
And Behavior

Recently, we reported differences in the expression pattern of the blue light-sensitive flavoprotein cryptochrome (CRY) and the neuropeptide pigment-dispersing factor (PDF) in the neuronal clock network of high-latitude Drosophila species, belonging to the Drosophila subgenus ( virilis-repleta radiation), compared with cosmopolitan D. melanogaster flies, belonging to the Sophophora subgenus. Alterations in rhythmic patterns of activity due to these differences might have adaptive significance for colonizing high-latitude habitats and, hence, adjusting to long photoperiods. Here, we show that these differing CRY/PDF expression patterns are only present in those species of the virilis-repleta radiation that colonized high latitudes. The cosmopolitan species D. mercatorum and D. hydei have a D. melanogaster-like clock network and behavior despite belonging to the virilis-repleta radiation. Similarly, 2 species of the holotropical Zaprionus genus, more closely related to the Drosophila subgenus than to the Sophophora subgenus, retain a D. melanogaster-like clock network and rhythmic behavior. We therefore suggest that the D. melanogaster-like clock network is the “ancestral fly clock phenotype” and that alterations in the CRY/PDF clock neurochemistry have allowed some species of the virilis-repleta radiation to colonize high-latitude environments.

scholarly journals NoRCE: non-coding RNA sets cis enrichment tool

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gulden Olgun ◽  
Afshan Nabi ◽  
Oznur Tastan
Keyword(s):  
Expression Patterns ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Fruit Fly ◽  
Relevant Information ◽  
R Package ◽  
Data Repository ◽  
Biologically Relevant ◽  
Gene Sets ◽  
Data Files

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

scholarly journals The circadian clock uses different environmental time cues to synchronize emergence and locomotion of the solitary bee Osmia bicornis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Katharina Beer ◽  
Mariela Schenk ◽  
Charlotte Helfrich-Förster ◽  
Andrea Holzschuh
Keyword(s):  
Circadian Clock ◽  
Circadian System ◽  
Evolutionary Adaptation ◽  
Solitary Bee ◽  
Daily Rhythms ◽  
Osmia Bicornis ◽  
Cavity Nesting ◽  
Impact On Survival ◽  
Life On Earth ◽  
And Behavior

AbstractLife on earth adapted to the daily reoccurring changes in environment by evolving an endogenous circadian clock. Although the circadian clock has a crucial impact on survival and behavior of solitary bees, many aspects of solitary bee clock mechanisms remain unknown. Our study is the first to show that the circadian clock governs emergence in Osmia bicornis, a bee species which overwinters as adult inside its cocoon. Therefore, its eclosion from the pupal case is separated by an interjacent diapause from its emergence in spring. We show that this bee species synchronizes its emergence to the morning. The daily rhythms of emergence are triggered by temperature cycles but not by light cycles. In contrast to this, the bee’s daily rhythms in locomotion are synchronized by light cycles. Thus, we show that the circadian clock of O. bicornis is set by either temperature or light, depending on what activity is timed. Light is a valuable cue for setting the circadian clock when bees have left the nest. However, for pre-emerged bees, temperature is the most important cue, which may represent an evolutionary adaptation of the circadian system to the cavity-nesting life style of O. bicornis.

Stability of the Synechococcus elongatus PCC 7942 circadian clock under directed anti-phase expression of the kai genes

Microbiology ◽  
2005 ◽  
Vol 151 (8) ◽  
pp. 2605-2613 ◽  
Author(s):  
Jayna L. Ditty ◽  
Shannon R. Canales ◽  
Breanne E. Anderson ◽  
Stanly B. Williams ◽  
Susan S. Golden
Keyword(s):  
Circadian Clock ◽  
Expression Patterns ◽  
Phase Relationship ◽  
Synechococcus Elongatus ◽  
Cycle Period ◽  
Rhythmic Expression ◽  
Core Components ◽  
Synechococcus Elongatus Pcc 7942 ◽  
Time Required ◽  
Pcc 7942

The kaiA, kaiB and kaiC genes encode the core components of the cyanobacterial circadian clock in Synechococcus elongatus PCC 7942. Rhythmic expression patterns of kaiA and of the kaiBC operon normally peak in synchrony. In some mutants the relative timing of peaks (phase relationship) between these transcription units is altered, but circadian rhythms persist robustly. In this study, the importance of the transcriptional timing of kai genes was examined. Expressing either kaiA or kaiBC from a heterologous promoter whose peak expression occurs 12 h out of phase from the norm, and thus 12 h out of phase from the other kai locus, did not affect the time required for one cycle (period) or phase of the circadian rhythm, as measured by bioluminescence reporters. Furthermore, the data confirm that specific cis elements within the promoters of the kai genes are not necessary to sustain clock function.

scholarly journals A54 THE CIRCADIAN CLOCK INFLUENCES JAK/STAT SIGNALING AND GUT PERMEABILITY

2021 ◽  
Vol 4 (Supplement_1) ◽  
pp. 11-12
Author(s):  
K Parasram ◽  
D Bachetti ◽  
P Karpowicz
Keyword(s):  
Circadian Clock ◽  
Clock Cycle ◽  
Intestinal Barrier ◽  
Fruit Fly ◽  
Cell Types ◽  
Time Of Day ◽  
Acute Injury ◽  
Intestinal Barrier Function ◽  
Intestinal Immunity ◽  
Stat Signaling

Abstract Background The circadian clock is a 24-hour feedback loop that drives rhythms in behaviours and physiological processes. This molecular timekeeper consists of the transcription factors, Clock-Cycle, that drive expression of thousands of clock-controlled genes, with two of these, Period and Timeless, acting as negative regulators of Clock-Cycle. This fundamental mechanism was initially characterized in the fruit fly, Drosophila melanogaster (Nobel Prize in Physiology & Medicine, 2017), and is highly conserved in humans. The intestine, or midgut, of Drosophila, is also similar to the human small intestine consisting of similar cellular lineage, signaling pathways, and physiological functions. The lineage of the Drosophila intestine contains the same four cell types as humans: intestinal stem cells (ISCs), progenitors called enteroblasts, enterocytes and enteroendocrine cells. This simplified lineage as well as the genetic tools available, make Drosophila an ideal model for intestinal regeneration in health and disease. We have previously shown that the circadian clock is active in ISCs, EBs and ECs during both homeostatic and regenerating conditions. Furthermore, the circadian clock regulates the mitosis of ISCs under regenerating conditions. Aims We sought to uncover if Jak/STAT signaling, one of the key pathways involved in ISC proliferation in the Drosophila intestine, shows a circadian rhythm and if there is a time-of-day difference in the regenerative response. Methods To test whether the clock regulates Jak/STAT during acute injury, we developed an irradiation assay that does not affect survival but acutely disrupts intestinal barrier function. Results Using a dynamic reporter of Jak/STAT activity we show that Period circadian clock mutants have low Jak/STAT signaling and a leaky gut phenotype. Wildtype controls show time-dependent gut leakiness upon irradiation, which is higher and time-independent in Period mutants. The level of Jak/STAT response differs depending on the time of irradiation in the controls, but is higher at all times in the mutants. Conclusions The Jak/Stat pathway regulates intestinal immunity and epithelial cell proliferation in humans, thus playing a role in colorectal cancer and inflammatory bowel disease. Our results suggest Jak/Stat is controlled by the circadian clock, which has implications for intestinal recovery following medical treatments, including radiation therapy. Funding Agencies NRC

High Latitude Dust: contemporary emissions and geomorphic interactions

2021 ◽  
Author(s):  
Joanna Bullard
Keyword(s):  
Remote Sensing ◽  
Environmental Change ◽  
High Latitude ◽  
Cold Climate ◽  
Sediment Supply ◽  
Future Research ◽  
Similar Proportion ◽  
High Latitudes ◽  
Dust Emissions ◽  
Dust Sources

<div> <p>The world’s largest contemporary dust sources are in low-lying, hot, arid regions, however the processes of dust production and emission also operate in cold climate regions at high latitudes and altitudes.  This lecture focuses on contemporary dust emissions originating from the high latitudes (≥50°N and ≥40°S) and explores three themes before setting out an integrated agenda for future research.  The first theme considers how much dust originates from the high latitudes and methods for determining this.  Estimates from field studies, remote sensing and modelling all suggest around 5% of contemporary global dust emissions originate in the high latitudes, a similar proportion to that from the USA (excluding Alaska) or Australia.  This estimate is a proportion of a highly uncertain figure as quantification of dust emissions from Eurasian high latitudes is limited, and the contribution of local and regional emissions (from any latitude) to the global total is thought to be considerably under-estimated.  Emissions are particularly likely to be under-estimated where dust sources are topographically constrained, and where cold climates reduce vertical mixing of dust plumes restricting the altitudes to which the dust can rise, because both these characteristics present particular challenges for modelling and remote sensing approaches. The second theme considers the drivers of contemporary high latitude dust emissions that reflect complex interactions among sediment supply, sediment availability and transport capacity across different geomorphic sub-systems.  These interactions determine the magnitude, frequency and timing of dust emissions at a range of time scales (diurnal, seasonal, decadal) but both the drivers and response can be nonlinear and hard to predict.  The third and final theme explores the importance of high latitude dust cycling for facilitating cross-boundary material fluxes and its impact in the atmosphere, cryosphere, and terrestrial and marine ecosystems.  This is influenced not only by the quantity and timing of dust emissions but also by dust properties such as particle-size and geochemistry.  Landscape sensitivity, spatial environmental transitions and temporal environmental change are highlighted for their importance in determining how the interactions among drivers and cycles are likely to change in response to future environmental change.</p> </div>

Emx1 and Emx2 functions in development of dorsal telencephalon

Development ◽  
1997 ◽  
Vol 124 (1) ◽  
pp. 101-111 ◽  
Author(s):  
M. Yoshida ◽  
Y. Suda ◽  
I. Matsuo ◽  
N. Miyamoto ◽  
N. Takeda ◽  
...  
Keyword(s):  
Dentate Gyrus ◽  
Expression Patterns ◽  
Lateral Shift ◽  
Cerebral Hemispheres ◽  
Limbic Cortex ◽  
Lateral Region ◽  
Gap Gene ◽  
Positive Region ◽  
Dorsal Telencephalon ◽  
And Behavior

The genes Emx1 and Emx2 are mouse cognates of a Drosophila head gap gene, empty spiracles, and their expression patterns have suggested their involvement in regional patterning of the forebrain. To define their functions we introduced mutations into these loci. The newborn Emx2 mutants displayed defects in archipallium structures that are believed to play essential roles in learning, memory and behavior: the dentate gyrus was missing, and the hippocampus and medial limbic cortex were greatly reduced in size. In contrast, defects were subtle in adult Emx1 mutant brain. In the early developing Emx2 mutant forebrain, the evagination of cerebral hemispheres was reduced and the roof between the hemispheres was expanded, suggesting the lateral shift of its boundary. Defects were not apparent, however, in the region where Emx1 expression overlaps that of Emx2, nor was any defect found in the early embryonic forebrain caused by mutation of the Emx1 gene, of which expression principally occurs within the Emx2-positive region. Emx2 most likely delineates the palliochoroidal boundary in the absence of Emx1 expression during early dorsal forebrain patterning. In the more lateral region of telencephalon, Emx2-deficiency may be compensated for by Emx1 and vice versa. Phenotypes of newborn brains also suggest that these genes function in neurogenesis corresponding to their later expressions.

scholarly journals Circadian Control of Global Transcription

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Shujing Li ◽  
Luoying Zhang
Keyword(s):  
Transcription Factors ◽  
Environmental Conditions ◽  
Fruit Fly ◽  
Biological Pathways ◽  
Model Organisms ◽  
Molecular Clocks ◽  
Rhythmic Expression ◽  
The Earth ◽  
Circadian Control ◽  
And Behavior

Circadian rhythms exist in most if not all organisms on the Earth and manifest in various aspects of physiology and behavior. These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs). CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. The transcription of CCGs is tuned by rhythmic actions of transcription factors and circadian alterations in chromatin. Here, we review the circadian control of CCG transcription in five model organisms that are widely used, including cyanobacterium, fungus, plant, fruit fly, and mouse. Comparing the similarity and differences in the five organisms could help us better understand the function of the circadian clock, as well as its output mechanisms adapted to meet the demands of diverse environmental conditions.

scholarly journals Transcriptome characterization analysis and molecular profiles of obligatory diapause induction of the Chinese citrus fruit fly,Bactrocera minax(Diptera: Tephritidae)

2019 ◽  
Author(s):  
Zhixiong Zhou ◽  
Xiaolin Dong ◽  
Chuanren Li
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Citrus Fruit ◽  
Pupal Stage ◽  
Fruit Fly ◽  
Diapause Induction ◽  
Regulation Mechanism ◽  
Pupal Diapause ◽  
Specific Stage

AbstractThe Chinese citrus fruit fly,Bactrocera minax, is a devastating citrus pest in China, Bhutan and India. It will enter obligatory pupal diapause in each generation at specific stage, while little is known about the course and the molecular mechanisms of diapause induction. To gain insight into possible mechanisms of obligatory pupal diapause induction, high-throughput RNA-seq data were generated from second-instar larvae (2L), third-instar larvae (3L) and pupal (P, one week after pupating). A total of 116,402 unigenes were assembled and researched against public databases, and 54,781 unigenes matched to proteins in the NCBI database using the BLAST search. Three pairwise comparisons were performed, and significantly differentially regulated transcripts were identified. Several differentially expressed genes (DEGs) expression patterns revealed that those highly or lowly expressed genes in pupal stage were predicted to be involved in diapause induction. Moreover, GO function and KEGG pathway analysis were performed on all DEGs and showed that 20-hydroxyecdysone (20E) biosynthesis, insulin signaling pathway, FoxO signaling pathway, cell cycle and metabolism pathway may be related to the obligatory diapause of the Chinese citrus fruit fly. This study provides valuable information about the Chinese citrus fruit fly transcriptome for future gene function research, and contributes to the in-depth elucidation of the molecular regulation mechanism of insect obligatory diapause induction.

scholarly journals Attenuated SIRT1 Activity Leads to PER2 Cytoplasmic Localization and Dampens the Amplitude of Bmal1 Promoter-Driven Circadian Oscillation

2021 ◽  
Vol 15 ◽  
Author(s):  
Atsushige Ashimori ◽  
Yasukazu Nakahata ◽  
Toshiya Sato ◽  
Yuichiro Fukamizu ◽  
Takaaki Matsui ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Circadian Clock ◽  
Posttranslational Modifications ◽  
Cultured Cells ◽  
Circadian Oscillation ◽  
Clock Proteins ◽  
Circadian Clock Proteins ◽  
Circadian Physiology ◽  
And Behavior ◽  
Robust Systems

The circadian clock possesses robust systems to maintain the rhythm approximately 24 h, from cellular to organismal levels, whereas aging is known to be one of the risk factors linked to the alternation of circadian physiology and behavior. The amount of many metabolites in the cells/body is altered with the aging process, and the most prominent metabolite among them is the oxidized form of nicotinamide adenine dinucleotide (NAD+), which is associated with posttranslational modifications of acetylation and poly-ADP-ribosylation status of circadian clock proteins and decreases with aging. However, how low NAD+ condition in cells, which mimics aged or pathophysiological conditions, affects the circadian clock is largely unknown. Here, we show that low NAD+ in cultured cells promotes PER2 to be retained in the cytoplasm through the NAD+/SIRT1 axis, which leads to the attenuated amplitude of Bmal1 promoter-driven luciferase oscillation. We found that, among the core clock proteins, PER2 is mainly affected in its subcellular localization by NAD+ amount, and a higher cytoplasmic PER2 localization was observed under low NAD+ condition. We further found that NAD+-dependent deacetylase SIRT1 is the regulator of PER2 subcellular localization. Thus, we anticipate that the altered PER2 subcellular localization by low NAD+ is one of the complex changes that occurs in the aged circadian clock.

scholarly journals Peripheral Sensory Organs Contribute to Temperature Synchronization of the Circadian Clock in Drosophila melanogaster

2021 ◽  
Vol 12 ◽  
Author(s):  
Rebekah George ◽  
Ralf Stanewsky
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Circadian Clock ◽  
Temperature Fluctuations ◽  
Fruit Fly ◽  
Circadian Clocks ◽  
Sensory Cells ◽  
Clock Gene Expression ◽  
External Time ◽  
Peripheral Sensory

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

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