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Journal articles on the topic 'Circadian cycle characterization'
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Masana, Monica I., Isabel C. Sumaya, Michael Becker-Andre, and Margarita L. Dubocovich. "Behavioral characterization and modulation of circadian rhythms by light and melatonin in C3H/HeN mice homozygous for the RORβ knockout." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 292, no. 6 (June 2007): R2357—R2367. http://dx.doi.org/10.1152/ajpregu.00687.2006.
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This study reports for the first time the effects of retinoid-related orphan receptors [RORβ; receptor gene deletion RORβ(C3H)−/−] in C3H/HeN mice on behavioral and circadian phenotypes. Pineal melatonin levels showed a robust diurnal rhythm with high levels at night in wild-type (+/+), heterozygous (+/−), and knockout (−/−) mice. The RORβ(C3H)−/− mice displayed motor (“duck gait,” hind paw clasping reflex) and olfactory deficits, and reduced anxiety and learned helplessness-related behaviors. Circadian rhythms of wheel-running activity in all genotypes showed entrainment to the light-dark (LD) cycle, and free running in constant dark, with RORβ(C3H)−/− mice showing a significant increase in circadian period ( tau). Melatonin administration (90 μg/mouse sc for 3 days) at circadian time (CT) 10 induced phase advances, while exposure to a light pulse (300 lux) at CT 14 induced phase delays of circadian activity rhythms of the same magnitude in all genotypes. In RORβ(C3H)−/− mice a light pulse at CT 22 elicited a larger phase advance in activity rhythms and a slower rate of reentrainment after a 6-h advance in the LD cycle compared with (+/+) mice. Yet, the rate of reentrainment was significantly advanced by melatonin administration at the new dark onset in both (+/+) and (−/−) mice. We conclude that the RORβ nuclear receptor is not involved in either the rhythmic production of pineal melatonin or in mediating phase shifts of circadian rhythms by melatonin, but it may regulate clock responses to photic stimuli at certain time domains.
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MENGER, GUS J., JOSEPH R. KOKE, and GREGORY M. CAHILL. "Diurnal and circadian retinomotor movements in zebrafish." Visual Neuroscience 22, no. 2 (March 2005): 203–9. http://dx.doi.org/10.1017/s0952523805222083.
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Key indicators of circadian regulation include the persistence of physiological rhythmicity in the absence of environmental time cues and entrainment of this rhythmicity by the ambient light cycle. In some teleosts, the inner segments of rod and cone photoreceptors contract and elongate according to changes in ambient lighting and the circadian cycle. Pigment granules in the retinal pigment epithelium (RPE) disperse and aggregate in a similar manner. Collectively, these movements are known as retinomotor movements. We report the histological characterization of diurnal and circadian retinomotor movements in zebrafish, Danio rerio. Adult fish subjected to a 14:10 light:dark (LD) cycle, constant darkness (DD), or constant light (LL) were sacrificed at 1–13 h intervals and processed for semithin sectioning of the retina. Using bright-field microscopy, 15 measurements of pigment granule position and the inner segment lengths of 30 rods and 30–45 cones were collected from the central third of the dorso-optic retina per time point. In LD, rods and cones followed a clear diurnal rhythm in their inner segment movements. Short-single, UV-sensitive cones were found to contract significantly 1 h before light onset in LD conditions. In DD conditions, the inner segments movements of short-single and double cones displayed statistically significant rhythms. RPE pigment granule movements are rhythmically regulated in both LD and DD although fluctuations are damped in the absence of photic cues. No significant retinomotor movements were observed in LL. These findings indicate retinomotor movements in zebrafish are differentially regulated by an endogenous oscillator and by light-dependent mechanisms.
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Stack, Nora, Jamie M. Zeitzer, Charles Czeisler, and Cecilia Diniz Behn. "Estimating Representative Group Intrinsic Circadian Period from Illuminance-Response Curve Data." Journal of Biological Rhythms 35, no. 2 (November 29, 2019): 195–206. http://dx.doi.org/10.1177/0748730419886992.
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The human circadian pacemaker entrains to the 24-h day, but interindividual differences in properties of the pacemaker, such as intrinsic period, affect chronotype and mediate responses to challenges to the circadian system, such as shift work and jet lag, and the efficacy of therapeutic interventions such as light therapy. Robust characterization of circadian properties requires desynchronization of the circadian system from the rest-activity cycle, and these forced desynchrony protocols are very time and resource intensive. However, circadian protocols designed to derive the relationship between light intensity and phase shift, which is inherently affected by intrinsic period, may be applied more broadly. To exploit this relationship, we applied a mathematical model of the human circadian pacemaker with a Markov-Chain Monte Carlo parameter estimation algorithm to estimate the representative group intrinsic period for a group of participants using their collective illuminance-response curve data. We first validated this methodology using simulated illuminance-response curve data in which the intrinsic period was known. Over a physiological range of intrinsic periods, this method accurately estimated the representative intrinsic period of the group. We also applied the method to previously published experimental data describing the illuminance-response curve for a group of healthy adult participants. We estimated the study participants’ representative group intrinsic period to be 24.26 and 24.27 h using uniform and normal priors, respectively, consistent with estimates of the average intrinsic period of healthy adults determined using forced desynchrony protocols. Our results establish an approach to estimate a population’s representative intrinsic period from illuminance-response curve data, thereby facilitating the characterization of intrinsic period across a broader range of participant populations than could be studied using forced desynchrony protocols. Future applications of this approach may improve the understanding of demographic differences in the intrinsic circadian period.
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Reis, Daniel, and Nazanin Bahraini. "0022 Characterization and Evaluation of Digital Dim Light Melatonin Onset in a Population-Based Sample." SLEEP 46, Supplement_1 (May 1, 2023): A9—A10. http://dx.doi.org/10.1093/sleep/zsad077.0022.
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Abstract Introduction Misalignment between circadian phase (i.e., timing) and the desired sleep window is associated with sleep disturbances including insomnia and circadian rhythm sleep-wake disorders. Identifying circadian-driven sleep disruption requires assessment of circadian phase, the gold-standard of which is dim light melatonin onset (DLMO). While DLMO is traditionally measured in the lab using saliva or blood sampled over multiple hours, novel methods of estimating DLMO using activity and light data obtained from wearable sensors (i.e., digital DLMO) have been recently validated in samples with both healthy and disordered sleep. Such methods could potentially provide pragmatic, low-burden ways of assessing circadian phase, which in turn could be used to aid diagnostic decisions and to adjust circadian-targeted interventions in real time. However, digital DLMO has yet to be characterized within the broader adult population, which is needed to differentiate between normative and clinically salient values. Therefore, this study will examine digital DLMO in a large, population-based sample, as well as explore the potential clinical utility of digital biomarkers related to circadian phase. Methods This study will be a secondary analysis of data obtained during the ancillary sleep study of the Multi-Ethnic Study of Atherosclerosis (i.e., MESA Sleep). Seven days of activity and light data, measured via wrist-worn actigraphy, were obtained from 2,237 participants. Digital DLMO will be estimated using the extended Kronauer limit-cycle model of the human circadian pacemaker. Phase angles, or the differences in clock time, between digital DLMO and the following will be calculated: self-reported in-bed time; and sleep onset, midpoint, and offset measured by actigraphy. The associations between these phase angles and sleep outcomes (i.e., sleep onset latency, sleep efficiency, and sleep quality) will be explored using linear regression. Covariates will include the age, gender, and race/ethnicity of the participant. Weekend and weekday averages will be evaluated separately. Results Results will include the distribution of digital DLMO in a population-based sample, as well as the associations between digital DLMO phase angles and sleep outcomes. Conclusion This study will inform future research into the clinical potential of digital circadian biomarkers. Support (if any)
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Vollenweider, Stephanie, Anna Wirz-Justice, Josef Flammer, Selim Orgül, and Kurt Kräuchi. "Chronobiological characterization of women with primary vasospastic syndrome: body heat loss capacity in relation to sleep initiation and phase of entrainment." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 294, no. 2 (February 2008): R630—R638. http://dx.doi.org/10.1152/ajpregu.00609.2007.
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Women with primary vasospastic syndrome (VS), but otherwise healthy, exhibit a functional disorder of vascular regulation (main symptom: cold extremities) and often suffer from difficulties initiating sleep (DIS). Diverse studies have shown a close association between distal vasodilatation before lights off and a rapid onset of sleep. Therefore, we hypothesized that DIS in women with VS could be due to a reduced heat loss capacity in the evening, i.e., subjects are physiologically not ready for sleep. The aim of the study was to elucidate whether women having both VS and DIS (WVD) or not (controls) show different circadian characteristics (e.g., phase delay of the circadian thermoregulatory system with respect to the sleep-wake cycle). Healthy young women ( n = 9 WVD and n = 9 control) completed a 40-h constant routine protocol (adjusted to habitual bedtime) before and after an 8-h sleep episode. Skin temperatures [off-line calculated as distal-proximal skin temperature gradient (DPG)] and core body temperature (CBT; rectal) were continuously recorded. Half-hourly saliva samples were collected for melatonin assay and subjective sleepiness was assessed on the Karolinska Sleepiness Scale (KSS). Compared with control, WVD showed no differences in habitual bed times, but a 1-h circadian phase delay of dim light-melatonin onset (hours after lights on: WVD 14.6 ± 0.3 h; control 13.5 ± 0.2 h; P = 0.01). Similar phase shifts were observed in CBT, DPG, and KSS ratings. In conclusion, WVD exhibit a phase delay of the endogenous circadian system with respect to their habitual sleep-wake cycle, which could be a cause of DIS.
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Zhang, Luoying, Arisa Hirano, Pei-Ken Hsu, Christopher R. Jones, Noriaki Sakai, Masashi Okuro, Thomas McMahon, et al. "A PERIOD3 variant causes a circadian phenotype and is associated with a seasonal mood trait." Proceedings of the National Academy of Sciences 113, no. 11 (February 22, 2016): E1536—E1544. http://dx.doi.org/10.1073/pnas.1600039113.
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In humans, the connection between sleep and mood has long been recognized, although direct molecular evidence is lacking. We identified two rare variants in the circadian clock gene PERIOD3 (PER3-P415A/H417R) in humans with familial advanced sleep phase accompanied by higher Beck Depression Inventory and seasonality scores. hPER3-P415A/H417R transgenic mice showed an altered circadian period under constant light and exhibited phase shifts of the sleep-wake cycle in a short light period (photoperiod) paradigm. Molecular characterization revealed that the rare variants destabilized PER3 and failed to stabilize PERIOD1/2 proteins, which play critical roles in circadian timing. Although hPER3-P415A/H417R-Tg mice showed a mild depression-like phenotype, Per3 knockout mice demonstrated consistent depression-like behavior, particularly when studied under a short photoperiod, supporting a possible role for PER3 in mood regulation. These findings suggest that PER3 may be a nexus for sleep and mood regulation while fine-tuning these processes to adapt to seasonal changes.
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Taroncher-Oldenburg, Gaspar, and Donald M. Anderson. "Identification and Characterization of Three Differentially Expressed Genes, Encoding S-Adenosylhomocysteine Hydrolase, Methionine Aminopeptidase, and a Histone-Like Protein, in the Toxic Dinoflagellate Alexandrium fundyense." Applied and Environmental Microbiology 66, no. 5 (May 1, 2000): 2105–12. http://dx.doi.org/10.1128/aem.66.5.2105-2112.2000.
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ABSTRACT Genes showing differential expression related to the early G1 phase of the cell cycle during synchronized circadian growth of the toxic dinoflagellate Alexandrium fundyensewere identified and characterized by differential display (DD). The determination in our previous work that toxin production inAlexandrium is relegated to a narrow time frame in early G1 led to the hypothesis that transcriptionally up- or downregulated genes during this subphase of the cell cycle might be related to toxin biosynthesis. Three genes, encodingS-adenosylhomocysteine hydrolase (Sahh), methionine aminopeptidase (Map), and a histone-like protein (HAf), were isolated. Sahh was downregulated, while Map and HAf were upregulated, during the early G1 phase of the cell cycle. Sahh andMap encoded amino acid sequences with about 90 and 70% similarity to those encoded by several eukaryotic and prokaryoticSahh and Map genes, respectively. The partialMap sequence also contained three cobalt binding motifs characteristic of all Map genes. HAf encoded an amino acid sequence with 60% similarity to those of two histone-like proteins from the dinoflagellate Crypthecodinium cohniiBiecheler. This study documents the potential of applying DD to the identification of genes that are related to physiological processes or cell cycle events in phytoplankton under conditions where small sample volumes represent an experimental constraint. The identification of an additional 21 genes with various cell cycle-related DD patterns also provides evidence for the importance of pretranslational or transcriptional regulation in dinoflagellates, contrary to previous reports suggesting the possibility that translational mechanisms are the primary means of circadian regulation in this group of organisms.
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Oh, Vera-Khlara S., and Robert W. Li. "Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data." Genes 12, no. 3 (February 27, 2021): 352. http://dx.doi.org/10.3390/genes12030352.
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Dynamic studies in time course experimental designs and clinical approaches have been widely used by the biomedical community. These applications are particularly relevant in stimuli-response models under environmental conditions, characterization of gradient biological processes in developmental biology, identification of therapeutic effects in clinical trials, disease progressive models, cell-cycle, and circadian periodicity. Despite their feasibility and popularity, sophisticated dynamic methods that are well validated in large-scale comparative studies, in terms of statistical and computational rigor, are less benchmarked, comparing to their static counterparts. To date, a number of novel methods in bulk RNA-Seq data have been developed for the various time-dependent stimuli, circadian rhythms, cell-lineage in differentiation, and disease progression. Here, we comprehensively review a key set of representative dynamic strategies and discuss current issues associated with the detection of dynamically changing genes. We also provide recommendations for future directions for studying non-periodical, periodical time course data, and meta-dynamic datasets.
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Naseri Kouzehgarani, Ghazal, Mikhail E. Kandel, Masayoshi Sakakura, Joshua S. Dupaty, Gabriel Popescu, and Martha U. Gillette. "Circadian Volume Changes in Hippocampal Glia Studied by Label-Free Interferometric Imaging." Cells 11, no. 13 (June 30, 2022): 2073. http://dx.doi.org/10.3390/cells11132073.
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Complex brain functions, including learning and memory, arise in part from the modulatory role of astrocytes on neuronal circuits. Functionally, the dentate gyrus (DG) exhibits differences in the acquisition of long-term potentiation (LTP) between day and night. We hypothesize that the dynamic nature of astrocyte morphology plays an important role in the functional circuitry of hippocampal learning and memory, specifically in the DG. Standard microscopy techniques, such as differential interference contrast (DIC), present insufficient contrast for detecting changes in astrocyte structure and function and are unable to inform on the intrinsic structure of the sample in a quantitative manner. Recently, gradient light interference microscopy (GLIM) has been developed to upgrade a DIC microscope with quantitative capabilities such as single-cell dry mass and volume characterization. Here, we present a methodology for combining GLIM and electrophysiology to quantify the astrocyte morphological behavior over the day-night cycle. Colocalized measurements of GLIM and fluorescence allowed us to quantify the dry masses and volumes of hundreds of astrocytes. Our results indicate that, on average, there is a 25% cell volume reduction during the nocturnal cycle. Remarkably, this cell volume change takes place at constant dry mass, which suggests that the volume regulation occurs primarily through aqueous medium exchange with the environment.
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Unruh, Benjamin A., and Shihoko Kojima. "The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in Mammals." Journal of Biological Rhythms 35, no. 6 (September 23, 2020): 519–29. http://dx.doi.org/10.1177/0748730420957498.
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The identification and characterization of rhythmically expressed mRNAs have been an active area of research over the past 20 years, as these mRNAs are believed to produce the daily rhythms in a wide range of biological processes. Circadian transcriptome studies have used mature mRNA as a primary readout and focused largely on rhythmic RNA synthesis as a regulatory mechanism underlying rhythmic mRNA expression. However, RNA synthesis, RNA degradation, or a combination of both must be rhythmic to drive rhythmic RNA profiles, and it is still unclear to what extent rhythmic synthesis leads to rhythmic RNA profiles. In addition, circadian RNA expression is also often tissue specific. Although a handful of genes cycle in all or most tissues, others are rhythmic only in certain tissues, even though the same core clock mechanism is believed to control the rhythmic RNA profiles in all tissues. This review focuses on the dynamics of rhythmic RNA synthesis and degradation and discusses how these steps collectively determine the rhythmicity, phase, and amplitude of RNA accumulation. In particular, we highlight a possible role of RNA degradation in driving tissue-specific RNA rhythms. By unifying findings from experimental and theoretical studies, we will provide a comprehensive overview of how rhythmic gene expression can be achieved and how each regulatory step contributes to tissue-specific circadian transcriptome output in mammals.
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Fernández, J. R., R. C. Hermida, and A. Mojón. "Chronobiological analysis techniques. Application to blood pressure." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 367, no. 1887 (October 22, 2008): 431–45. http://dx.doi.org/10.1098/rsta.2008.0231.
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Most variables of clinical interest show predictable changes with different frequencies, mainly, but not exclusively, along the rest–activity cycle (circadian variation). Methods of linear least-squares estimation have been designed for the detection of periodic components in sparse and noisy time series (as they are usually present in clinical situations). They include the single and population-mean cosinor methods. In cases where more than one period is statistically significant over the span of time investigated, or when the waveform is non-sinusoidal, the use of multiple components analysis to fit a model consisting of several cosine functions (harmonics or not from a given fundamental period) is recommended. We describe these methods, from the characterization of the underlying models to the process of parameter estimation. As an application example, we describe the modelling of the circadian variation of blood pressure (BP). In most individuals, BP presents a morning increase, a small postprandial valley and a deeper descent during nocturnal rest. This pattern can be easily modelled by means of a model with periods of 24 and 12 hours. Individuals that differ from this model might be considered to present increased cardiovascular risk.
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Zhao, Bin, Claudia Schneid, Dobromir Iliev, Eva-Maria Schmidt, Volker Wagner, Franziska Wollnik, and Maria Mittag. "The Circadian RNA-Binding Protein CHLAMY 1 Represents a Novel Type Heteromer of RNA Recognition Motif and Lysine Homology Domain-Containing Subunits." Eukaryotic Cell 3, no. 3 (June 2004): 815–25. http://dx.doi.org/10.1128/ec.3.3.815-825.2004.
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ABSTRACT The RNA-binding protein CHLAMY 1 from Chlamydomonas reinhardtii binds specifically to UG(≥7) repeat sequences situated in the 3′ untranslated regions of several mRNAs. Its binding activity is controlled by the circadian clock. The biochemical purification and characterization of CHLAMY 1 revealed a novel type of RNA-binding protein. It includes two different subunits (named C1 and C3), whose interaction appears necessary for RNA binding. One of them (C3) belongs to the proteins of the CELF (CUG-BP-ETR-3-like factors) family and thus bears three RNA recognition motif domains. The other is composed of three lysine homology domains and a protein-protein interaction domain (WW). The subunits C1 and C3 have theoretical molecular masses of 45 and 52 kDa, respectively, and are present in nearly equal amounts during the circadian cycle. At the beginning of the subjective night, both can be found in protein complexes of 100 to 160 kDa. However, during subjective day when binding activity of CHLAMY 1 is low, the C1 subunit in addition is present in a high-molecular-mass protein complex of more than 680 kDa. These data indicate posttranslational control of the circadian binding activity of CHLAMY 1. Notably, the C3 subunit shows significant homology to the rat CUG-binding protein 2. Anti-C3 antibodies can recognize the rat homologue, which can also be found in a protein complex in this vertebrate.
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Brunelle, Stephanie A., E. Starr Hazard, Erik E. Sotka, and Frances M. Van Dolah. "CHARACTERIZATION OF A DINOFLAGELLATE CRYPTOCHROME BLUE-LIGHT RECEPTOR WITH A POSSIBLE ROLE IN CIRCADIAN CONTROL OF THE CELL CYCLE." Journal of Phycology 43, no. 3 (June 2007): 509–18. http://dx.doi.org/10.1111/j.1529-8817.2007.00339.x.
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van der Schalie, Ellena A., Francesca E. Conte, Karla E. Marz, and Carla B. Green. "Structure/Function Analysis of Xenopus Cryptochromes 1 and 2 Reveals Differential Nuclear Localization Mechanisms and Functional Domains Important forInteraction with and Repression of CLOCK-BMAL1." Molecular and Cellular Biology 27, no. 6 (January 8, 2007): 2120–29. http://dx.doi.org/10.1128/mcb.01638-06.
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ABSTRACT Circadian rhythms control the temporal arrangement of molecular, physiological, and behavioral processes within an organism and also synchronize these processes with the external environment. A cell autonomous molecular oscillator, consisting of interlocking transcriptional/translational feedback loops, drives the approximately 24-hour duration of these rhythms. The cryptochrome protein (CRY) plays a central part in the negative feedback loop of the molecular clock by translocating to the nucleus and repressing CLOCK and BMAL1, two transcription factors that comprise the positive elements in this cycle. In order to gain insight into the inner workings of this feedback loop, we investigated the structure/function relationships of Xenopus laevis CRY1 (xCRY1) and xCRY2 in cultured cells. The C-terminal tails of both xCRY1 and xCRY2 are sufficient for their nuclear localization but achieve it by different mechanisms. Through the generation and characterization of xCRY/photolyase chimeras, we found that the second half of the photolyase homology region (PHR) of CRY is important for repression through facilitating interaction with BMAL1. Characterization of these functional domains in CRYs will help us to better understand the mechanism of the known roles of CRYs and to elucidate new intricacies of the molecular clock.
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Al-anbagi, Mina Shihab, Nawal A. Rajab, Mohammed Abd-Alhussein Aljodah, and Zaid Al-Attar. "Preparation and Characterization of Sumatriptan Timed Delivery System Using Combination of Natural and Synthetic Polymers." Open Access Macedonian Journal of Medical Sciences 10, A (February 15, 2022): 432–43. http://dx.doi.org/10.3889/oamjms.2022.8358.
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BACKGROUND: Pulsatile drug delivery systems are time-controlled dosage forms that release active pharmaceutical component after a predefined period in order to synchronize circadian cycle of illness. Migraine has a diurnal cycle, with episodes peaking between 6 a.m. and 8 a.m. Sumatriptan acts as a selective agonist for 5-Hydroxytryptamine1 (serotonin) receptors. Thus, it is an effective therapy for acute migraine episodes. AIM: The objective of the study is to create a time-controlled press-coated tablet containing two sumatriptan pulses. The first pulse demonstrated 100% active component release within 2 min, followed by the second sumatriptan pulse after just 5.5-h lag period. MATERIALS AND METHODS: We prepared eleven formulations for rapid dissolving core tablets and thirty-three formulations for press-coated tablet that were manufactured by direct compression technique. The third layer was then squeezed onto press-coated tablet to create a two-pulse-time-controlled system. The qualities of core tablets and coatings were examined using a variety of criteria. RESULTS: The formula F7 of core tablet was chosen because it had the lowest disintegration duration (8.8 s) with the quickest drug release within 2 min. In addition, formula C28 of the pectin-containing press-coated tablet: EC 100 mpa.s: HPMCK4M in concentrations of 20mg, 100 mg, and 80 mg were chosen as optimal coating layer. CONCLUSIONS: Utilizing pulsatile delivery system for sumatriptan is an effective strategy in resolving migraine attacks.
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Zanfino, Gioia, Concetto Puzzo, Vincenzo de Laurenzi, and Walter Adriani. "Characterization of Behavioral Phenotypes in Heterozygous DAT Rat Based on Pedigree." Biomedicines 11, no. 9 (September 18, 2023): 2565. http://dx.doi.org/10.3390/biomedicines11092565.
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Dopamine is an essential neurotransmitter whose key roles include movement control, pleasure and reward, attentional and cognitive skills, and regulation of the sleep/wake cycle. Reuptake is carried out by the dopamine transporter (DAT; DAT1 SLC6A3 gene). In order to study the effects of hyper-dopaminergia syndrome, the gene was silenced in rats. DAT-KO rats show stereotypical behavior, hyperactivity, a deficit in working memory, and an altered circadian cycle. In addition to KO rats, heterozygous (DAT-HET) rats show relative hypofunction of DAT; exact phenotypic effects are still unknown and may depend on whether the sire or the dam was KO. Our goal was to elucidate the potential importance of the parental origin of the healthy or silenced allele and its impact across generations, along with the potential variations in maternal care. We thus generated specular lines to study the effects of (grand) parental roles in inheriting the wild or mutated allele. MAT-HETs are the progeny of a KO sire and a WT dam; by breeding MAT-HET males and KO females, we obtained subjects with a DAT -/- epigenotype, named QULL, to reflect additional epigenetic DAT modulation when embryos develop within a hyper-dopaminergic KO uterus. We aimed to verify if any behavioral anomaly was introduced by a QULL (instead of KO) rat acting as a direct father or indirect maternal grandfather (or both). We thus followed epigenotypes obtained after three generations and observed actual effects on impaired maternal care of the offspring (based on pedigree). In particular, offspring of MAT-HET-dam × QULL-sire breeding showed a compulsive and obsessive phenotype. Although the experimental groups were all heterozygous, the impact of having a sire of epigenotype QULL (who developed in the uterus of a KO grand-dam) has emerged clearly. Along the generations, the effects of the DAT epigenotype on the obsessive/compulsive phenotype do vary as a function of the uterine impact on either allele in one’s genealogical line.
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Shen, Wen-Hui, Yves Parmentier, Hanjo Hellmann, Esther Lechner, Aiwu Dong, Jean Masson, Fabienne Granier, Loı̈c Lepiniec, Mark Estelle, and Pascal Genschik. "Null Mutation of AtCUL1 Causes Arrest in Early Embryogenesis in Arabidopsis." Molecular Biology of the Cell 13, no. 6 (June 2002): 1916–28. http://dx.doi.org/10.1091/mbc.e02-02-0077.
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The SCF (for SKP1, Cullin/CDC53,F-box protein) ubiquitin ligase targets a number of cell cycle regulators, transcription factors, and other proteins for degradation in yeast and mammalian cells. Recent genetic studies demonstrate that plant F-box proteins are involved in auxin responses, jasmonate signaling, flower morphogenesis, photocontrol of circadian clocks, and leaf senescence, implying a large spectrum of functions for the SCF pathway in plant development. Here, we present a molecular and functional characterization of plant cullins. TheArabidopsis genome contains 11 cullin-related genes. Complementation assays revealed that AtCUL1 but not AtCUL4 can functionally complement the yeast cdc53 mutant.Arabidopsis mutants containing transfer DNA (T-DNA) insertions in the AtCUL1 gene were shown to display an arrest in early embryogenesis. Consistently, both the transcript and the protein of the AtCUL1 gene were found to accumulate in embryos. The AtCUL1 protein localized mainly in the nucleus but also weakly in the cytoplasm during interphase and colocalized with the mitotic spindle in metaphase. Our results demonstrate a critical role for the SCF ubiquitin ligase inArabidopsis embryogenesis.
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Almutairi, Zainab M. "In Silico Identification and Characterization of B12D Family Proteins in Viridiplantae." Evolutionary Bioinformatics 18 (January 2022): 117693432211067. http://dx.doi.org/10.1177/11769343221106795.
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B12D family proteins are transmembrane proteins that contain the B12D domain involved in membrane trafficking. Plants comprise several members of the B12D family, but these members’ numbers and specific functions are not determined. This study aims to identify and characterize the members of B12D protein family in plants. Phytozome database was retrieved for B12D proteins from 14 species. The total 66 B12D proteins were analyzed in silico for gene structure, motifs, gene expression, duplication events, and phylogenetics. In general, B12D proteins are between 86 and 98 aa in length, have 2 or 3 exons, and comprise a single transmembrane helix. Motif prediction and multiple sequence alignment show strong conservation among B12D proteins of 11 flowering plants species. Despite that, the phylogenetic tree revealed a distinct cluster of 16 B12D proteins that have high conservation across flowering plants. Motif prediction revealed 41 aa motif conserved in 58 of the analyzed B12D proteins similar to the bZIP motif, confirming that in the predicted biological process and molecular function, B12D proteins are DNA-binding proteins. Cis-regulatory elements screening in putative B12D promoters found various responsive elements for light, abscisic acid, methyl jasmonate, cytokinin, drought, and heat. Despite that, there is specific elements for cold stress, cell cycle, circadian, auxin, salicylic acid, and gibberellic acid in the promoter of a few B12D genes indicating for functional diversification for B12D family members. The digital expression shows that B12D genes of Glycine max have similar expression patterns consistent with their clustering in the phylogenetic tree. However, the expression of B12D genes of Hordeum vulgure appears inconsistent with their clustering in the tree. Despite the strong conservation of the B12D proteins of Viridiplantae, gene association analysis, promoter analysis, and digital expression indicate different roles for the members of the B12D family during plant developmental stages.
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Beckwith, Esteban J., Katherine R. Lelito, Yun-Wei A. Hsu, Billie M. Medina, Orie Shafer, M. Fernanda Ceriani, and Horacio O. de la Iglesia. "Functional Conservation of Clock Output Signaling between Flies and Intertidal Crabs." Journal of Biological Rhythms 26, no. 6 (November 30, 2011): 518–29. http://dx.doi.org/10.1177/0748730411420242.
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Intertidal species have both circadian and circatidal clocks. Although the behavioral evidence for these oscillators is more than 5 decades old, virtually nothing is known about their molecular clockwork. Pigment-dispersing hormones (PDHs) were originally described in crustaceans. Their insect homologs, pigment-dispersing factors (PDFs), have a prominent role as clock output and synchronizing signals released from clock neurons. We show that gene duplication in crabs has led to two PDH genes (β -pdh-I and β -pdh-II). Phylogenetically, β -pdh-I is more closely related to insect pdf than to β -pdh-II, and we hypothesized that β-PDH-I may represent a canonical clock output signal. Accordingly, β-PDH-I expression in the brain of the intertidal crab Cancer productus is similar to that of PDF in Drosophila melanogaster, and neurons that express PDH-I also show CYCLE-like immunoreactivity. Using D. melanogaster pdf-null mutants ( pdf01) as a heterologous system, we show that β -pdh-I is indistinguishable from pdf in its ability to rescue the mutant arrhythmic phenotype, but β -pdh-II fails to restore the wild-type phenotype. Application of the three peptides to explanted brains shows that PDF and β-PDH-I are equally effective in inducing the signal transduction cascade of the PDF receptor, but β-PDH-II fails to induce a normal cascade. Our results represent the first functional characterization of a putative molecular clock output in an intertidal species and may provide a critical step towards the characterization of molecular components of biological clocks in intertidal organisms.
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Zera, Anthony J., and Zhangwu Zhao. "Morph-associated JH titer diel rhythm in Gryllus firmus: Experimental verification of its circadian basis and cycle characterization in artificially selected lines raised in the field." Journal of Insect Physiology 55, no. 5 (May 2009): 450–58. http://dx.doi.org/10.1016/j.jinsphys.2008.11.012.
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Cowley, Allen W., Carol Moreno, Howard J. Jacob, Christine B. Peterson, Francesco C. Stingo, Kwang Woo Ahn, Pengyuan Liu, et al. "Characterization of biological pathways associated with a 1.37 Mbp genomic region protective of hypertension in Dahl S rats." Physiological Genomics 46, no. 11 (June 1, 2014): 398–410. http://dx.doi.org/10.1152/physiolgenomics.00179.2013.
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The goal of the present study was to narrow a region of chromosome 13 to only several genes and then apply unbiased statistical approaches to identify molecular networks and biological pathways relevant to blood-pressure salt sensitivity in Dahl salt-sensitive (SS) rats. The analysis of 13 overlapping subcongenic strains identified a 1.37 Mbp region on chromosome 13 that influenced the mean arterial blood pressure by at least 25 mmHg in SS rats fed a high-salt diet. DNA sequencing and analysis filled genomic gaps and provided identification of five genes in this region, Rfwd2, Fam5b, Astn1, Pappa2, and Tnr. A cross-platform normalization of transcriptome data sets obtained from our previously published Affymetrix GeneChip dataset and newly acquired RNA-seq data from renal outer medullary tissue provided 90 observations for each gene. Two Bayesian methods were used to analyze the data: 1) a linear model analysis to assess 243 biological pathways for their likelihood to discriminate blood pressure levels across experimental groups and 2) a Bayesian graphical modeling of pathways to discover genes with potential relationships to the candidate genes in this region. As none of these five genes are known to be involved in hypertension, this unbiased approach has provided useful clues to be experimentally explored. Of these five genes, Rfwd2, the gene most strongly expressed in the renal outer medulla, was notably associated with pathways that can affect blood pressure via renal transcellular Na+ and K+ electrochemical gradients and tubular Na+ transport, mitochondrial TCA cycle and cell energetics, and circadian rhythms.
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Rozner, Reut, Janna Vernikov, Shelley Griess-Fishheimer, Tamar Travinsky, Svetlana Penn, Betty Schwartz, Ronit Mesilati-Stahy, Nurit Argov-Argaman, Ron Shahar, and Efrat Monsonego-Ornan. "The Role of Omega-3 Polyunsaturated Fatty Acids from Different Sources in Bone Development." Nutrients 12, no. 11 (November 13, 2020): 3494. http://dx.doi.org/10.3390/nu12113494.
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N-3 polyunsaturated fatty acids (PUFAs) are essential nutrients that must be obtained from the diet. We have previously showed that endogenous n-3 PUFAs contribute to skeletal development and bone quality in fat-1 mice. Unlike other mammals, these transgenic mice, carry the n-3 desaturase gene and thus can convert n-6 to n-3 PUFAs endogenously. Since this model does not mimic dietary exposure to n-3 PUFAs, diets rich in fish and flaxseed oils were used to further elucidate the role of n-3 PUFAs in bone development. Our investigation reveals that dietary n-3 PUFAs decrease fat accumulation in the liver, lower serum fat levels, and alter fatty acid (FA) content in liver and serum. Bone analyses show that n-3 PUFAs improve mechanical properties, which were measured using a three-point bending test, but exert complex effects on bone structure that vary according to its source. In a micro-CT analysis, we found that the flaxseed oil diet improves trabecular bone micro-architecture, whereas the fish oil diet promotes higher bone mineral density (BMD) with no effect on trabecular bone. The transcriptome characterization of bone by RNA-seq identified regulatory mechanisms of n-3 PUFAs via modulation of the cell cycle and peripheral circadian rhythm genes. These results extend our knowledge and provide insights into the molecular mechanisms of bone remodeling regulation induced by different sources of dietary n-3 PUFAs.
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Scaliusi, Santiago F., Luis Gimenez, Pablo Pérez, Daniel Martín, Alberto Olmo, Gloria Huertas, F. Javier Medrano, and Alberto Yúfera. "From Bioimpedance to Volume Estimation: A Model for Edema Calculus in Human Legs." Electronics 12, no. 6 (March 14, 2023): 1383. http://dx.doi.org/10.3390/electronics12061383.
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Heart failure (HF) is a severe disease and one of the most important causes of death in our society nowadays. A significant percentage of patients hospitalized for decompensation of heart failure are readmitted after some weeks or months due to an expected bad and uncontrolled HF evolution due to the lack of the patient supervision in real time. Herein is presented a straightforward electric model useful for volume leg section calculus based on the bioimpedance test as a way to assist with the acute HF patient’s supervision. The method has been developed for time-evolution edema evaluation in patients’ corresponding legs. The data are picked up with a wearable device specifically developed for acute heart failure patients. As an initial step, a calibration method is proposed to extract the extracellular volume component from bioimpedance measurements done in healthy subjects, and then applied to unhealthy ones. The intra- and extracellular resistance components are calculated from fitted Cole–Cole model parameters derived from BI spectroscopy measurements. Results obtained in a pilot assay, with healthy subjects and heart failure subjects, show sensitivities in leg volume [mL/Ω], with much lower values for healthy than in unhealthy people, being an excellent biomarker to discriminate between both. Finally, circadian cycle evolution for leg volume has been measured from the bioimpedance test as an extension of the work, enabling an alternative parameter for the characterization of one day of human activity for any person.
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Yao, Wenjing, Chuanzhe Li, Shuyan Lin, Li Ren, Yawen Wan, Li Zhang, and Yulong Ding. "Morphological Characteristics and Transcriptome Comparisons of the Shoot Buds from Flowering and Non-Flowering Pleioblastus pygmaeus." Forests 11, no. 11 (November 23, 2020): 1229. http://dx.doi.org/10.3390/f11111229.
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Bamboo plants have a distinctive life cycle with long flowering periodicity. Many species remain in vegetative growth for decades, followed by large-scale flowering and subsequent death. Floral transition is activated while shoot buds are still dormant in bamboo plants. In this study, we performed morphological characterization and transcriptome analysis of the shoot buds at different growth stages from flowering and non-flowering Pleioblastus pygmaeus. The morphological and anatomical structures of the dormant shoot buds were similar in flowering and non-flowering plants, while there was an obvious difference between the flower buds from flowering plants and the leaf buds from non-flowering plants. The transcriptomes of the dormant shoot buds, germinated shoots, and flower buds from flowering P. pygmaeus, and the dormant shoot buds, germinated shoots, and leaf buds from non-flowering P. pygmaeus were profiled and compared by RNA-Seq. The identified sequences were mostly related to metabolic synthesis, signal transmission, translation, and other functions. A total of 2434 unigenes involved in different flowering pathways were screened from transcriptome comparisons. The differentially expressed unigenes associated with the photoperiod pathway were related to circadian rhythm and plant hormone signal transduction. Moreover, the relative expression levels of a few key flowering-related genes such as CO, FT, FLC, and SOC1 were quantified by qRT-PCR, which was in accordance with RNA-Seq. The study revealed morphological differences in the shoot buds at different growth stages and screened flowering-related genes by transcriptome comparisons of the shoot buds from flowering and non-flowering P. pygmaeus, which will enrich the research on reproductive biology of bamboo plants and shed light on the molecular mechanism of the floral transition in bamboo plants.
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Kim, Nan-Sun, Jihyeon Yu, Sangsu Bae, Hyang Suk Kim, Soyoung Park, Kijong Lee, Soo In Lee, and Jin A. Kim. "Identification and Characterization of PSEUDO-RESPONSE REGULATOR (PRR) 1a and 1b Genes by CRISPR/Cas9-Targeted Mutagenesis in Chinese Cabbage (Brassica rapa L.)." International Journal of Molecular Sciences 23, no. 13 (June 23, 2022): 6963. http://dx.doi.org/10.3390/ijms23136963.
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The CRISPR/Cas9 site-directed gene-editing system offers great advantages for identifying gene function and crop improvement. The circadian clock measures and conveys day length information to control rhythmic hypocotyl growth in photoperiodic conditions, to achieve optimal fitness, but operates through largely unknown mechanisms. Here, we generated core circadian clock evening components, Brassica rapa PSEUDO-RESPONSE REGULATOR (BrPRR) 1a, 1b, and 1ab (both 1a and 1b double knockout) mutants, using CRISPR/Cas9 genome editing in Chinese cabbage, where 9–16 genetic edited lines of each mutant were obtained. The targeted deep sequencing showed that each mutant had 2–4 different mutation types at the target sites in the BrPRR1a and BrPRR1b genes. To identify the functions of BrPRR1a and 1b genes, hypocotyl length, and mRNA and protein levels of core circadian clock morning components, BrCCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) and BrLHY (LATE ELONGATED HYPOCOTYL) a and b were examined under light/dark cycles and continuous light conditions. The BrPRR1a and 1ab double mutants showed longer hypocotyls, lower core circadian clock morning component mRNA and protein levels, and a shorter circadian rhythm than wildtype (WT). On the other hand, the BrPRR1b mutant was not significantly different from WT. These results suggested that two paralogous genes may not be associated with the same regulatory function in Chinese cabbage. Taken together, our results demonstrated that CRISPR/Cas9 is an efficient tool for achieving targeted genome modifications and elucidating the biological functions of circadian clock genes in B. rapa, for both breeding and improvement.
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Yalçin, Müge, and Angela Relógio. "Sex and age-dependent characterization of the circadian clock as a potential biomarker for physical performance: A prospective study protocol." PLOS ONE 18, no. 10 (October 24, 2023): e0293226. http://dx.doi.org/10.1371/journal.pone.0293226.
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Introduction Circadian rhythms (CR) regulate daily cycles in behavior, physiology and molecular processes. CRs are endogenous and vary across individuals. Seasonal changes can influence CR. Accordingly, rhythms with different characteristics (amplitude, phase) are depicted during the summer months, as compared to winter. Increasing evidence points to an influence of circadian regulation on physical performance. Here, we aim to obtain a comprehensive circadian gene expression profile for physically active individuals, which can potentially be used for the identification of optimal time intervals for physical exercise. Methods and analysis To explore these different aspects, we propose a study where we will carry out a molecular analysis of CR by measuring the expression of specific clock and clock-controlled genes, based on a non-invasive approach using RNA extracted from saliva in physically active, healthy participants. We will collect data across two seasons and use computational algorithms to integrate the molecular data with hormonal data (cortisol and melatonin), and generate a profile of CR in healthy individuals of different sex and age groups. Finally, we will use computational tools to predict optimal time intervals for physical performance based on the above-described data, thereby retrieving valuable data on the circadian clock as a key factor for health maintenance and optimization.
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Mullegama, Sureni, Joseph Alaimo, Michael Fountain, Brooke Burns, Amanda Balog, Li Chen, and Sarah Elsea. "RAI1 Overexpression Promotes Altered Circadian Gene Expression and Dyssomnia in Potocki–Lupski Syndrome." Journal of Pediatric Genetics 06, no. 03 (March 7, 2017): 155–64. http://dx.doi.org/10.1055/s-0037-1599147.
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Abstract Retinoic acid induced 1 (RAI1) encodes a dosage-sensitive gene that when haploinsufficient results in Smith–Magenis syndrome (SMS) and when overexpressed results in Potocki–Lupski syndrome (PTLS). Phenotypic and molecular evidence illustrates that haploinsufficiency of RAI1 disrupts circadian rhythm through the dysregulation of the master circadian regulator, circadian locomotor output cycles kaput (CLOCK), and other core circadian components, contributing to prominent sleep disturbances in SMS. However, the phenotypic and molecular characterization of sleep features in PTLS has not been elucidated. Using the Pittsburgh Sleep Quality Index (PSQI), caregivers of 15 school-aged children with PTLS reported difficulties in initiating sleep. Indeed, more than 70% of individuals manifested moderate to severe sleep latency, as defined by the PSQI. Moreover, these individuals manifested difficulties in sleep maintenance, with middle of the night and early morning awakenings. When assessing daytime sleepiness through the Epworth Sleepiness Scale, approximately 21% of the individuals manifested excessive daytime somnolence. This indicates that mild dyssomnia characterizes the majority of the sleep phenotype, with occasionally problematic daytime somnolence, a phenotype different than that expressed by individuals with SMS, where daytime sleepiness is a chronic problem. Gene expression analysis of the core circadian machinery in the hypothalamus of the PTLS mouse model (Rai1-Tg) found significant dysregulation of the transcriptional activators, Clock and Arntl, and the transcriptional repressors, Per1–3 and Cry1/2, during both light and dark phases. These findings suggest a partial loss of circadian entrainment typically evoked by environmental photic cues. Examination of circadian clock gene expression in the Rai1-Tg mouse heart, liver, and kidney found unchanged expression of Clock and most of its downstream targets during both light and dark phases, suggesting an asynchronized circadian rhythm. Furthermore, examination of circadian gene expression in synchronized PTLS lymphoblasts revealed reduced transcripts of the Period (PER1–3) family and normal expression of CRY1/2. The finding that central circadian gene expression was altered while many peripheral circadian components were intact suggests a tissue-specific circadian uncoupling of the circadian machinery due to Rai1 overexpression. Overall, our results demonstrate that overexpression of RAI1 results in sleep deficiencies in individuals with PTLS due to a lack of properly regulated circadian machinery gene expression and highlight the importance of evaluating sleep concerns in individuals with PTLS.
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Yalçin, Müge, Ana Rita Peralta, Carla Bentes, Cristiana Silva, Tiago Guerreiro, Joaquim J. Ferreira, and Angela Relógio. "Molecular characterization of the circadian clock in patients with Parkinson’s disease–CLOCK4PD Study protocol." PLOS ONE 19, no. 7 (July 19, 2024): e0305712. http://dx.doi.org/10.1371/journal.pone.0305712.
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Introduction Circadian rhythms (CRs) orchestrate intrinsic 24-hour oscillations which synchronize an organism’s physiology and behaviour with respect to daily cycles. CR disruptions have been linked to Parkinson’s Disease (PD), the second most prevalent neurodegenerative disorder globally, and are associated to several PD-symptoms such as sleep disturbances. Studying molecular changes of CR offers a potential avenue for unravelling novel insights into the PD progression, symptoms, and can be further used for optimization of treatment strategies. Yet, a comprehensive characterization of the alterations at the molecular expression level for core-clock and clock-controlled genes in PD is still missing. Methods and analysis The proposed study protocol will be used to characterize expression profiles of circadian genes obtained from saliva samples in PD patients and controls. For this purpose, 20 healthy controls and 70 PD patients will be recruited. Data from clinical assessment, questionnaires, actigraphy tracking and polysomnography will be collected and clinical evaluations will be repeated as a follow-up in one-year time. We plan to carry out sub-group analyses considering several clinical factors (e.g., biological sex, treatment dosages, or fluctuation of symptoms), and to correlate reflected changes in CR of measured genes with distinct PD phenotypes (diffuse malignant and mild/motor-predominant). Additionally, using NanoStringⓇ multiplex technology on a subset of samples, we aim to further explore potential CR alterations in hundreds of genes involved in neuropathology pathways. Discussion CLOCK4PD is a mono-centric, non-interventional observational study aiming at the molecular characterization of CR alterations in PD. We further plan to determine physiological modifications in sleep and activity patterns, and clinical factors correlating with the observed CR changes. Our study may provide valuable insights into the intricate interplay between CR and PD with a potential to be used as a predictor of circadian alterations reflecting distinct disease phenotypes, symptoms, and progression outcomes.
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Bae, Kiho, Choogon Lee, David Sidote, Keng-yu Chuang, and Isaac Edery. "Circadian Regulation of a Drosophila Homolog of the Mammalian Clock Gene: PER and TIM Function as Positive Regulators." Molecular and Cellular Biology 18, no. 10 (October 1, 1998): 6142–51. http://dx.doi.org/10.1128/mcb.18.10.6142.
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ABSTRACT The Clock gene plays an essential role in the manifestation of circadian rhythms (≅24 h) in mice and is a member of the basic helix-loop-helix (bHLH) PER-ARNT-SIM (PAS) superfamily of transcription factors. Here we report the characterization of a novelDrosophila bHLH-PAS protein that is highly homologous to mammalian CLOCK. (Similar findings were recently described by Allada et al. Cell 93:791–804, 1998, and Darlington et al., Science 280:1599–1603, 1998.) Transcripts from this putative Clockortholog (designated dClock) undergo daily rhythms in abundance that are antiphase to the cycling observed for the RNA products from the Drosophila melanogaster circadian clock genes period (per) and timeless(tim). Furthermore, dClock RNA cycling is abolished and the levels are at trough values in the absence of either PER or TIM, suggesting that these two proteins can function as transcriptional activators, a possibility which is in stark contrast to their previously characterized role in transcriptional autoinhibition. Finally, the temporal regulation of dClock expression is quickly perturbed by shifts in light-dark cycles, indicating that this molecular rhythm is closely connected to the photic entrainment pathway. The isolation of a Drosophila homolog ofClock together with the recent discovery of mammalian homologs of per indicate that there is high structural conservation in the integral components underlying circadian oscillators in Drosophila and mammals. Nevertheless, because mammalian Clock mRNA is constitutively expressed, our findings are a further example of striking differences in the regulation of putative circadian clock orthologs in different species.
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Chowdhury, Debajyoti, Yip Hiu Fung, Chao Wang, Xue Cheng TAI, and Aiping LU*. "015 Modulating melatonin dynamics at transcription level using virtual knockout approaches: an advanced perspective in sleep medicine." Sleep 44, Supplement_2 (May 1, 2021): A8. http://dx.doi.org/10.1093/sleep/zsab072.014.
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Abstract Introduction Sleep disorders, the most neglected public-health issues, are threatening overall health. It is tightly associated with the individual’s exposures to the light/dark (LD)-cycles linked to their circadian rhythms. Lifestyle, shift-work, frequent travels, and post-pandemic-stress lead unintentional compromise of sleep, thus circadian homeostasis. Melatonin (MT), a pivotal natural hormone for circadian and sleep health, attains acrophase in the dark. MT mediates LD-triggered circadian rhythms through its dynamic expressions. Circadian phases are greatly reflected by MT-dynamics. Dim-light-MT-onsets (DLMO) act as a marker, reporting internal circadian-timing in mammals. Estimating this is essential in therapeutic-designing against misaligned circadian conditions. Despite many experimental approaches, there is still a slit hacking the MT-dynamics from molecules to systems. Inclusive perspectives on endogenous factors affecting MT’s synthesis, secretions and bioavailability over time-course are not extensively exposed. MT-dynamics has multiplexed stochastic interactions across numerous genes, TFs, and regulators, and they are coupled non-linearly. Small changes used to compound through the genetic networks and reflected in systems-wide events marking distinct signalling response dynamics. Understanding such responses is challenging yet imperative. A robust quantitative model is inevitable to investigate such stochastic intricacy. Methods We proposed a quantitative framework to model MT signalling networks using diverse kinetic parameters linked in its genetic circuits and perturbing them must alter the MT-dynamics. We used a robust computational approach, LogicTRN to decode the systematic controls of the MT-dynamics. It combines multi-layered transcriptome-wide data as input. Computing this returned the regulatory TF-logics in the transcriptional regulatory networks for MT. We developed transcriptional simulations with virtual-knockout mutants and performed genetic network perturbation study. Results The results showed the reconstruction of robust quantitative regulatory networks decrypting transcriptional controls for MT-dynamics to estimate the influence of the multiple kinetically distinct inputs affecting those dynamics. This offered competitive advantages in terms of scalability, robustness, and iterations to characterize the effective molecular-targets to modulate the genetic circuit of MT-dynamics effectually. Conclusion Quantitative reconstruction and characterization of the regulatory interactome of MT may facilitate us to strategize the adjustments of regulatory controls to effectively modulate MT-dynamics. This foundation may enhance the advancement of circadian and sleep medicine in future. Support (if any):
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Skene, Debra J., Elena Skornyakov, Namrata R. Chowdhury, Rajendra P. Gajula, Benita Middleton, Brieann C. Satterfield, Kenneth I. Porter, Hans P. A. Van Dongen, and Shobhan Gaddameedhi. "Separation of circadian- and behavior-driven metabolite rhythms in humans provides a window on peripheral oscillators and metabolism." Proceedings of the National Academy of Sciences 115, no. 30 (July 10, 2018): 7825–30. http://dx.doi.org/10.1073/pnas.1801183115.
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Misalignment between internal circadian rhythmicity and externally imposed behavioral schedules, such as occurs in shift workers, has been implicated in elevated risk of metabolic disorders. To determine underlying mechanisms, it is essential to assess whether and how peripheral clocks are disturbed during shift work and to what extent this is linked to the central suprachiasmatic nuclei (SCN) pacemaker and/or misaligned behavioral time cues. Investigating rhythms in circulating metabolites as biomarkers of peripheral clock disturbances may offer new insights. We evaluated the impact of misaligned sleep/wake and feeding/fasting cycles on circulating metabolites using a targeted metabolomics approach. Sequential plasma samples obtained during a 24-h constant routine that followed a 3-d simulated night-shift schedule, compared with a simulated day-shift schedule, were analyzed for 132 circulating metabolites. Nearly half of these metabolites showed a 24-h rhythmicity under constant routine following either or both simulated shift schedules. However, while traditional markers of the circadian clock in the SCN—melatonin, cortisol, and PER3 expression—maintained a stable phase alignment after both schedules, only a few metabolites did the same. Many showed reversed rhythms, lost their rhythms, or showed rhythmicity only under constant routine following the night-shift schedule. Here, 95% of the metabolites with a 24-h rhythmicity showed rhythms that were driven by behavioral time cues externally imposed during the preceding simulated shift schedule rather than being driven by the central SCN circadian clock. Characterization of these metabolite rhythms will provide insight into the underlying mechanisms linking shift work and metabolic disorders.
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Noya, Sara B., David Colameo, Franziska Brüning, Andrea Spinnler, Dennis Mircsof, Lennart Opitz, Matthias Mann, Shiva K. Tyagarajan, Maria S. Robles, and Steven A. Brown. "The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep." Science 366, no. 6462 (October 10, 2019): eaav2642. http://dx.doi.org/10.1126/science.aav2642.
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Neurons have adapted mechanisms to traffic RNA and protein into distant dendritic and axonal arbors. Taking a biochemical approach, we reveal that forebrain synaptic transcript accumulation shows overwhelmingly daily rhythms, with two-thirds of synaptic transcripts showing time-of-day–dependent abundance independent of oscillations in the soma. These transcripts formed two sharp temporal and functional clusters, with transcripts preceding dawn related to metabolism and translation and those anticipating dusk related to synaptic transmission. Characterization of the synaptic proteome around the clock demonstrates the functional relevance of temporal gating for synaptic processes and energy homeostasis. Unexpectedly, sleep deprivation completely abolished proteome but not transcript oscillations. Altogether, the emerging picture is one of a circadian anticipation of messenger RNA needs in the synapse followed by translation as demanded by sleep-wake cycles.
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Spitschan, Manuel, Karin Smolders, Benjamin Vandendriessche, Brinnae Bent, Jessie P. Bakker, Isaac R. Rodriguez-Chavez, and Céline Vetter. "Verification, analytical validation and clinical validation (V3) of wearable dosimeters and light loggers." DIGITAL HEALTH 8 (January 2022): 205520762211448. http://dx.doi.org/10.1177/20552076221144858.
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Background Light exposure is an important driver and modulator of human physiology, behavior and overall health, including the biological clock, sleep-wake cycles, mood and alertness. Light can also be used as a directed intervention, e.g., in the form of light therapy in seasonal affective disorder (SAD), jetlag prevention and treatment, or to treat circadian disorders. Recently, a system of quantities and units related to the physiological effects of light was standardized by the International Commission on Illumination (CIE S 026/E:2018). At the same time, biometric monitoring technologies (BioMeTs) to capture personalized light exposure were developed. However, because there are currently no standard approaches to evaluate the digital dosimeters, the need to provide a firm framework for the characterization, calibration, and reporting for these digital sensors is urgent. Objective This article provides such a framework by applying the principles of verification, analytic validation and clinical validation (V3) as a state-of-the-art approach for tools and standards in digital medicine to light dosimetry. Results This article describes opportunities for the use of digital dosimeters for basic research, for monitoring light exposure, and for measuring adherence in both clinical and non-clinical populations to light-based interventions in clinical trials.
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Martinez, Jessy, Donald Popke, Marcus Donnelly, Daniel Torres, Brittany Clawson, Sha Jiang, and Sara Aton. "054 Characterization of Sleep Phenotypes and Sleep-Dependent Memory Consolidation in a Mouse Model of Fragile X Syndrome." Sleep 44, Supplement_2 (May 1, 2021): A22—A23. http://dx.doi.org/10.1093/sleep/zsab072.053.
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Abstract Introduction Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by disruption of Fmr1 gene function, leading to intellectual disability. FXS individuals report increased incidence of sleep disruptions such as loss of NREM sleep, irregular sleep/wake cycles, and circadian rhythm disturbances that warrant pharmacological intervention. Since sleep has critical roles in the promotion of memory consolidation, it is unknown whether disrupted cognitive function in FXS is exacerbated by abnormal sleep. We characterized the link between sleep loss phenotypes and cognition in FXS mice (Fmr1 KO). We hypothesized that normalizing sleep in Fmr1 KO mice could improve sleep-dependent cognitive function. Because direct activation of G-protein inward rectifying potassium (GIRK) channels by ML297 has been found to promote NREM sleep, we tested how ML297 affected sleep and memory consolidation phenotypes in Fmr1 KO mice. Methods Wild type (WT) and Fmr1 KO were implanted with electrodes for electroencephalogram/electromyogram (EEG/EMG) recording of wakefulness, NREM and REM sleep. Sleep-dependent memory consolidation was measured using single-trial contextual fear conditioning (CFC). ML297 or vehicle was administered after CFC training to measure the effects on sleep and fear memory consolidation. Results Fmr1 KO mice showed reduced sleep in the hours following CFC learning compared to wild type littermates, and reduced contextual fear memory consolidation. Post-CFC sleep deprivation disrupted memory consolidation in wild type littermates, but not Fmr1 KO mice. Both NREM sleep time and NREM bout length were reduced in Fmr1 KO mice, and preliminary data suggest reduced NREM delta (0.5–4 Hz) power in the prefrontal cortex. These deficits were present at baseline and also following CFC. Post-CFC training administration of ML297 rescued NREM sleep and contextual fear memory deficits in Fmr1 KO mice. Conclusion Our study showed a strong link between NREM sleep loss and cognitive deficits in Fmr1 KO mice. Critically, normalization of NREM sleep through direct activation of GIRK channels rescues cognitive deficits seen in Fmr1 KO mice, suggesting a new therapeutic approach to treating cognitive deficits associated with FXS. Support (if any) This work was supported by a Rackham Merit Fellowship to JDM.
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Gombert-Labedens, Marie, Elisabet Alzueta, Evelyn Perez-Amparan, Dilara Yuksel, Orsolya Kiss, Massimiliano de Zambotti, Katharine Simon, et al. "Using Wearable Skin Temperature Data to Advance Tracking and Characterization of the Menstrual Cycle in a Real-World Setting." Journal of Biological Rhythms, May 20, 2024. http://dx.doi.org/10.1177/07487304241247893.
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The menstrual cycle is a loop involving the interplay of different organs and hormones, with the capacity to impact numerous physiological processes, including body temperature and heart rate, which in turn display menstrual rhythms. The advent of wearable devices that can continuously track physiological data opens the possibility of using these prolonged time series of skin temperature data to noninvasively detect the temperature variations that occur in ovulatory menstrual cycles. Here, we show that the menstrual skin temperature variation is better represented by a model of oscillation, the cosinor, than by a biphasic square wave model. We describe how applying a cosinor model to a menstrual cycle of distal skin temperature data can be used to assess whether the data oscillate or not, and in cases of oscillation, rhythm metrics for the cycle, including mesor, amplitude, and acrophase, can be obtained. We apply the method to wearable temperature data collected at a minute resolution each day from 120 female individuals over a menstrual cycle to illustrate how the method can be used to derive and present menstrual cycle characteristics, which can be used in other analyses examining indicators of female health. The cosinor method, frequently used in circadian rhythms studies, can be employed in research to facilitate the assessment of menstrual cycle effects on physiological parameters, and in clinical settings to use the characteristics of the menstrual cycles as health markers or to facilitate menstrual chronotherapy.
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Kervezee, Laura, Fernando Gonzales-Aste, Phillipe Boudreau, and Diane B. Boivin. "The relationship between chronotype and sleep behavior during rotating shift work: a field study." Sleep 44, no. 4 (February 4, 2021). http://dx.doi.org/10.1093/sleep/zsaa225.
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Abstract Shift work, an essential part of our 24/7 society, inevitably leads to displacement of the habitual sleep period and thereby to misalignment of the internal circadian timing system with the rest–activity cycle and the environment. How interindividual differences in circadian organization affect sleep duration and timing during rotating shift work is not fully understood. The objective of this study was to assess the effect of chronotype, shift type, and their interaction on actigraphy-based sleep behavior in 74 police officers (20 women and 54 men; age [mean ± SD]: 32.1 ± 5.4 years) involved in rotating shift work throughout a 28- to 35-day work cycle consisting of morning, evening, and night shifts. Using linear mixed modeling, we found that chronotype was associated with sleep duration depending on the shift type: increasing morningness was correlated with longer sleep duration during series of consecutive morning shifts, while increasing eveningness was correlated with longer sleep duration during series of evening shifts. During series of night shifts, increasing eveningness was associated with a longer duration of the main sleep episode, but this relationship was attenuated and no longer significant when naps were taken into account due to increased napping in morning chronotypes during series of night shifts. Providing a detailed within-subject characterization of sleep behavior across a complete work cycle consisting of morning, evening, and night shifts, this study advances the understanding of the relationship between chronotype and sleep in rotating shift workers and supports the implementation of work schedules that take into account chronobiological principles.
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Calligaro, Hugo, Azarin Shoghi, Xinyue Chen, Keun-Young Kim, Hsin Liu Yu, Brian Khov, Benjamin Finander, Hiep Le, Mark H. Ellisman, and Satchidananda Panda. "Ultrastructure of synaptic connectivity within sub-regions of the suprachiasmatic nucleus revealed by a genetically encoded tag and Serial Blockface Electron Microscopy." eneuro, July 27, 2023, ENEURO.0227–23.2023. http://dx.doi.org/10.1523/eneuro.0227-23.2023.
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The hypothalamic suprachiasmatic nucleus (SCN) is the central circadian pacemaker in vertebrates. The SCN receives photic information exclusively through melanopsin-expressing retinal ganglion cells (mRGC) to synchronize circadian rhythms with the environmental light cycles. The SCN is composed of two major peptidergic neuron types in the core and shell regions of the SCN. Determining how mRGCs interact with the network of synaptic connections onto and between SCN neurons is key to understand how light regulates the circadian clock and to elucidate the relevant local circuits within the SCN. To map these connections, we used a newly developed Cre-dependent electron microscopy reporter, APEX2, to label the mitochondria of mRGC axons. Serial blockface scanning electron microscopy was then used to resolve the fine 3D structure of mRGC axons and synaptic boutons in the SCN of a male mouse. The resulting maps reveal patterns of connectomic organization in the core and shell of the SCN. We show that these regions are composed of different neuronal subtypes and differ with regard to the pattern of mRGC input, as the shell receives denser mRGC synaptic input compared to the core. This finding challenges the present view that photic information coming directly from the retina is received primarily by the core region of the SCN.Signification statementThe hypothalamic suprachiasmatic nucleus (SCN) in the vertebrate brain serves as the central pacemaker regulating circadian rhythm throughout the body and as the principal hub for entraining circadian rhythm with the ambient light:dark cycle. Cellular and molecular studies have suggested heterogeneity of the SCN neurons and their connectivity, yet an ultrastructural characterization of the SCN connectivity is still lacking. In order to systematically investigate the connectivity within the SCN, we used a recently developed Cre-dependant electron microscopy reporter, APEX2, to specifically label mitochondria of mRGCs, and SBEM to produce image volumes of the two functional sub-regions of the SCN, the core and the shell. Our findings unveil several differences between the sub-regions, including synaptic input (retinal and non-retinal), the density of network of dendrites forming dendro-dendritic synapses. In addition, we established morphological criteria for discriminating between different types of axonic boutons.
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Peng, Ziqing, Yaxin Liu, Haiying Ma, Shiwei Xiao, Allan Au-Yeung, Liang Zhang, Qinglu Zeng, and Yusong Guo. "Characterization of extracellular vesicles released from Prochlorococcus MED4 at the steady state and under a light–dark cycle." Philosophical Transactions of the Royal Society B: Biological Sciences 380, no. 1918 (January 23, 2025). https://doi.org/10.1098/rstb.2023.0339.
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Bacterial extracellular vesicles (EVs) are vesicles secreted by bacteria into the extracellular environment. Containing DNA, RNA and proteins, EVs are implicated to mediate intercellular communications. The marine cyanobacterium Prochlorococcus , the most abundant photosynthetic organism in marine ecosystems, has been shown to generate EVs continuously during cell growth. However, biogenesis and functions of EVs released by Prochlorococcus remain largely unclear. Here, we isolated and characterized EVs released by Prochlorococcus MED4 culture. We found that the majority of MED4 EVs are elliptical and enriched with specific proteins performing particular cellular functions. The light–dark cycle has been demonstrated to affect the cell cycle of Prochlorococcus , with cell division occurring at night time. Interestingly, we found that the net production of MED4 EVs was faster during the night time. Moreover, we revealed that MED4 EVs that are released or absorbed in the night time are enriched with distinct proteins, suggesting the release and absorbance of EVs are influenced by the diel cycle. We found that inhibiting cell division decreased the net production of MED4 EVs during the night time, suggesting that cell division is important for the biogenesis of MED4 EVs. These analyses provide novel insights into biogenesis and functions of EVs released from bacteria. This article is part of the Theo Murphy meeting issue ‘Circadian rhythms in infection and immunity’.
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Karsai-Rektenwald, Flóra, Khongorzul Odgerel, Jeny Jose, and Zsófia Bánfalvi. "In Silico Characterization and Expression Analysis of GIGANTEA Genes in Potato." Biochemical Genetics, March 11, 2022. http://dx.doi.org/10.1007/s10528-022-10214-7.
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AbstractGIGANTEA (GI) genes are ubiquitous in the plant kingdom and are involved in diverse processes from flowering during stress responses to tuberization; the latter occurs in potato (Solanum tuberosum L.). GI genes have a diurnal cycle of expression; however, no details on the regulation of GI gene expression in potato have been reported thus far. The aim of our work was the analysis of the GI promoter sequence and studying GI expression in different organs and under abiotic stress conditions in potato. Two GI genes homologous to Arabidopsis GI located on chromosomes 4 and 12 (StGI.04 and StGI.12) were identified in the genome-sequenced potato S. phureja. The GI promoter regions of the commercial potato cultivar ‘Désirée’ were cloned and found to be almost identical to the S. phureja GI promoter sequence. More than ten TF families binding to the GI promoters were predicted. EVENING ELEMENT and ABSCISIC ACID RESPONSE ELEMENT LIKE elements related to circadian regulation and a binding site for POTATO HOMEOBOX 20 presumably involved in tuber initiation were detected in both GI promoters. However, the locations of these elements and several other cis-acting regulatory elements as well as the organ-specific expression and responses of the genes to abiotic stresses and abscisic acid were different. Thus, we presume that the function of StGI.04 and StGI.12 are at least partially different. This study lays foundation for further investigation of the roles of GI genes in potato.
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AYGÖREN, Ahmed Sidar, Recep AYDINYURT, Sümeyra UÇAR, Ayşe Gül KASAPOĞLU, Esra YAPRAK, Burak Muhammed ÖNER, Selman MUSLU, et al. "Fasulyede Tuz ve Kuraklık Stresi Altında PIF Gen Ailesinin Genom Çapında Analizi ve Karakterizasyonu." Türkiye Tarımsal Araştırmalar Dergisi, October 18, 2022. http://dx.doi.org/10.19159/tutad.1109558.
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Plant growth and development are regulated by light, which is a significant environmental component. It is involved in seedling de-etiolation, phototropism, shadow escaping, seed germination, circadian rhythms, and blooming timing, among other reactions in the plant life cycle (collectively termed photomorphogenesis). These light responses are controlled by phytochromes, which interact with a variety of partner proteins. The purpose of this study was to identify and describe members of the phytochrome-interacting factors (PIFs) gene family including the basic helix loop helix (bHLH) binding site in Phaseolus vulgaris plants, as well as to investigate their responses to salt and drought stress. Various tools in silico approaches were used to identify five Pvul-PIF gene families in the P. vulgaris genome. This gene family contained 324 to 726 amino acids and has molecular weights ranging from 35.11 kDa to 77.67 kDa. The theoretical isoelectric points range from 6.03 (Pvul-PIF-3.3) to 8.30 (Pvul-PIF-3.2). Pvul-PIF proteins were shown to be clustered in three main groups with Arabidopsis thaliana, Populus trichocarpa, Solanum lycopersicum, Zea mays, Arachis hypogaea L., Oryza sativa, Vitis vinifera, Glycine max, and Phaseolus vulgaris species as a result of the phylogenetic study. Segmental duplication was detected between Pvul-PIF-3.2, Pvul-PIF-3.3 and Pvul-PIF-3.1 genes, Pvul-PIF-4.1 and Pvul-PIF-4.2 genes and Pvul-PIF-3.3 and Pvul-PIF-3.1 genes. When the expression patterns of the Pvul-PIF genes were examined, it was observed that they had different levels of expression under salt and drought stress and that they may be involved in specific biological and molecular processes in response to different abiotic and biotic stresses. The results of this research, which were established for the first time in the response to salt and drought stress in P. vulgaris of the PIF gene family, will be a valuable source of knowledge and additional information in the fields of plant biotechnology, agricultural biotechnology, and molecular biology.
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Kaur, Harleen, Pooja Manchanda, Gurupkar S. Sidhu, and Parveen Chhuneja. "Genome-wide identification and characterization of flowering genes in Citrus sinensis (L.) Osbeck: a comparison among C. Medica L., C. Reticulata Blanco, C. Grandis (L.) Osbeck and C. Clementina." BMC Genomic Data 25, no. 1 (February 20, 2024). http://dx.doi.org/10.1186/s12863-024-01201-5.
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Abstract Background Flowering plays an important role in completing the reproductive cycle of plants and obtaining next generation of plants. In case of citrus, it may take more than a year to achieve progeny. Therefore, in order to fasten the breeding processes, the juvenility period needs to be reduced. The juvenility in plants is regulated by set of various flowering genes. The citrus fruit and leaves possess various medicinal properties and are subjected to intensive breeding programs to produce hybrids with improved quality traits. In order to break juvenility in Citrus, it is important to study the role of flowering genes. The present study involved identification of genes regulating flowering in Citrus sinensis L. Osbeck via homology based approach. The structural and functional characterization of these genes would help in targeting genome editing techniques to induce mutations in these genes for producing desirable results. Results A total of 43 genes were identified which were located on all the 9 chromosomes of citrus. The in-silico analysis was performed to determine the genetic structure, conserved motifs, cis-regulatory elements (CREs) and phylogenetic relationship of the genes. A total of 10 CREs responsible for flowering were detected in 33 genes and 8 conserved motifs were identified in all the genes. The protein structure, protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to study the functioning of these genes which revealed the involvement of flowering proteins in circadian rhythm pathways. The gene ontology (GO) and gene function analysis was performed to functionally annotate the genes. The structure of the genes and proteins were also compared among other Citrus species to study the evolutionary relationship among them. The expression study revealed the expression of flowering genes in floral buds and ovaries. The qRT-PCR analysis revealed that the flowering genes were highly expressed in bud stage, fully grown flower and early stage of fruit development. Conclusions The findings suggested that the flowering genes were highly conserved in citrus species. The qRT-PCR analysis revealed the tissue specific expression of flowering genes (CsFT, CsCO, CsSOC, CsAP, CsSEP and CsLFY) which would help in easy detection and targeting of genes through various forward and reverse genetic approaches.
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Burckard, Odile, Michèle Teboul, Franck Delaunay, and Madalena Chaves. "Benchmark for quantitative characterization of circadian clock cycles." BioSystems, November 2024, 105363. http://dx.doi.org/10.1016/j.biosystems.2024.105363.
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Liu, Zhe, Xiaoxuan Zhu, Weijuan Liu, Kaijie Qi, Zhihua Xie, Shaoling Zhang, Juyou Wu, and Peng Wang. "Characterization of the REVEILLE family in Rosaceae and role of PbLHY in flowering time regulation." BMC Genomics 24, no. 1 (January 28, 2023). http://dx.doi.org/10.1186/s12864-023-09144-4.
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Abstract Background The circadian clock integrates endogenous and exogenous signals and regulates various physiological processes in plants. REVEILLE (RVE) proteins play critical roles in circadian clock system, especially CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) and LHY (LATE ELONGATED HYPOCOTYL), which also participate in flowering regulation. However, little is known about the evolution and function of the RVE family in Rosaceae species, especially in Pyrus bretschneideri. Results In this study, we performed a genome-wide analysis and identified 51 RVE genes in seven Rosaceae species. The RVE family members were classified into two groups based on phylogenetic analysis. Dispersed duplication events and purifying selection were the main drivers of evolution in the RVE family. Moreover, the expression patterns of ten PbRVE genes were diverse in P. bretschneideri tissues. All PbRVE genes showed diurnal rhythms under light/dark cycles in P. bretschneideri leaves. Four PbRVE genes also displayed robust rhythms under constant light conditions. PbLHY, the gene with the highest homology to AtCCA1 and AtLHY in P. bretschneideri, is localized in the nucleus. Ectopic overexpression of PbLHY in Arabidopsis delayed flowering time and repressed the expression of flowering time-related genes. Conclusion These results contribute to improving the understanding and functional research of RVE genes in P. bretschneideri.
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Stefanelli, Chiara, Davide Colaianni, Gabriella M. Mazzotta, Gabriele Sales, Cristiano Bertolucci, Bettina Meyer, Alberto Biscontin, and Cristiano De Pittà. "Functional characterization of the second feedback loop in the circadian clock of the Antarctic krill Euphausia superba." BMC Biology 22, no. 1 (December 23, 2024). https://doi.org/10.1186/s12915-024-02099-2.
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Abstract Background The Antarctic krill Euphausia superba is a keystone species in the Southern Ocean ecosystem. This crustacean has an ancestral clock whose main components have been identified and characterized in the past few years. However, the second feedback loop, modulating clock gene expression through two transcription factors, VRI and PDP1, has yet to be described. The presence of this second regulatory mechanism is suggested by the identification of its negative component, vrille, at the transcriptional level. Results Here, we describe the second feedback loop of krill by identifying the positive component, pdp1, and functionally characterizing both pdp1 and vrille. Starting from the online transcriptome database KrillDB2, we identified and cloned three putative pdp1 sequences which were subsequently analyzed for tissue expression and functional activity using luciferase assays, individually and in combination with two vrille isoforms. Among the pdp1 isoforms, Espdp1_3 displayed higher expression levels in relevant circadian districts than the other two. Furthermore, EsPDP1_3 and EsVRI_2 exhibited the expected positive and negative regulation of the V/P-box in our in vitro system. Finally, Espdp1_3 and Esvrille also showed rhythmic expression in light–dark cycles, supporting their involvement in the regulation of the main circadian clock of the Antarctic krill. Conclusions This study expands our knowledge about the molecular architecture of the Antarctic krill circadian clock by defining the components that take part in the modulation of clock expression, establishing a second feedback loop.
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Hua, Xiuting, Qiaochu Shen, Yihan Li, Dong Zhou, Zhe Zhang, Sehrish Akbar, Zhengchao Wang, and Jisen Zhang. "Functional characterization and analysis of transcriptional regulation of sugar transporter SWEET13c in sugarcane Saccharum spontaneum." BMC Plant Biology 22, no. 1 (July 22, 2022). http://dx.doi.org/10.1186/s12870-022-03749-9.
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Abstract Background Sugarcane is an important crop for sugar production worldwide. The Sugars Will Eventually be Exported Transporters (SWEETs) are a group of sugar transporters recently identified in sugarcane. In Saccharum spontaneum, SsSWEET13c played a role in the sucrose transportation from the source to the sink tissues, which was found to be mainly active in the mature leaf. However, the function and regulation of SWEETs in sugarcane remain elusive despite extensive studies performed on sugar metabolism. Results In this study, we showed that SsSWEET13c is a member of SWEET gene family in S. spontaneum, constituting highest circadian rhythm-dependent expression. It is a functional gene that facilitates plant root elongation and increase fresh weight of Arabidopsis thaliana, when overexpressed. Furthermore, yeast one-hybrid assays indicate that 20 potential transcription factors (TFs) could bind to the SsSWEET13c promoter in S. spontaneum. We combined transcriptome data from developmental gradient leaf with distinct times during circadian cycles and stems/leaves at different growth stages. We have uncovered that 14 out of 20 TFs exhibited positive/negative gene expression patterns relative to SsSWEET13c. In the source tissues, SsSWEET13c was mainly positively regulated by SsbHLH34, SsTFIIIA-a, SsMYR2, SsRAP2.4 and SsbHLH035, while negatively regulated by SsABS5, SsTFIIIA-b and SsERF4. During the circadian rhythm, it was noticed that SsSWEET13c was more active in the morning than in the afternoon. It was likely due to the high level of sugar accumulation at night, which was negatively regulated by SsbZIP44, and positively regulated by SsbHLH34. Furthermore, in the sink tissues, SsSWEET13c was also active for sugar accumulation, which was positively regulated by SsbZIP44, SsTFIIIA-b, SsbHLH34 and SsTFIIIA-a, and negatively regulated by SsERF4, SsHB36, SsDEL1 and SsABS5. Our results were further supported by one-to-one yeast hybridization assay which verified that 12 potential TFs could bind to the promoter of SsSWEET13c. Conclusions A module of the regulatory network was proposed for the SsSWEET13c in the developmental gradient of leaf and circadian rhythm in S. spontaneum. These results provide a novel understanding of the function and regulation of SWEET13c during the sugar transport and biomass production in S. spontaneum.