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https://www.readbyqxmd.com/read/29219623/usual-normalization-strategies-for-gene-expression-studies-impair-the-detection-and-analysis-of-circadian-patterns
#1
Diego de Siqueira Figueredo, Mayara Rodrigues Barbosa, Daniel Gomes Coimbra, José Luiz Araújo Dos Santos, Ellyda Fernanda Lopes Costa, Bruna Del Vechio Koike, Magna Suzana Alexandre Moreira, Tiago Gomes de Andrade
Recent studies have shown that transcriptomes from different tissues present circadian oscillations. Therefore, the endogenous variation of total RNA should be considered as a potential bias in circadian studies of gene expression. However, normalization strategies generally include the equalization of total RNA concentration between samples prior to cDNA synthesis. Moreover, endogenous housekeeping genes (HKGs) frequently used for data normalization may exhibit circadian variation and distort experimental results if not detected or considered...
December 8, 2017: Chronobiology International
https://www.readbyqxmd.com/read/29186676/the-circadian-clock-regulates-adipogenesis-by-a-per3-crosstalk-pathway-to-klf15
#2
Abhishek Aggarwal, Maria José Costa, Belén Rivero-Gutiérrez, Lijuan Ji, Stefanie L Morgan, Brian J Feldman
The generation of new adipocytes from precursor cells (adipogenesis) has implications for systemic metabolism and is a commonly used model for studying the process of cell differentiation in vitro. Previous studies from us and others suggested that the peripheral circadian clock can influence adipogenesis in vitro, but the mechanisms driving this activity and the relevance for adipogenesis in vivo are unknown. Here we reveal that mouse adipocyte precursor cells (APCs) contain a circadian clock that oscillates in vivo...
November 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/29176713/rapid-resetting-of-human-peripheral-clocks-by-phototherapy-during-simulated-night-shift-work
#3
Marc Cuesta, Philippe Boudreau, Nicolas Cermakian, Diane B Boivin
A majority of night shift workers have their circadian rhythms misaligned to their atypical schedule. While bright light exposure at night is known to reset the human central circadian clock, the behavior of peripheral clocks under conditions of shift work is more elusive. The aim of the present study was to quantify the resetting effects of bright light exposure on both central (plasma cortisol and melatonin) and peripheral clocks markers (clock gene expression in peripheral blood mononuclear cells, PBMCs) in subjects living at night...
November 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29172740/the-choroid-plexus-harbors-a-circadian-oscillator-modulated-by-estrogens
#4
Telma Quintela, Tânia Albuquerque, Gabriella Lundkvist, Andrea Carmine Belin, Daniela Talhada, Isabel Gonçalves, Eva Carro, Cecília R A Santos
The suprachiasmatic nucleus (SCN) of the hypothalamus is considered the master circadian oscillator in mammals. However, extra-SCN structures in the brain also display daily rhythms. Recently, we have demonstrated that the choroid plexus (CP) expresses core clock genes that are subjected to circadian regulation in a sex-dependent manner. By using CP explants cultured from female knock-in mice carrying the Period-luciferase transgene, we show that CP exhibits endogenous circadian rhythms of PERIOD2::LUCIFERASE expression...
November 27, 2017: Chronobiology International
https://www.readbyqxmd.com/read/29165002/adrenal-dependent-and-independent-stress-induced-per1-mrna-in-hypothalamic-paraventricular-nucleus-and-prefrontal-cortex-of-male-and-female-rats
#5
Lauren E Chun, Jenny Christensen, Elizabeth R Woodruff, Sarah J Morton, Laura R Hinds, Robert L Spencer
Oscillating clock gene expression gives rise to a molecular clock that is present not only in the body's master circadian pacemaker, the hypothalamic suprachiasmatic nucleus (SCN), but also in extra-SCN brain regions. These extra-SCN molecular clocks depend on the SCN for entrainment to a light:dark cycle. The SCN has limited neural efferents, so it may entrain extra-SCN molecular clocks through its well-established circadian control of glucocorticoid hormone secretion. Glucocorticoids can regulate the normal rhythmic expression of clock genes in some extra-SCN tissues...
November 22, 2017: Stress: the International Journal on the Biology of Stress
https://www.readbyqxmd.com/read/29157002/effects-of-circadian-clock-protein-per1b-on-zebrafish-visual-functions
#6
Ke Nie, Kun Wang, Deng-Feng Huang, Yu-Bin Huang, Wu Yin, Da-Long Ren, Han Wang, Bing Hu
The circadian clock is an endogenous and entrainable time-keeping mechanism with a period of approximately 24 h, operated by transcription/translation feedback loops composed of circadian clock genes and their proteins. The visual system displays robust circadian changes. Relatively little, however, is known about the mechanisms underlying visual circadian rhythmicity. Zebrafish period1b (per1b), as a canonical circadian clock gene, is involved in circadian regulation. Here, we observed that zebrafish per1b mutants exhibit visual defects including reduced behavioral contrast sensitivity and significant retinal dopaminergic deficiency...
November 20, 2017: Chronobiology International
https://www.readbyqxmd.com/read/29144171/circadian-gene-methylation-in-rotating-shift-nurses-a-cross-sectional-study
#7
Edyta Reszka, Edyta Wieczorek, Monika Przybek, Ewa Jabłońska, Paweł Kałużny, Agnieszka Bukowska-Damska, Shanbeh Zienolddiny, Beata Pepłońska
Investigating the methylation status of the circadian genes may contribute to a better understanding of the shift work-related circadian disruption in individuals exposed to artificial light at night. In the present study, we determined the methylation status of the circadian genes associated with a shift work pattern among nurses and midwives participating in a cross-sectional study in Lodz, Poland. Quantitative methylation polymerase chain reaction assays were used to assess promoter CpG methylation in PER1, PER2, PER3, CRY1, CRY2, BMAL1, CLOCK, and NPAS2 in genomic DNA from whole blood of 347 women having a rotating-shift work schedule and 363 women working days only...
November 16, 2017: Chronobiology International
https://www.readbyqxmd.com/read/29138967/mice-lacking-egr1-have-impaired-clock-gene-bmal1-oscillation-locomotor-activity-and-body-temperature
#8
Casper Schwartz Riedel, Birgitte Georg, Henrik L Jørgensen, Jens Hannibal, Jan Fahrenkrug
Early growth response transcription factor 1 (EGR1) is expressed in the suprachiasmatic nucleus (SCN) after light stimulation. We used EGR1-deficient mice to address the role of EGR1 in the clock function and light-induced resetting of the clock. The diurnal rhythms of expression of the clock genes BMAL1 and PER1 in the SCN were evaluated by semi-quantitative in situ hybridization. We found no difference in the expression of PER1 mRNA between wildtype and EGR1-deficient mice; however, the daily rhythm of BMAL1 mRNA was completely abolished in the EGR1-deficient mice...
November 14, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/29138421/mperiod2-brdm1-and-other-single-period-mutant-mice-have-normal-food-anticipatory-activity
#9
Julie S Pendergast, Robert H Wendroth, Rio C Stenner, Charles D Keil, Shin Yamazaki
Animals anticipate the timing of food availability via the food-entrainable oscillator (FEO). The anatomical location and timekeeping mechanism of the FEO are unknown. Several studies showed the circadian gene, Period 2, is critical for FEO timekeeping. However, other studies concluded that canonical circadian genes are not essential for FEO timekeeping. In this study, we re-examined the effects of the Per2 (Brdm1) mutation on food entrainment using methods that have revealed robust food anticipatory activity in other mutant lines...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29121225/time-dependent-glucocorticoid-administration-differently-affects-peripheral-circadian-rhythm-in-rats
#10
Tao Wu, Zhengwei Fu
There is a growing recognition that glucocorticoid (GC) acts as an internal timing signal for peripheral circadian oscillators. However, the transcription process of GC-related clock gene in the peripheral tissues is not fully understood. The present study was designed to explore the potential role of clock genes in the GC-induced peripheral circadian gene expression invivo. Real-time RT-PCR analysis indicated that the transcript levels of Per1 and Dec1 were rapidly up-regulated within 0.5 and 1 h in the heart and kidney respectively after stimulation with dexamethasone (Dex)...
November 7, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/29113166/expression-of-circadian-clock-genes-in-human-colorectal-adenoma-and-carcinoma
#11
Tomoyuki Momma, Hirokazu Okayama, Masaru Saitou, Hidekazu Sugeno, Nobuhiro Yoshimoto, Yuji Takebayashi, Shinji Ohki, Seiichi Takenoshita
Circadian rhythms are fundamental biological systems in most organisms. Epidemiological and animal studies have demonstrated that disruption of circadian rhythms is linked to tumor progression and mammalian tumorigenesis. However, the clinical significance of in situ clock gene expression in precancerous and cancerous colorectal lesions remains unknown. The present study aimed to investigate mRNA transcript levels of circadian clock genes within human colorectal cancer and adenoma tissue sections. Using in situ hybridization, the expression of key clock genes, including period circadian protein homolog (Per) 1 and 2, cryptochrome 1 (Cry1), circadian locomoter output cycles protein kaput (Clock), brain and muscle ARNT-like protein 1 (Bmal1) and casein kinase 1ε (CK1ε) were retrospectively examined in 51 cases of colorectal carcinoma and 10 cases of adenoma...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29106308/sleep-quality-and-methylation-status-of-core-circadian-rhythm-genes-among-nurses-and-midwives
#12
Agnieszka Bukowska-Damska, Edyta Reszka, Pawel Kaluzny, Edyta Wieczorek, Monika Przybek, Shanbeh Zienolddiny, Beata Peplonska
ABSTARCT Poor sleep quality or sleep restriction is associated with sleepiness and concentration problems. Moreover, chronic sleep restriction may affect metabolism, hormone secretion patterns and inflammatory responses. Limited recent reports suggest a potential link between sleep deprivation and epigenetic effects such as changes in DNA methylation profiles. The aim of the present study was to assess the potential association between poor sleep quality or sleep duration and the levels of 5-methylcytosine in the promoter regions of PER1, PER2, PER3, BMAL1, CLOCK, CRY1 CRY2 and NPAS2 genes, taking into account rotating night work and chronotype as potential confounders or modifiers...
2017: Chronobiology International
https://www.readbyqxmd.com/read/29070825/melanopsin-a-canonical-light-receptor-mediates-thermal-activation-of-clock-genes
#13
Maria Nathália Moraes, Leonardo Vinícius Monteiro de Assis, Keila Karoline Magalhães-Marques, Maristela Oliveira Poletini, Leonardo Henrique Ribeiro Graciani de Lima, Ana Maria de Lauro Castrucci
Melanopsin (OPN4) is a photo-pigment found in a small subset of intrinsically photosensitive ganglion cells (ipRGCs) of the mammalian retina. These cells play a role in synchronizing the central circadian pacemaker to the astronomical day by conveying information about ambient light to the hypothalamic suprachiasmatic nucleus, the site of the master clock. We evaluated the effect of a heat stimulus (39.5 °C) on clock gene (Per1 and Bmal1) expression in cultured murine Melan-a melanocytes synchronized by medium changes, and in B16-F10 melanoma cells, in the presence of the selective OPN4 antagonist AA92593, or after OPN4 knockdown by small interfering RNA (siRNA)...
October 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29061672/mir-6883-family-mirnas-target-cdk4-6-to-induce-g1-phase-cell-cycle-arrest-in-colon-cancer-cells
#14
Amriti R Lulla, Michael J Slifker, Yan Zhou, Avital Lev, Margret B Einarson, David T Dicker, Wafik S El-Deiry
CDK4/6 targeting is a promising therapeutic strategy under development for various tumor types. In this study, we used computational methods and TCGA dataset analysis to identify novel miRNAs that target CDK4/6 and exhibit potential for therapeutic development in colorectal cancer (CRC). The 3'UTR of CDK4/6 mRNAs are targeted by a family of miRNAs which includes miR-6883-5p, miR-149*, miR-6785-5p and miR-4728-5p. Ectopic expression of miR-6883-5p or miR-149* downregulated CDK4 and CDK6 levels in human CRC cells...
October 23, 2017: Cancer Research
https://www.readbyqxmd.com/read/29044990/transcriptome-analysis-for-uvb-induced-phototoxicity-in-mouse-retina
#15
Mi-Jin An, Chul-Hong Kim, Gyu-You Nam, Dae-Hyun Kim, Sangmyung Rhee, Sung-Jin Cho, Jung-Woong Kim
Throughout life, the human eye is continuously exposed to sunlight and artificial lighting. Ambient light exposure can lead to visual impairment and transient or permanent blindness. To mimic benign light stress conditions, Mus musculus eyes were exposed to low-energy UVB radiation, ensuring no severe morphological changes in the retinal structure post-exposure. We performed RNA-seq analysis to reveal the early transcriptional changes and key molecular pathways involved before the activation of the canonical cell death pathway...
October 17, 2017: Environmental Toxicology
https://www.readbyqxmd.com/read/29027702/per1-gup1-and-cwh43-of-methylotrophic-yeast-ogataea-minuta-are-involved-in-cell-wall-integrity
#16
Xin-Xin Xu, Akiko Komatsuzaki, Yasunori Chiba, Xiao-Dong Gao, Takehiko Yoko-O
In eukaryotes, the glycosylphosphatidylinositol (GPI) modification of many glycoproteins on the cell surface is highly conserved. The lipid moieties of GPI-anchored proteins undergo remodeling processes during their maturation. To date, the products of the PER1, GUP1, and CWH43 genes of the yeast Saccharomyces cerevisiae have been shown to be involved in the lipid remodeling. Here, we focus on the putative GPI remodeling pathway in the methylotrophic yeast Ogataea minuta. We found that the O. minuta homologs of PER1, GUP1, and CWH43 are functionally compatible with those of S...
October 13, 2017: Yeast
https://www.readbyqxmd.com/read/29023516/hypothalamic-control-systems-show-differential-gene-expression-during-spontaneous-daily-torpor-and-fasting-induced-torpor-in-the-djungarian-hamster-phodopus-sungorus
#17
Ceyda Cubuk, Hanna Markowsky, Annika Herwig
Djungarian hamsters are able to use spontaneous daily torpor (SDT) during the winter season as well as fasting-induced torpor (FIT) at any time of the year to cope with energetically challenging environmental conditions. Torpor is a state of severely reduced metabolism with a pronounced decrease in body temperature, which enables animals to decrease their individual energy requirements. Despite sharing common characteristics, such as reduced body mass before first torpor expression and depressed metabolism and body temperature during the torpid state, FIT and SDT differ in several physiological properties including torpor bout duration, minimal body temperature, fuel utilization and circadian organization...
2017: PloS One
https://www.readbyqxmd.com/read/29021622/the-circadian-transcriptome-of-marine-fish-sparus-aurata-larvae-reveals-highly-synchronized-biological-processes-at-the-whole-organism-level
#18
M Yúfera, E Perera, J A Mata-Sotres, J Calduch-Giner, G Martínez-Rodríguez, J Pérez-Sánchez
The regulation of circadian gene expression remains largely unknown in farmed fish larvae. In this study, a high-density oligonucleotide microarray was used to examine the daily expression of 13,939 unique genes in whole gilthead sea bream (Sparus aurata) larvae with fast growth potentiality. Up to 2,229 genes were differentially expressed, and the first two components of Principal Component Analysis explained more than 81% of the total variance. Clustering analysis of differentially expressed genes identified 4 major clusters that were triggered sequentially, with a maximum expression at 0 h, 3 h, 9-15 h and 18-21 h zeitgeber time...
October 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28992069/local-delivery-of-liposomal-prednisolone-leads-to-an-anti-inflammatory-profile-in-renal-ischaemia-reperfusion-injury-in-the-rat
#19
Carla M A van Alem, Mark Boonstra, Jurriën Prins, Taisiya Bezhaeva, Mieke F van Essen, Jurjen M Ruben, Alexander L Vahrmeijer, Eric P van der Veer, Johan W de Fijter, Marlies E Reinders, Onno Meijer, Josbert M Metselaar, Cees van Kooten, Joris I Rotmans
Background: Treatment of inflammatory kidney diseases with systemic high-dose glucocorticoids (GCs) has severe side effects. Liposomal encapsulation could facilitate local delivery of GCs to the inflamed kidney, as liposomes encapsulate their payload until extravasation at sites of inflammation, potentially resulting in local bioactivity. Our aim was to evaluate the ability of liposomes to accumulate locally after renal ischaemia-reperfusion injury in the rat and to study its effect on macrophages...
July 8, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/28981604/an-individual-12-h-shift-of-the-light-dark-cycle-alters-the-pancreatic-and-duodenal-circadian-rhythm-and-digestive-function
#20
Liang Xu, Tao Wu, Haifeng Li, Yinhua Ni, Zhengwei Fu
In mammals, behavioral and physiological rhythms are controlled by circadian clocks which are entrained by environmental light and food signals. However, how the environmental cues affect digestive tract's circadian clock remains poorly understood. Therefore, in order to elucidate the effect of light cue on the resetting of the peripheral clocks, we investigated the expressions of clock genes (Bmal1, Cry1, Rev-erbα, Per1, and Per2) and digestive function genes (Cck, Cck-1r, Sct, Sctr, and Ctrb1) in the pancreas and duodenum of rats after the light-dark (LD) cycle reversal for 7 days...
October 1, 2017: Acta Biochimica et Biophysica Sinica
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