Questions related to Circadian Biology
I worked with Chronolab program, but this program is for Mac and it's old. Is there some similar program for PC or some latter version of Chronolab? Thanks
Biomechanics face grand challenges due to the intricacy of living things. We need multidiciplinary approach (mechanical, chemical, electrical, and thermal ) to unravel these intricacies. We need to integrate observations from multiple length scales - from organ level to, tissue level, cell level, molecular level, atomic level, and then to energy level) Over these intricacies, their dynamism, the complexity of their response makes it very difficult to correlate empirical data with theoretical models. Among these challenges, which is the most important challenge. If we solve the most important challenge, we could solve most of the other challenges easily.
The research that we are performing is using 2-times cortisol (8 AM - 10 PM) as circadian biomarker for acute sleep deprivation. The thing is, we ask them to avoid the ingestion of any caffeine-based substances (beverages or medications) the day before the test, but we want to know if the caffeine ingestion can anyhow "reset", or modify the cortisol curve after the first sample collected. Does anyone knows if there are any papers assessing the effects of caffeine over the cortisol circadian curve?
I want to localize the pinealocytes, using immunohistochemistry. Generally, the pineal organ of the catfish is very tiny and thread like appearance. Sectioning of the pineal organ is too difficult.Can you provide me any protocol to study the localization of the pinealocytes using confocal microscopy?
I noticed that most study on sleep (including sleep deprivation and rebound) use a photoperiod of LD 12:12. In this way, for sleep deprivation, they usually choose to deprive 6, 12, 24h. Is that like a convention we should follow?
For me I want to raise them under different photoperiod, like longday and shortday photoperiod (e.g. LD 11:13, 15:9..). I am not sure whether it is OK. Thanks for your kind and useful answer!
Besides the previously discovered circadian clock (the 24-hour timekeeper) is there another master regulator clock controlling aging and other time scheduled events of life, such as fetal development and puberty (and ultimately over-watching the whole cycle of aging) which are precisely time-dependent, by keeping the track of solar “years” passed?
After a long bibliographic search I could not find any data with regard on the performance of Ewoks on the novel object recognition (NOR) test. Any information would be greatly appreciated.
These animals seem pretty hostile to novel stimuli (i.e. stormtroopers) so I wonder if longer habituation sessions would be needed to avoid their neo-phobia.
I also have concerns on the housing light conditions, and preferred stage of the light cycle for the test. I am unfamiliar with the light cycle hours in their natural environment. They also seem pretty active at night.
I have list of genes with their phase of expression. Frequency of phase distributions shows two distinct phase clusters. I would like to calculate the mean of each phase clusters (circular phase) What I understand is simple averaging is not right for this type of directional data.
It would be great if someone can help me to calculate the mean circular phase of phase clusters. what I have with me is phase of expression of each gene and frequency of each phase.
Is there any type of circadian clock rhythmic expression happens due to different colors of light? Or different intensity of the light can affects?
Kindly give me any suggestion.
I am curious from the point of view of those who may take sleep-aiding/soporific drugs to hasten adaptation to new time-zones?
Is it possible that the value of circadian amplitude higher than circadian MESOR? or depends upon the variable such as physiological (blood pressure) or biochemical (ex. melatonin)?
Does anybody know works where two or more circadian genes were overexpressed multiplexly and lifespan of a model was observed? Probably somebody knows groups solving the problem of combined overexpression for life extension, I would be grateful to recieve any information.
I am hoping to find answers for an issue that I am facing when using LumiCycle from Actimetrics. I have been using U2OS cells with Per2-Luciferase in it, which has given me stable rhythmic outputs consistently. Over the last few months, I have encountered a strange problem when the signal dies off at the end of Day 3 after plating while previously it used to continue till day 7. This problem is erratic as it comes and goes. I have changed the batch of my cells, used fresh lumicycle media, luciferin, cell densities while plating etc. When the signal is lost, the cells still look healthy and there is definitely no contamination in the media, nor is there any loss in the volume of the media since they were set up. The problem is at times seen on all the channels or in some channels while the other channels are just fine.
I was wondering if anyone experienced in working with this instrument has encountered any similar problem and would appreciate any assistance or direction to resolve this issue.
I'm looking for raw data of weight change over the course of a single day/night. How does weight change hour-to-hour, minute-to-minute, over the course of a single day? I know of one guy who has done an overnight weight loss study in Brazil but his work appears to be ignored by mainstream science at this point.
Keywords: Circadian biology, weight flux, weight loss, metabolism.
As already established that our performance rhythms in various cognitive domains are the outcome of two processes- homoeostasis and circadian timing system (CTS). Having said that, if we assess the influence of CTS in cognitive performance through time-of-day protocol method preferably over other two methods i.e. forced de-synchronization and constant routine, can we make sure that both the aforementioned processes are individually unmasked, if not completely, then even partially?
I am currently working with activity data on European badger (Meles meles). They are nocturnal, and begin their winter sleep (not true hibernation) approx. early November lasting to early March. Their activity in the winter is limited indirectly by low temperature (frost) and snow cover due to less access to food (e.g. digging after earthworms).
This circannual rhythm of activity might be endogenously generated, although external cues such as photoperiod, temperature or snow cover can function to entrain a circannual rhythm.
I working with data from wild badgers and I will not be able to control for the different variables experimentally.
I am planning to test if the decrease in activity in the fall and increased activity in spring could be explained by the time of the year, photoperiod, temperature and snow cover.
However, I will not be able to separate photoperiod from time of the year, but temperature and snow cover do varies. I am seeking the most parsimonious model to explain what causes the badgers to go to winter sleep.
I wish to discuss and get advice on how I should treat the data.
Activity index (numbers of observations adjusted for monitoring effort).
Time of the year
Time of the year is the variable I find challenging and I want to hear your opinions. I am in particular interested in the fall vs winter and winter vs. spring. Could one solution be to split the data set into summer and winter solstice, i.e. June and December solstice (Northern Hemisphere)? Then I could use days until winter solstice and days since winter solstice as an explanatory variables respectively in addition to temperature and snow.
Melatonin and Circadian Typology
What are the causes behind the late secretion (i.e. 2-3 hours) of melatonin hormone in owls as compared to that of larks?
Clock genes are controlled by the temperature and photoperiod. But I wanted to know different temperatures like 150 c,250 c,350 c so on.How to regulate the expression of clock genes of different temperatures? Kindly anyone tell me or send me any research article regarding this.
What are the connections between the reticular nucleus of the thalamus and the reticular formation of the brain stem, the hypothalamus and the cerebral cortex? What role does GABA play?
Hello, I like to ask for information about genetic markers of time perception, internal clock or duration representation or trials in rat model.
In the same way, ask for specific trials in rat model that can be linked with duration process or internal clocking.
I really appreciate your help!
I am analyzing microarray data for circadian experiments (8 timepoints, 4-hour sampling resolution) and I would like to do a COSOPT analysis. I could not find the COSOPT code or the email of Dr. Straume. Do you have acess to that code in a programming language? I wonder if someone can share the algorithm source. I already analyzed the data using JTK_Cycle. Do you know any other program for analyzing periodic patterns in genome-scale data sets?
Abrupt changes from weekend to weekday and vice versa worsen circadian disruption as several days of a stable sleep schedule is required to shift the hormone rhythms completely?...and is the latter part correct or just an assumption?
Everywhere is clear that melatonin is produced mainly at nighttime, and its production decreases with age almost half from 25 to 50 years old. However the absolute amount of produced melatonin remains unclear for me. I would appreciate very much any information on that. Maximum concentrations in blood in young or old individuals would help also!
We found in our recent study (in prep.) an indication that the daylight's brightness suppresses activity of a nocturnal/crepuscular insect, not any other environmental factor. In other words, the period of inactivity matches exactly the peak of brightness, while peaks of temperature/humidity and wind speed don't match as nicely.
Are there any existing studies that we can cite to support this assertion? It's not central to our research question, but would be useful to elaborate. The only references I could find deal with seasonal patterns of activity entrained by daylight duration on longer time scales. But what about diel patterns of activity? Any pointer would be much appreciated.
Hello Good People!
For my thesis purpose, I need to measure some LED lights (blue LED, and also others, except IR LED, UV LED). My main purpose to find out the non-visual effect of LED light on human circadian rhythm such like melanopic lux and so on. I need to compare LED spectrum with the light spectrum (D65).
Now, my main need to measure the light both horizontal and vertical directions. Can anyone suggest the proper methods how can I measure the LED lights?
I know about LL and DD condition which can disturb normal circadian cycle of light. when we are talking about rat as a model, how much change is ok in light/dark cycle of animal ? I mean, is it possible to have below schedule time for D and L sequences in different groups?
12D/12L in one group, 6D/6L in other group or 48 D/48L?
Does any role exist in this model?
Thanks for your help
There is very little information on dormancy in woody species in tissue culture systems. I am more after bud dormancy and apical dominance. In nature, the axillary buds are often dormant and this is controlled by sucrose, water supply to the bud and more than anything hormonal balances. In tissue culture, we give the same photoperiod and temperature throughout the year and conditions are ideal for all the buds to grow, but still we find that apical dominance exists more often than not. Has anyone studied these aspects in detail - biochemistry, gene regulation etc.? I am asking because when we test the tolerance to vitrification solution, axillary buds tend to be more tolerant than the apical buds. Any clues?
Thanks in advance
I am working on the circadian rhythym of recovery after fatigue. I have seen many researches in this area but still not satisfied with the work done. Can somebody suggest something who have worked in this area?
I am doing some experiments about clock gene in broiler. And I need some relative articles. Articles in relation to clock gene,cry gene,per gene and bmal gene are best. Thanks.
from : Lei Liu,China Agriculture University, BeiJing,China
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Moon gravity influences plants, animal reproduction, human behavior, etc. It is time to demonstrate to the scientific world that the cosmic and lunar periodicities significantly affects, even in the field of biological clocks.
Since 2014 they are beginning to appear incredibly many studies about these topics before then were almost nonexistent since the nineties.
I have just started with analysing daily periodicity in animal behaviour and I'm a bit confused about the use of the term "Circadian rhythms. There seems to be two different definitions, see below.
I wonder if it is common to use circadian to describe observations of animals in their natural environment (no experiment controlling for light-dark cycles)? Or should I just use "diel" or " daily" activity when describing behaviour throughout a 24 h cycle?
“Circadian rhythms are by definition endogenous rhythms with a period of about 24 hours that persist even with the loss of external synchronizers, that is, under constant conditions (1). In the absence of such experimental evidence, characterizing the locomotor activity pattern of juvenile Alligator mississippiensis as circadian is premature.
We are designing a neuroimaging study to test hypothesised circadian moderation of reward function in humans. Seems like our hypothesis is best tested using resting state methods, ideally with the hypothalamic suprachiasmatic nucleus as a 'seed region' to investigate correlations with brain reward centres (particularly ventral striatum).
I understand that small, deep brain centres are difficult to image.
I have recently started analyzing animal circadian activity (24 hours). I started my analyzes with the use of GAM (or more precise GAMM, with random term (animal ID)). However, I'm now aware that some use cosine curve fitting when working with circadian data. What is the best approach?
My activity data is nest attendance in breeding birds. I have repeated measurements of several breeding pairs. And I look at nest visits per hour block (activity index). From this I would like to model the circadian activity throughout the day, and try to see if there are some peaks.
I have used the following script in R:
Cosine curve fitting#
M1 <- lme(Activity ~ I(cos(2*pi*Time/24))+I(sin(2*pi*Time/24))+
random =~ 1 | ID,
data = observations, method = "REML")
Note: fixed at 2 harmonics gave the best fit.
M2 <- gamm(Activity ~ s(Time),
random = list(ID=~1),
data = observations, method = "REML")
From what I understand there is approximately 2 hours in the sleep/wake cycle of the 'lark' and 'owl' but I am trying to find out how this affects the timing of other biological clocks. I am a design student - I hope I am not asking an obvious question.
Also antibodies for PACAP and calbindin. What are other neuronal phenotypes in the SCN?
I would like to investigate a possible relationship between the daily activity patterns of an animal and the timing and amount of daylight experiences by the animal. I do not have light-logger data per animal, so I am searching for a free data source. Ideally this data would be location specific (I'm working near Albany, New York, USA) and available per minute. Can any one suggest a data source? Perhaps something widely accepted within the circadian biology community?
Costa/Lievore reported in (10.1080/00140138908966104): "Conversely, morningness appeared to be
unrelated to long-term tolerance, but did influence circadian adjustments and
sleep behaviour." in their abstract.
We're interested in using WI-38 cells to establish an assay. We are interested in a human fibroblast cell line which is haploid and has been previously used in circadian experiments. The assay will require us to transfect or infect the cells and then to create clonal populations. Does anyone have experience with WI-38 cells and can speak to the ease/difficulty of working with WI-38 cells?