Archive for February, 2015

More links between food, circadian rhythm, and health?

February 14, 2015 Leave a comment

My research is broadly focused in circadian rhythm, and as a second year graduate student, I am still expanding my knowledge in this field. The more I read, the more I realize that everything is connected! Circadian rhythm can be described at many levels. There are transcriptional cycles, translational cycle, post-translational modification cycles, and even metabolic cycles. As it turns out, all to of these circadian rhythms are not coincidental, but rather, they are mostly a result of environmentally regulated mechanism such as light, nutrition, and hormonal stimuli. For the average animal, cycles of daylight, eating, and hormone release are set to the pace of their environment, and evolution has been selective for organisms that can anticipate their environments. Thus, circadian rhythms are highly conserved across the animal kingdoms. Although circadian regulation occurs at each level of gene expression, it all begins with transcription. The transcriptional circadian cycle can be attributed to transcription factors (CLOCK and CYCLE/BMAL) which bind to E-box elements and promote downstream gene expression. Of these genes, two of them (PERIOD and TIMELESS/CRYPTOCHROME) return to the nucleus to inhibit CLOCK and CYCLE activity and their own transcription. This negative feedback loop takes approximately 24h and defines the circadian period. One of the most important regulatory mechanism underlying this cycle is that of post-translational modifications (PTM) which establish the timing of PERIOD and TIMELESS inhibitory activity.

PTM regulation has been well defined in terms of phosphorylation, but the field of PTM regulatory mechanisms has barely scratched the surface. There are numerous ways a protein can be modified and even more ways in which this can affect protein activities. The articles I have selected provide an example for the importance of PTM in the circadian cycles of the liver. Metabolic health is a growing concern worldwide due to the number of people who suffer from metabolic diseases or malnutrition. The first article is a study from 2013 that illustrates the dramatic shift in transcriptional and metabolic outputs in response to nutritional challenges. It is compelling to consider what implications this has for people who regularly face “nutritional challenges” such as high fat diets. The second article is a review that discusses how high sugar and other nutritional challenges can affect enzyme activity in the liver by disrupting the PTM profile of those enzymes. Together, these articles support the notion that healthy eating is an important component of healthy protein function. There are a number of other ways that good nutrition supports healthy cells, metabolism, and hormone balance, but when it comes to my area of focus, I see it all through the lens of protein regulation by PTM. Perhaps a full profile of PTM in healthy and unhealthy people could establish new guidelines for future healthcare as a point of diagnostics and therapeutics. Then again, it might be easier to just eat a salad every now and then.

Cheers to good food and good PTM!

Adam Contreras

BMCDB Graduate Group, UC Davis

Categories: Uncategorized

Breakthrough in understanding folding of single stranded viral RNAs could lead to cure for the common cold

February 9, 2015 Leave a comment

Pretty cool stuff, not only is it the primary sequence, but all the secondary structural interacts are absolutely key for folding and assembly into the viral partciel.

Title overstates the case but excerpt from: Scientists have figured out how to stop the common cold in its tracks

“We have understood for decades that the RNA carries the genetic messages that create viral proteins, but we didn’t know that, hidden within the stream of letters we use to denote the genetic information, is a second code governing virus assembly,” one of the team, biophysicist Roman Tuma from the University of Leeds in the UK, told Laura Donnelly at The Telegraph. “It is like finding a secret message within an ordinary news report and then being able to crack the whole coding system behind it.”

Single-stranded RNA viruses are the most simple type of viruses known to science, and it’s thought that they were probably one of the first to evolve. And being around for a long time means they’re super-effective at what they do. Rhinovirus, which is the predominant cause of the common cold, is responsible for 1 billion infections per year – in the US alone.

Revealing the density of encoded functions in a viral RNA

We present direct experimental evidence that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism. We show that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid self-assembly in vitro. These experiments confirm that the selective advantages for viral yield and encapsidation specificity, predicted from previous modeling of packaging signal-mediated assembly, are found in Nature. Regions of the genome that act as packaging signals also function in translational and transcriptional enhancement, as well as directly coding for the coat protein, highlighting the density of encoded functions within the viral RNA. Assembly and gene expression are therefore direct molecular competitors for different functional folds of the same RNA sequence. The strongest packaging signal in the test fragment, encodes a region of the coat protein that undergoes a conformational change upon contact with packaging signals. A similar phenomenon occurs in other RNA viruses for which packaging signals are known. These contacts hint at an even deeper density of encoded functions in viral RNA, which if confirmed, would have profound consequences for the evolution of this class of pathogens.