Thursday, June 22, 2017

Why does spicy "burn"?

https://www.scientificamerican.com/article/why-is-it-that-eating-spi/

Sunday, June 18, 2017

The Search for Alien Megastructures

You guys might remember the huge internet explosion about alien megastructes back in 2015 when scientists suggested the unusual dimming patterns of a distant star, KIC 8462852, may be due to alien megastructures or Dyson Spheres hypothisized by physacist Freeman Dyson in 1960. Dyson Spheres or alien megastructures are hypothetical massive structures built around a star to harvest its energy, sounds awesome right? Well the search for alien megadtructures has continued since the excitement in 2015 and along with it, the observation of KIC 8462852. Perhaps the main argument against the dimming patterns of KIC 8462852 being due to an alien megastructure is the lack of infrared radiation detected from the star. If there was a massive alien structure absorbing the star's energy it would give off more energy than the star alone. Hope is not lost in the search for alien megastructures though; physicist Zaza Osmanov pointed out it would be better to build one of these energy-harvesting megastructures around the reminants of the dead stellar heart of a once giant star, a pulsar. Pulsars radiate their energy in narrow beams akin to the beams of a light house, which would enable extraterrestrials to build ring-like structures to harvest the energy as opposed to something that would encapsulate an entire star. Pulsars may be the best possibility to investigate in our search for alien megastructures.

Article info is from: https://www.theguardian.com/science/across-the-universe/2017/jun/15/alien-megastructures-where-we-should-look-next

Chimeric Pancreases Used to Cure Diabetes in Mice

This year the first human-pig chimera was made. This could be a huge step for regenerative medicine because if we could manipulate animals such as pigs to grow human organs it would eliminate the need for organ donors and organ wait lists. Human transplants are likely still a long ways off, but this February researchers sucessfully created rats with pancreases made from mouse pluripotent stem cells. They first used CRISPR to create rats without the ability to make their own pancreases, then injected the rat embryos with mouse stem cells which sucsessfully formed normally-functioning pancreases in the rats. From there they surgically removed the rat-mouse pancreases and transplanted them into diabetic mice. The transplanted pancreases succesfully normalized to the mice and maintained normal blood glucose levels in the host mice. The mice survived for over a year without immunosuppressants. This is the first time a chimeric organ has been used to treat a disease. This line of research shows promise for developing a long-term cure for diabetes.

Article: http://www.nature.com/nature/journal/v542/n7640/full/nature21070.html#affil-auth

Behavioral Switch Genes

I'm sure you guys have heard of HOX, the set of growth genes active during early development almost entirely responsible for determining the physical proportions of the body (body plan). HOX genes are physical switch genes regulating growth and physical development. There is clearly a genetic basis to certain aspects of behavior but is there anything a drastic as HOX genes? Are there behavioral switch genes? The answer remains debatable for humans, but the fru gene in Drosophila has been identified as one such gene. The fruitless (fru) gene is spliced sex-specifically in Drosophila giving rise to distinct male and female proteins. Male Drosophila preform an elaborate, innate mating ritual that shows almost no variation between individuals and is always directed towards females but when fru is mutated this mating ritual can is often disrupted even though physically the males show no mutations. Females never engage in courting behavior. Researchers created male Drosophila with forced female splicing of fru and found the males no longer showed courtship behavior; they were behaviorally female in mating. The males showed no significant differences in their anatomy. They then created female Drosophila with forced male splicing of fru and found the females displayed the male courtship behavior, performing the entire, elaborate male courtship ritual directed towards other females without changing their anatomy. These experiments demonstrate the sex-specific splicing of fru in Drosophila is both necissary and sufficent to confer mating behavior and sexual preference. These findings not only raise questions about the existence of behavior switch genes in other more complex animals, including humans but also about the basis of sexual orientation. Is it possible sexual orientation is controlled by a similar behavioral switch gene in humans? Behavioral switch genes are extremely hard to locate because our understanding of the biological basis of behavior is still so limited, however, the discovery of the fru gene's role in sexual orientation/mating preference in Drosophila may provide clues to the identification of related behavioral switch genes in other animals.

Here's the original paper:  fruitless Splicing Specifies Male Courtship Behavior in Drosophila
File

Monday, June 12, 2017

WHY BATS MATTER

So, my grandmother has this huge fear of bats. And, as she and my grandfather lived in the mountains for about 10 years of my childhood, we all experienced plenty of bats both inside and outside the house. (Yes, a cute little bat family decided that a great nesting area would be the attic!!!) Let's just say my grandmother wasn't ecstatic.
Anyhow, I was thinking about bat pollination. Yes, some bats eat insects mainly, but some are also huge pollinators. I found a cool website that explains so many reasons as to WHY BATS MATTER. So many reasons having to do with pest reduction (aka eating insects), but also to do with pollination. I think I might share this with my grandmother to a) get a laugh out of her reaction b) perhaps change her negative opinion on bats c) educate her on their helpfulness within ecosystems.
Some cool, common bat pollinated flowers (these just happen to turn in to fruit!!) are as follows:
MANGO
BANANA
COCOA (though I can't quite appreciate this one, as I am allergic to chocolate)
DURIAN
GUAVA
AGAVE (fun fact folks, this is used to make tequila)
I'd say bats are pretty important, personally.
http://www.bats.org.uk/pages/why_bats_matter.html

Sympathetic Touch?!

I thought that this was a really cool article. It has to do with synesthesia, and it was found that even simply watching another person being touched stimulates a neural circuit, which some people then said caused them to feel the sensation of touch as well. This correlated with a higher empathic ability, so this showed a consistency with the idea that simulation allows us to empathize with others. Some people who experienced this synesthesia felt the touch on their left cheek when the left cheek of the person being touched was poked, (lol, it also amused me that they just poked people's cheeks), but some felt it on the right, thereby feeling sensation as one would in a mirror image.

Sunday, June 11, 2017

Are these bees going to a rave?

     No! They just happen to be fluorescent thanks to science! This experiment discusses the ways to track bees for ecological purposes and compares fluorescent powders to protein powders. The bees were marked using a tube placed at the entrance of the beehive that would coat the bees in either a fluorescent powder or a protein powder made with egg whites or powdered milk as they leave. This allows for scientists to track where bees are for the purposes of counting populations, determining spread of pollination, and many other tracking reasons.
     The paper determined that the fluorescent powders were significantly more accurate in coating the bees than the protein coatings and was easier to recognize later as well as produced a lower false positive percentage. This method of marking bees could be used widely in ecology and is an important look into the ways we can continue to SAVE THE BEES!

https://academic.oup.com/jinsectscience/article-lookup/doi/10.1673/031.011.14301

Increased risk of sepsis due to vitamin D deficiency

     I mean, obviously we need the sun to live. But what happens when we don't get enough of it? Often, this leads to vitamin D deficiency. This can lead to a whole range of issues. One of these is actually incredibly scary(so get some sun!). A lack of vitamin D can lead to an increased risk of sepsis, according to one paper from 2017 by Zeljic et.al. which outlines the way this happens. Sepsis is a phenomenon that often occurs in hospitalized patients when the body begins to become inflamed due to a foreign virus or organism which can be fatal. Vitamin D receptors are a major key in many biological functions, including inflammatory responses, which is how sepsis occurs, as well as maintaining homeostasis during sepsis.
     Zeljic et.al. 2017 details that genetic predispositions to sepsis have been found but this experiment looks into vitamin D receptor(VDR) deformations may affect the likelihood of sepsis. It was found that homozygous CC genotypes had an increased risk of sepsis in comparison to a TT genotype of  VDR. This is incredibly important because, while we try our best to get into the sun and get vitamin D in as many ways as possible, some people may just be destined to have a deficiency(a little morbid, I know). However, this can lead to more research questions about how we can use dna sequencing and gene splicing to possibly eradicate this issue in the future.

Link to paper: http://onlinelibrary.wiley.com/doi/10.1111/iji.12318/full

Thursday, June 8, 2017

This isn't directly related to biology but it is a thing that just happened and its an incredibly cool feat and testament to the crazy complexity and ability of the human body. So Kristen and I rock climb (generally bouldering without harnesses on a 12 foot wall) and so related to that, this rock climber, Alex Honnold, just basically did what we do, but on a way more insane scale. 

Steps for fully fathoming what this amazing man's body is doing:
1) Take that 12 foot wall that Kristen and I are climbing and then multiply that by 250 (!!!).
2) Take a breath down here at 35cm (give or take) above sea level. Then picture what it's like to breathe at 7000ft above sea level (the top of El Capitan is at 7569 feet above sea level). For reference,  Acute Mountain Sickness symptoms may set in at any altitude above an average of 6,000 feet, information that can be found through any basic google search.
3) Now picture what its like to breathe for the last 1500ft of a 3000ft climb above an altitude of 6000ft while wedged into a crack in natural rock with all of your muscles engaged at one point or another keeping you from falling.

Hopefully you have envisioned all of these things and are now not having a panic attack but most importantly recognizing the amazing, crazy way our muscular, skeletal, nervous, respiratory, circulatory and all the rest are working synergistically to get this man up the wall.

Also everyone should try rock climbing because it is a fun way to make friends and stay healthy and accomplish really cool things!!

Watch Alex on part of his journey up this crazy wall

Food and colors!

So this is not about animal behavior I promise. This is about the topic I talked about today in class where our brain loves to see warm colored foods because we associate it with being safe, fresh and nutritional. This study plays with our perception of foods and colors changing the backgrounds to see what attracts these participants, which 93% go to Brigham Young University.
http://www.sciencedirect.com/science/article/pii/S0950329316302178

Image result for color affect food perception

Titi Monkey from Ecuador

I am honestly obsessed with animal behavior so this is yet another post about animal behavior.
There was a study conducted in Ecuador on Titi Monkeys and the male-female relationship before and after they have had an infant together. It shows that the father is actually a bigger part of the infants life than the mother and that the mother actually finds ways to avoid being with their infant! For more information on this topic here is the paper I read on it: https://link.springer.com/article/10.1007/s10329-015-0489-8

Image result for titi monkey

The few benefits of being a parent (as a seahorse)

So when we talked about Behavioral Ecology week 3 the topic of seahorses came up because of the parental care that the males put in. Well this paper talks about how this parental care improves their immune system! While mating competition does reduce the male's immunity, parenting is there to help improve it. If you want to know more check out this paper!
http://www.sciencedirect.com/science/article/pii/S1050464816306325 

Image result for seahorse

Kylie back at it again with a walking fish!!!!!

As the provider of all things marine (whether you like it or not), I am back at it this quarter with yet another fish that appears to walk across the substrate (as a reference, last quarter I bestowed upon you all facts about the lobe-finned frogfish).

This quarter I bring to you *myyyysteryyyyy* in the form of what experts are potentially labeling as some species of stingfish, although without direct examination of the organism, it is unclear what exactly this bi-pedal creature is. As shown in the video (linked below), this little guy uses modified, crab-leg-esque pectoral fin appendages (that was a mouthful) to scuttle along the substrate. If this is in fact a species of stingfish, this organism possesses nasty spines that can stab and inject a venom into whomever is the unfortunate fool to touch them.

Watch the video for cool footage of this little guy as well as some cool facts:

Mysterious stingfish(?)

Wednesday, June 7, 2017

Farmed Fish Stomach Anomaly

When we briefly talked about the digestive system during our nutrition section, I became interested in the morphological and physiological changes within an organism that have an artificially modified diet. An easy example would be humans in the developed world given genetically modified food and other modifications made to our diets since the evolution of the modern human. However, a paper I discovered talked about an abnormality scene in farmed rainbow trout. Fish within the farm were developing extremely large stomachs. Scientists became interested in the possible osmoregulatory and nutritional changes within the stomachs of these fish. If you are interested in the subject, I have provided a link.
Link: http://www.sciencedirect.com/science/article/pii/004484869090257N

Tuesday, June 6, 2017

Sliding Filament Theory as a Middle School Dance

Approximately 2 hours ago I got really excited in class about the prospect of posting this video... HERE IT IS!
This is one of the old school Crash Course videos, created in 2012. In it, they talk about the sliding filament theory as though the actin and myosin filaments were middle schoolers trying to get jiggy with it at a dance. At around 5:00 the first mention of the middle school dance analogy takes place, but then there is an aside that discusses the discovery of the sliding filament model. This little "biolo-graphy" is really interesting, but if you want to skip it, the true simile begins around 8:25.
Check it out! It's informational and funny (aka memorable!).

Attention all Coffee and/or Tea Lovers!!

Do you love starting the day with a nice hot cup of coffee? Or, perhaps, ending a long day at work with a sweet cup of tea? Do you happen to dislike chronic liver disease, the 12th leading cause of death in the world?

Then this article is for you!!!

A recent study in New Amsterdam of 2000+ adults (over the age of 45) tested the effects of coffee and tea on healthiness of the liver. The study predicted that drinking coffee or tea daily may prevent stiffness and scarring in the liver, helping to protect against liver fibrosis. People were split into groups of heavy vs moderate coffee drinkers, heavy vs moderate tea drinkers, and neither coffee or tea drinkers, and the scar tissue and health states of their livers were analyzed. The data collected showed that frequent coffee and tea drinkers had "significantly lower odds of high liver stiffness values independent of lifestyle, metabolic and environmental traits."



Although there are more than 100 components in coffee, making it difficult to tell what causes these effects on the liver, I think it's safe to say that coffee just got even more fantastic. I'll drink (coffee and/or tea) to that!!!

Built in "Deet"

These Amazonian frogs have chemicals in their skin that serve as ant repellant! The way they do it is actually really cool, because they imitate the ants' own chemical signals, "blending in" with the ants. This way, the ants will pass by Lithodytes Lineatus but attack any other frog or insect in their way. The two species coexist and have a symbiotic relationship, specifically commensalism, because the frog benefits from the higher humidity of the anthills for their eggs. In order to read more about the scientific study that suggests this use of chemicals in the skin to blend in with ants, read this paper: https://link.springer.com/article/10.1007%2Fs00265-016-2223-y



Racism in Medicine

The Tuskegee syphilis study is infamous, but the intersection of racism and medical treatment extends far beyond that. Science and history are always tied together, and scientific racism has helped shape both history and the world we experience today, so here are two papers describing just a bit of this phenomenon.

Tuskegee Study: http://www.jstor.org/stable/pdf/3561468.pdf?refreqid=excelsior%3A312f38214409327e1508fda1047bda73

Racism in medical treatment: http://www.pnas.org/content/113/16/4296.full

Also to look up:

  • Dr. Sim's and development of modern gynecology through forced experimentation on enslaved women
  • Resistance to malaria and the advent of slavery in the Americas




Monday, June 5, 2017

"Pain!" (said in Spock voice) or lack thereof...

Hello, bio people! I was looking back at my scrawlings in the margins of my bio notes and one of them says "How common is that thing where people can't feel pain?" And as eloquent as that was.. this paper is much better. Have a good time learning about congenital insensitivity to pain!

http://bjj.boneandjoint.org.uk/content/jbjsbr/84-B/2/252.full.pdf

Image result for spock pain gif

What if you couldn't recognize your own mother?

There have been many studies dedicated to determining which part of the brain is in charge of face recognition, as it is an important evolutionary skill to be able to quickly recognize faces. In fact, if an infant is put in front of a paddle with scribbles and a paddle resembling an extremely basic face, they will automatically gravitate towards the face. At an early age, babies develop the ability to recognize their mothers scent and facial features, as their mother is typically the most important figure in their early lives.
Prosopagnosia, or face blindness, is an inability to recognize people's faces, no matter how often you interact with them. Instead, people with prosopagnosia rely on things like scent, hairstyle, or voice to distinguish people from each other. The experience of living with face blindness has been compared to looking at a picture like the one below, where faces are flipped upside down. Even though we should be able to immediately recognize these faces, it is extremely hard to do without turning your head in some way.
Through various studies, psychologists have determined that there is a section of the brain dedicated to face recognition, coined the fusiform face area, in the occipital lobe. Oftentimes, genetic prosopagnosia is reported alongside other afflictions such as the inability to recognize objects, or colorblindness.

Axolotl Limb Regeneration

During our discussion about animal physiology, I pondered what interesting traits some other animals possessed. I eventually came across a paper about ambystoma mexicanum, otherwise known as the axolotl salamander. This amphibian never loses its gills and remains aquatic its entire life cycle, has never been documented with cancer, and these animals can regenerate entire limbs. The ability to regenerate limbs is a trait that seen in other amphibians and it is a trait that is very interesting to scientists. The paper discusses the nature if limb regeneration within these animals. Different amputation, reattachment, and regeneration methods were used in the research of the pluripotent stem cells within the damaged and amputated tissue sites. If you are interested in reading this paper, I have provided a link.  
Link: http://search.proquest.com/docview/204463860/fulltext/4BA77EE3E7684378PQ/1?accountid=14522

Sunday, June 4, 2017

Not Only Obesity, But also Brian Aging

Even though I didn't rise my hands up in class when Claudia asked about who loved diet coke, since I used it to replace consumption of regular Pepsi for a while, I started to worried about my eating habit. Unfortunately, I researched it on the internet, and found that diet soda not only will ruin my weight control, but also increase risk of developing stroke and dementia. A research conducted by Boston University found that people who drink diet soda daily will be three times as likely to develop stroke and dementia when compared to those who did not. In this research, they mainly analyzed data that has been collected, and although they didn't find correlation between diet soda consumption and stroke or dementia, they found people who drank at least one diet soda per day were three times as likely to develop stroke and dementia.

Probably, I am going to drink water only.

More information, click here.  

A New(2011) Discovery of Immune Cell Type

Immunology system is vital to human beings and it is so complicated that needs scientists to keep researching on it. In 2011, biologists at University of Melbourne discovered a new type of cell in the immune system, which can contribute to further development of drugs that specifically focus on certain types of infectious organisms. We know that the immune system focus on proteins from viruses and bacteria to recognize their types. Among those cells, some T-cells(NKT) can recognize lipid-based molecules, and the a new type of NKT cell was identified which specifically target lipids that exist in cell walls of bacteria, including Mycobacteria. 

Further information, click here.  

Friday, June 2, 2017

Fossilized anatomical systems... cuz fossils...

Hey, here's this (always have to relate our lectures to paleontology somehow, right?).

A nearly complete respiratory, circulatory, and excretory system preserved in small Late Cretaceous octopods (Cephalopoda) from Lebanon

http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=GeneralSearch&qid=2&SID=2FSiBEJmXEfekD9kUhl&page=1&doc=1

Thursday, June 1, 2017

Preventing Premature Labor

Although we have not quite covered the musculoskeletal system in class, I thought I would make a post on the topic since I will be leaving early this quarter. Thus, I will be writing about pregnancy.

The myometrium - the smooth muscle of the uterus - is a key player in the maintenance of pregnancy. Throughout pregnancy, the myometrium is kept in a relaxed state by the steroidal hormone progesterone. However, unbeknownst to most of the world, there is battle going on during pregnancy, a viscous brawl between progesterone (which would like to maintain pregnancy) and estriol (which would like to violently end it by stimulating the myometrium to contract). Once estriol overtakes progesterone, labor begins and pregnancy soon terminates. Once this begins, there really is no stopping the process.

This presents an issue when mothers go into labor prematurely - if the mother goes into labor too early, the fetus will be underdeveloped when born. Being born prematurely presents a host of potential medical issues to the newborn baby. Thus, we would like to prevent this from occurring. Much research has therefore been done on the matter.

Smooth muscle contracts when an action potential is generated by the muscle cell after signaling from a neuron - calcium enters the smooth muscle cell which facilitates the binding of phosphate groups to the myosin filaments in the cell. This causes a shape change in the myosin which pulls on the actin filaments of the muscle cell- causing the cell to contract.

Therefore, if we want to stop the contraction of the myometrium, we must stop this process from occurring in some way - and, as you can see, there are multiple places at which we could do this. Nitric oxide (NO) and androgens (such as testosterone)  have recently been shown to stimulate relax of the myometrium by blockage of these processes. Both molecules have been shown to somehow alter the ion channels which facilitate the entry of Ca2+ and other ions into the cell. Androgens may also regulate at the level of the phosphorylation of the myosin, preventing it from occurring.

Hopefully, not too long from now, these chemicals will find applicable use in preventing premature labor in humans, but more research needs to be done before human trials can begin.

If you want to read more on the matter, here are a couple papers:
https://academic.oup.com/jcem/article-lookup/doi/10.1210/jc.2015-2851
http://onlinelibrary.wiley.com/doi/10.1038/sj.bjp.0704226/full

Wednesday, May 31, 2017

Silica Affecting the Physiology of the Lungs

In class, we briefly discussed the physiology of the respiratory system within animals. I decided to look into some papers that involved the respiratory system. I eventually came across an old paper that talked about how exposing the lungs to different forms of silica can lead to increase tissue production. Originally this was thought to have been a possible therapeutic, however, when the authors decided to run these experiments on mice, most died. However, some rats did experience increase tissue production. If you are curious about this topic, I have provided a link.
Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1037436/?page=1

Acidic Soap???

Acidic soap - I thought it would have been a good idea. 

Last week in class we learned about the innate immune system. One component of this was the skin and its acidic environment which deters microbes such as bacteria from entering our body. Therefore, when we wash our hands with soap, which is typically basic, we are essentially buffering or neutralizing this natural defense that we have.

So why don't we use acidic soap? That's the question I asked myself as I pictured a row of neatly stacked, yellow, soapy lemon bars sitting enticingly upon a bathroom counter-top. However, this isn't the case in our everyday lives. Why? 

Because it turns out that it doesn't really make a difference. A study done in 2013 in an intensive care unit recruited two groups of ICU patients -one group of patients which used an acidic hand wash and another group which used a normal hand soap. It was found that there was no significant difference in the micro-flora of the hands between these two groups, indicating that the basicity of soap doesn't have any long lasting effects on the bacterial levels or composition of the hands. However, it was found that the pH of the skin was consistently higher on those patients that used normal soaps than those who used the acidic cleanser. While this increased pH of the skin did not lead to an increase in bacterial colonization or an altered micro-flora, this pH increase may have other consequences. 

If you want to read more about the study, here's a link to the paper: http://www.sciencedirect.com/science/article/pii/S0964339713000268

Tuesday, May 30, 2017

Want to lose weight? Simple - Don't Eat

After talking today about metabolism and the twinkie diet that Professor Mark Haub went on, I did some research and found a guy that actually didn't eat for 1 year and 17 days in order to lose weight. He ended up losing 275 lbs and went from from 456 to 181!

In 1965 in Scotland, the anonymous man went to the hospital at Dundee and told the doctors his plan and, despite the doctors advising against it, he went through with it and had the doctors monitor him throughout. He was only fed yeast, multivitamins, and potassium tablets over the time period. He also only defecated every 40 to 50 days.

Article on it

Unfortunately the event was not scientifically documented so I couldn't find any official information on it beyond random articles online. Even though some of the specific details are different throughout different articles the general story is the same, and there are also multiple other accounts of people doing something similar.

Interesting AMA on Reddit of a man that went through this

There are also (as expected) a large number of health risks that go along with this. The man who posted on reddit most likely has kidney disease, an unstable heart rate, and has had to undergo multiple surgeries. There are also others who have attempted starvation and have died from heart failure, small bowel obstruction, and lactic acidosis from refeeding after the fast.

Even though starving has worked for a couple people, it is still extremely dangerous and is likely to cause death. However it is pretty incredible to see people that have survived this to act as a testament for what the human body is capable of.

Saturday, May 27, 2017

Living Fossils

At the Museum of Natural History we learned that the California Condor's huge size made it much better adapted to the Pleistocene (when the average carcass was much larger) than to it's present day environment. So much so that in order to sustain wild populations dead cows are often carted out to condor habitats just so the condors have enough to eat.

This story reminded me of an article I read recently on evolutionary anachronisms. This term refers to characteristics of living species that are probably the result of co-evolution with another species that is now extinct. The remaining species is then left with some ridiculous adaption that probably requires significant energy expense and has no feasible benefit in it's current environment.

Here are a couple familiar examples:

Image result for avocados
Avocados- Avocados are clearly designed for animal dispersal with seeds covered in nutrient rich flesh. Unfortunately, the seeds are so big that most animals cannot swallow them without choking (except the occasional hungry jaguar) and don't often make it far from the parent tree. The 20 ft tall giant ground sloth was probably the avocado's original disperser but it went extinct over 13,000 years ago.


Related image
North American Pronghorn Antelope- Second fastest land animal in the world. Able run much faster than any known predator in North America. However, extinct predator's such as the American lion, the giant short-faced bear, the American Cheetah, or the Chasmaporthetes Hyena could have given the pronghorn's a run for their money (pun intended) when they were still around.


There are many more interesting examples of this phenomenon. Check out the Wikipedia page here!

If you're from Fresno you should read this. If you're not you should still read this.

So what's up with Fresno? Other than having a solid agricultural industry and an uncomfortable number of cows, you'd probably guess that not much is going on there. Guess again. You may not have known, but Fresno is the second most-polluted city in the US; and that's only because who can compete with a valley home to almost 4 million people surrounded by mountains that literally trap the smog in? Yea, Los Angeles will always be the dirtiest of them all (don't tell Las Vegas).

We all know pollution is bad, for the environment and for us, but what exactly is pollution doing to our bodies? It turns out, according to a recent study that came out in May of this year (Lee et. al, 2017) that exposure to the ubiquitous air pollutant produced by motor vehicles, polycyclic aromatic hydrocarbons (PAH), is shortening telomeres in children and adolescents. The authors selected 14 children and adolescents living in Fresno both with and without asthma based on their average annual PAH level and then measured their relative telomere lengths using peripheral blood mononuclear cells (PBMC). An inverse linear relationship was found between PAH levels and telomere length as well as age and telomere length. In addition, subjects with asthma had shorter mean telomere length than those without.

So what's the take home? Pollution is shortening your telomeres. And if you live in Fresno, you may want to move.

http://insights.ovid.com/crossref?an=00043764-201705000-00004


Friday, May 26, 2017

Some Things to Know About Your Gut Microbiota

If you read my previous post on tyhpoid fever's ability to inhibit the mammalian anorexic response, which as a facet of the innate immune system attempts to starve out bacterial invaders, then you'll notice that there is a bit of a gut microbes theme here.

Regardless, below are some neat facts about the microbes in your gut, gathered from this review paper from Cell:
  • Certain bacteria, like Christensenellaceae, proliferate in hosts with low body mass indices, and when cultivated in mouse models, cause a reduction in weight gain. This could signal a some epigenetic and phenotypic bacteria-host relations, as well as some element of heredity because Christensenellaceae is, according to the authors, one of the most heritable gut bacteria.
  • Your original microbiota is inherited from your parents, but becomes fixed during your early childhood. That means that the diversity of bacteria within your gut doesn't undergo any significant development past childhood, and that if for some reason (perhaps because of intense antibiotics) some of the bacteria is wiped out, it is possible that it will not ever return to its pervious state. 
  • The microbiota of mice models were observed after some mice were fed a "Western" diet, that was high in fats and simple carbohydrates and others were fed a "Traditional" diet. Those that were fed a "Traditional" diet had higher microbiota diversity.
To learn more specifics about how these results were determined and to learn more about host-associated microbial communities, read the article linked above.


Pathogen-Mediated Inhibition of Anorexia

Have you ever gotten sick with some bacterial gut infection and lost your appetite? Well this is a natural response, because when your inflammasome (which is responsible for the innate immune response to common bacterial traits such as flagella) is activated, it activates an enzyme called IL-1B, a cytokinase, which both facilitates inflammation and interacts with the vagus nerve, which connects your gut and your brain through the central nervous system. When the vagus nerve is stimulated by IL-1B, you lose your appetite and starve out the invading bacteria. Brilliant, right?

Wrong. The bacteria are tricky. Salmonella Typhimurium (also known as typhoid fever) has developed an enzyme called Salmonella Leucine Rich Repeat Protein (SlrP) which inhibits the activation of IL-1B, which inhibits your ability to mount an anorexic response. This means that the bacteria not only continues to be nourished by your natural bodily functions, but it is more capable of spreading than before.

This is particularly bad for mice, because S. Typhimurium spreads via fecal matter, and mice eat one another's poop. There's a happy thought for your memorial day weekend!

If you want all of the fascinating details, check our this article. It's not a tough read and I thought it was quite exciting!
http://www.cell.com/cell/abstract/S0092-8674(17)30054-5

Wednesday, May 24, 2017

Sponges Reclaim Their "Rightful" Place on the Tree of Life

So in 7th grade I remember being taught that sponges were "the first group of animals to evolve" - or more aptly put now - the earliest branching animal lineage. This thus made the sponges the sister group to all other animals, and I went on believing this lie for many years. But then my whole life was uprooted when, in CCS bio, John enlightened us to the current interpretation of the tree of life where ctenophores (comb jellies) kicked sponges out of their original position on the tree of life. I was shook. But as I was looking further into this topic after class, I found a recently published paper which discussed a new phylogenetic analysis that took place and restored sponges to their original position on the tree of life. Yay!

The new analysis used a much larger and more robust data set for their phylogenetic analysis than any other previous study tackling the issue - using a set of 1,719 "high quality" genes and 79 species. The researchers found that the most parsimonious interpretation of their results yields a tree of life where sponges branch off first in the metazoans and are monophyletic. These results also remove the implication that neurons and muscle cells had to evolve twice in the animal lineage - once in the ctenophores, then being lost in sponges, and evolving once again in bilaterals - as would have been the case if ctenophores branched first.

Previous phylogenetic analysis studies likely developed a different view of the tree of life due to an artifact or error known as long branch attraction which occurs when organisms with a high rate of molecular evolution, such as ctenophores, are grouped together simply because of this high rate of molecular evolution. This groups lineages that are not necessarily related together and thus produces errors.

If you want to look into this study in greater depth, here is a link to the article: http://www.sciencedirect.com/science/article/pii/S0960982217301999

Monday, May 8, 2017

What your parents aren't telling you about weed.

Weed. Marijuana. Mary Jane. Whatever you call it, it's a drug; it comes from a plant; and it can make you high. It's also used as a pain killer. You probably already knew all of this. But what I bet you didn't know is that new research suggests that marijuana may be able to reverse aging!! This is probably because WHO WOULD HAVE THOUGHT and also
because the paper was just published today. Believe it or not, researchers were able to return the state of old mice to that of two-month-old mice with prolonged low-doses of THC. They are now looking to start clinical trials in people. This novel role for marijuana holds exciting possibilities for the development of future treatments for age-related diseases such as dementia. Read the full article at the link below. Crazy stuff man!

https://www.sciencedaily.com/releases/2017/05/170508112400.htm

Tuesday, May 2, 2017

Fancy New Species

Hey guys!
So after Claudia talked about the cool new species in class I did some research to see what else was discovered recently.
My personal favorites are

Lasiognathus Dinema - this is a type of Angler fish living at depths below 500m. The thing that drew me to this was how crazy it looked! I feel like most biologists have an idea of what an angler fish is supposed to look like (especially with movies like Finding Nemo) but check this out!

Lasiognathus dinema, female about 30 mm long. Image credit: Theodore Pietsch.

It was discovered very recently so there aren't really any papers on it, but here's an article talking about its discovery.

Phyllopteryx Dewysea - also known as the Ruby Seadragon. Not only does this look pretty cool since it is related to seahorses, but it is only known from 4 preserved specimens!

Image result for Phyllopteryx dewysea

Recently it was found in the ocean and they actually got a video of it! Check out the video here.

Anyways, I thought these were pretty cool. Unfortunately there isn't too much research on either of these due to a lack of availability (only 4 ruby seadragons found, and the angler fish is super deep and very rare/hard to find) but hey if you're interested it seems like a cool area of research!



Tuesday, April 25, 2017

Chaos! It's weird

So today in class when we were talking about chaos, I attempted to describe this gif:

It's pretty cool and illustrates lag pretty well. The top rod goes back and forth (duh) but the bottom rod lags behind and over compensates for the changes, leading to the cool pattern. According to wikipedia this is "one of the simplest dynamical systems that has chaotic solutions." The article has lots of math, but some other very cool visuals, some of which I do not understand.

Also this shell apparently looks like a representation of chaos called rule 30, which was developed by the guy behind Wolfram Alpha.  If you're looking for a fin Wikipedia hole to fall down, chaos theory is a good place to start.

Thursday, April 20, 2017

A BUNCH OF PALEONTOLOGISTS ARGUE OVER WHETHER OR NOT PROTOTAXITES WAS A GIANT FUNGUS OR A ROLL OF MOSS!!!!

Remember when we learned about that enigma fossil prototaxites? The one that maybe looked like a giant... well... it looked vaguely phallic. Some say it was actually a roll of liverwort moss. I'm skeptical of this, but the way I found these articles on the Web of Science is hilarious.

At the bottom of the page was this article:
http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=OneClickSearch&qid=29&SID=1F9ceq7GOkeWkpBd6Et&page=1&doc=10
with the title: STRUCTURAL, PHYSIOLOGICAL, AND STABLE CARBON ISOTOPIC EVIDENCE THAT THE ENIGMATIC PALEOZOIC FOSSIL PROTOTAXITES FORMED FROM ROLLED LIVERWORT MATS

Above that, was an article by the same people from later that year:
http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=OneClickSearch&qid=32&SID=1F9ceq7GOkeWkpBd6Et&page=1&doc=9
with the title:
ROLLED LIVERWORT MATS EXPLAIN MAJOR PROTOTAXITES FEATURES: RESPONSE TO COMMENTARIES

Directly above was an article from the SAME ISSUE AS THE LAST:
entitled: THE ENIGMATIC DEVONIAN FOSSIL PROTOTAXITES IS NOT A ROLLED-UP LIVERWORT MAT: COMMENT ON THE PAPER BY GRAHAM ET AL. (AJB 97: 268-275)

Wow. So much salt. 

Wednesday, April 19, 2017

CRISPR and Human Gene Therapy

Hey guys!
So this doesn't have as much to do with our current topics in the class, but I think it is a pretty important area of modern Biology (it was first discovered only in 2005) so I thought I would post about it (and it's kind of about biodiversity in bacteria and archaea).
I recently started working at the Arias lab that works in virology primarily with CRISPR-Cas9.
Many bacteria and archaea have a section of DNA known as CRISPR (Clustered regularly interspaced short palindromic repeats) that will produce RNA that will create a complex with a protein called Cas9. This complex is designed to find and cut apart foreign DNA from phages or plasmids and is a powerful form of defense for these organisms. Scientists have managed to develop our own versions of this complex; one of the most exciting parts of the CRISPR-Cas9 complex is that it can actually be engineered to cut out specific parts of a genome and then that area can be potentially replaced with whatever the scientist chooses. Our usage of this complex is not too advanced yet, but the potential for gene therapy and the ability to literally design a complex that can entirely cut out a genetic disorder in a developing baby is pretty huge. This is currently one of the primary contenders for gene therapy and it will be exciting to see how the technology develops in  the future.

Cool video explaining how it works


Tuesday, April 18, 2017

Endosymbiosis of the Powerhouse of the Cell

Does anyone else find it entertaining when you mention the mitochondrion during a discussion entirely in context and someone instinctively blurts out "mitochondria are the powerhouses of the cell"? Well, as we discussed just last week, they weren't always the powerhouses of eukaryotic cells. It turns out that the scientific community currently has more questions than answers about when, why, and how endosymbiosis most likely occurred.

Summary of this review paper, entitled "The origin and early evolution of mitochondria"

  • Organism with genetically "richest" mitochondrial genome (most likely resembles ancestral protist that underwent symbiosis) is called Reclinomonas americana
  • Like viruses, mitochondrial genomes underwent "reductive evolution," in which their genomes decreased in size by throwing out genetic information that was redundant within the host cell's genome
  • Genome sequencing alludes to the possibility that ALL mitochondria are derived from a single mitochondrion, meaning that this relationship arose only once in evolution
  • While it is not clear when exactly the mitochondrion entered the eukaryotic cell, the evidence is clear that they primarily evolved together to create the Eukarya domain
  • Mitchondria likely arose from a parasitic intracellular alpha-proteobacteria
While all of this is exciting, the evidence needs to be considered with a skeptical frame of mind. Much of the data to support the claims above came from genome sequencing, and the parts determined to be ancestral to the original mitochondrion may well just be ancestral to the universal common ancestor (for argument can be made that some of the genetic material in the mitochondrion that was considered in these studies have very far relatives in bacteria, archea, and eukarya).

So while it was an interesting read, and I think a lot was learned, not a lot was definitively claimed. But so is science.

Saturday, April 15, 2017

Since when was the tundra biome considered aesthetically pleasing?

I personally have never found the cold, barren plains of the tundra biome to be very beautiful, especially when compared to the others, such as chaparral (yep that's us! aka Santa Barbara, one of the most desirable places to live in the world). Last time I checked, people weren't jumping to pay millions of dollars for small houses on even smaller lots nestled in the most barren areas of Alaska or Canada or Russia...you get the point. However, contrary to my belief that the tundra biome could rarely be considered "aesthetically pleasing," a study in 2007 found that college students actually favor the tundra and coniferous forest biomes!! To be honest, I had to read that twice. Maybe my opinion is in the minority though, so what do you think? Is the tundra biome actually a gem?

http://journals.sagepub.com/doi/abs/10.1177/0013916506292016

Thursday, April 13, 2017

Octopusnuff part 2

The following paper may be inappropriate for people who think dolphins are kind and gentle creatures and/or people who really like octopuses and/or dolphins.

Things I did not know a few minutes ago:

1. Dolphins predate octopuses
2. There is a field of study called "prey handling" which is about how predators kill their prey
3. There have been observed cases where still kind of alive octopuses have suffocated dolphins trying to eat them.

Of course, there is some ecological analysis included about where (in more costal waters over sand, mud, and slit) and why dolphins are eating octopuses (likely because octopuses are the deadly kale of the marine world and because in the spring they are less equipped to fight back since they've been brooding).

And of course, this study took place in Australia.

Wednesday, April 12, 2017

Research/Outreach help

Hey everybody,
It just so happens that one of the labs I work in needs some peer reviews on harmful algal blooms and since we just recently went over dinoflagellates, and other types of phyto/zooplankton, I was hoping some of you could take some time to review our outreach materials! These are just drafts but we want to make sure it makes sense for someone who has limited knowledge on the subject. Email me at ddpunsal@gmail.com if you would like to help with reviews! Or you could just enjoy this poster...


Tuesday, April 11, 2017

Parasite Brain Manipulation

There's a cool book called "This is Your Brain on Parasites" that I never really finished reading. BUT today in class when we talked about the life cycle of that malaria causing organism, and how it has to move from the gut to the salivary gland of the mosquito, it reminded me of a story in the beginning of this book.  In this account, it describes how a trematode needs to first be in an ant and then in a sheep to mature, and how the trematode will basically take control of the ant's brain to make this happen. Unfortunately, I can't share the whole book, but I found an interview with the author, Kathleen McAuliffe, where she briefly describes this idea:

"Trematode are basically a parasitic worm, but they have three hosts often, or two hosts, different species, and there's a very interesting case of a trematode that when it gets into an ant's brain it instructs the ant to leave its colony at night and climb to the top of a blade of grass, lock on to it, and just hang there overnight. If nothing happens, it goes back down to the colony the next day and he returns the next evening and he will do that again and again until a sheep comes by and happens to eat that blade of grass with the ant attached, and when that happens the parasite gets into the sheep, specifically into its bile duct, which is exactly where it wants to be because that's the only place it can reproduce."

You can check out the rest of the interview here. And though I didn't finish the book, I would recommend it!

Saturday, April 8, 2017

Octopuses Rewrite Their RNA

I guess this discovery has been out for a few years now, but I recently learned that octopuses seem to have the ability to rewrite their RNA! This can be used for a lot of cool survival mechanisms, like individuals in polar environments changing neurons to function better in cold temperatures.
Here are a couple links:

  • http://www.sciencemag.org/news/2012/01/octopuses-rewrite-their-rna-beat-cold
  • http://science.sciencemag.org/content/335/6070/848

Friday, April 7, 2017

New Virus Discovery Sparks Debate Over Tree of Life

A newly discovered group of giant viruses, Klosneuviruses, may contradict our definition of viruses. Check out the article here.

Thursday, March 23, 2017

Art, Math, Nature and Politics

Saw a video on Facebook about this and decided to look further into it. I love that this artist combines so many aspects into her project!

SHELLters

Wednesday, March 22, 2017

Can stress affect your gut microbiota, and vice versa?

I found this interesting when we briefly talked about the human gut microbiota at the beginning of the quarter, so I did a little digging. Turns out there is quite a substantial amount of communication between the gut microbiome and the HPA (Hypothalamic-pituitary-adrenal axis), which is the center of the neuroendocrine system. This means that the composition of your gut bacteria can affect stress levels in your brain. Meaning a person's diet can affect their stress response.
The following article from the Psychoneuroendocrinology (yes, this is a real word- three words jammed into one) Journal explains this phenomenon in great detail.
Abstract: There is now an expanding volume of evidence to support the view that commensal organisms within the gut play a role in early programming and later responsivity of the stress system. The gut is inhabited by 10¹³-10¹⁴ micro-organisms, which is ten times the number of cells in the human body and contains 150 times as many genes as our genome. It has long been recognised that gut pathogens such as Escherichia coli, if they enter the gut can activate the HPA. However, animals raised in a germ-free environment show exaggerated HPA responses to psychological stress, which normalises with monocolonisation by certain bacterial species including Bifidobacterium infantis. Moreover, increased evidence suggests that animals treated with probiotics have a blunted HPA response. Stress induces increased permeability of the gut allowing bacteria and bacterial antigens to cross the epithelial barrier and activate a mucosal immune response, which in turn alters the composition of the microbiome and leads to enhanced HPA drive. Increasing data from patients with irritable bowel syndrome and major depression indicate that in these syndromes alteration of the HPA may be induced by increased gut permeability. In the case of irritable bowel syndrome the increased permeability can respond to probiotic therapy. Detailed prospective studies in patients with mood disorders examining the gut microbiota, immune parameters and HPA activity are required to throw further light on this emerging area. It is however clear that the gut microbiota must be taken into account when considering the factors regulating the HPA.

Tuesday, March 21, 2017



Is the Holocene Epoch over? Are we now in the Anthropocene Epoch?

So the topic I chose to talk about as you may or not have remembered was about the Anthropocene debate, whether we are in it or not. The Environmentalists make a compelling argument that the Anthropocene is the epoch that is to proceed due to all the changes that humans have caused including mass extinction of certain animals and plants. So I guess the problem is really what we define as change and how we define when a new epoch is to be called upon.




My sources include:

Monday, March 20, 2017

Tiny Toasty Mammals

Though not quite the fossils used in the study, if this dog were
to keep overheating like this for about 10,000 years, we might
start to see a smaller version of it!
     We sure do love looking at small animals, from puppies to miniature pigs to that small mouse we obsessed over in CCS bio that one time. It seems that we could be heading in the direction of smaller mammals again! You might think this is great news, but of course, it's yet another result of good old global warming. This paper by Ambrosia et.al. (2107) looks into the fossil record to find if and how mammals have changed size in the past based on the average temperature of the earth. The paper focuses on the time periods known as the Paleocene-Eocene Thermal Maximum(PETM) about 56 million years ago and the Eocene Thermal Maximum 2(EMT2) about 53 million years ago. These two time periods were chosen because they were known as global warming periods. After looking at the tooth size of various fossils found to be from these two time periods, it was found that they decreased significantly in size as the periods went on, more so during the EMT2 time period as opposed to the PETM most likely due to the fact that EMT2 was more of an extreme change in temperature. Why do we care about this stuff? Because it's super cool! Animals get tiny because it gets hot and they need to conserve and that's just wild! It's also an important aspect to look into as we get further into our current global warming period and we need to think about how it could affect the earth and ecosystems over an extended period of time. Read the study to find out a ton more and learn about cool(or hot...) science!
http://advances.sciencemag.org/content/3/3/e1601430.full

Life Throughout Deep Time

"The Palaeos website is organised along two themes; time, being the geological timescaledeep time, which spans not the mere centuries or millennia of world history, but millions or even billions of years, and mapping out the evolution, specifically the evolution of life on Earth; the diversity of organisms that constitute the tree of life, beginning with simple bacteria and proceeding to ever more complex forms from there, as well as the interrelations between them. There is no reason to doubt that life could also have evolved elsewhere in the cosmos, and we also explore this topic. However, most of Palaeos is devoted to a detailed consideration of the history of life on Earth. "

http://palaeos.com/

Vernal Pools are Really Cool! (Ha.)

Vernal pools are an interesting landmark in Santa Barbara, but surprisingly not well known. If you live in the dorms, these unique ecosystems are just a couple hundred steps away. Vernal pools are, essentially, basins that fill up and drain over time, which creates a unique environment for flora, as pictured here:


 The pools are home to many endemic species, such as mole salamanders and fairy shrimp. Due to the nature in which they form, vernal pools usually do not have any fish and are thus able to support species that would not be able to survive in other aquatic environments.

In California, over ninety percent of vernal pools have been destroyed or otherwise damaged by human activity. Thus, restoration efforts have been necessary and have helped to account for some damage. On campus, all of the vernal pools are restored and surveyed by CCBER. 

One paper compares different types of vernal pool restoration and their effectiveness and gives a more in-depth insight on restoration specifically in Santa Barbara.

CCBER Website



Sunday, March 19, 2017

Nonhuman Primate "Talk" Hints at the Evolution of Human Speech

A recent paper in Science ("Learning from monkey 'talk'") described how there are aspects of primate communication that correlate with how humans speak. One of the more interesting points discussed was how nonhuman primate babies babble in the same way that humans do, and if the parents respond to only the appropriately formulated babbles of their babies, the babies will develop adult calls much earlier. This has been seen in humans, too! 

It is also possible that monkeys do not take turns when speaking because this turn-taking is a learned behavior. This particular finding is hard to prove, however, because the two studies that looked into it had opposing conclusions, and rather different methods. Nonetheless, it's an interesting concept to take into consideration. 

Another bit that I found quite cool was how humans and songbirds both have a set of genes involved in rapid articulation and sound sequencing that other species do not. The author, Charles T. Snowden, predicts that this could be the reason for monkeys not exhibiting similarly complex speech. But in reality, we don't know why other primates don't talk as we do. Yay for the unknown!

A link to the article, if you're curious: http://science.sciencemag.org/content/355/6330/1120.full

P.S. Sorry to post so much so late... I thought we were only supposed to post 2 times. Completely my fault. 

Cool Stuff in Wolfram Alpha

Wolfram Alpha is a great assistant to those of us suffering through tedious MATH 3B homework (so...many...integrals..), but there is a much larger wealth of knowledge and tools that are easily accessible. Some of the cooler things are locked behind Pro, like Wolfram Genomics Assistant, but a broad variety of information is available to an average user. 

Some examples:



Input Output
DNA Sequence Amino acid sequence, melting temperature, occurrence on human genome
Plant Name, image, natural occurrences (and if it occurs in your estimated location!!), distribution, detailed taxonomy
Species X, Species Y, Species Z Compares species, too much information to list