BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Evolution (Page 1 of 3)

Sour Science!

Have you ever enjoyed an orange and wondered what causes its amazing citrus flavor? Well, scientists have recently discovered the origins of citrus’s sour taste. 

Scientists have recently discovered the origins of citrus fruits like oranges and lemons. In their study, they discovered a specific gene, PH4, that influences the fruits’ taste by regulating the fruits’ citric acid levels. Additionally, the researchers traced the fruits’ evolutionary journey from the Indian subcontinent to south-central China over millions of years and discussed influences that environments may have had on the citrus.

There are many reasons why these fruits evolved the way they did. One reason discussed in the article is human interference through selective breeding. Thousands of years ago, humans selectively bred certain types of citrus for food and medicinal purposes. Another reason they might have evolved to have more citric acid is to prevent bacterial infections. Bacteria, generally, prefer neutral environments with a pH of about 7. o.  Citric acid has a pH of about 3.2. Therefore, the more citric acid a fruit has the less likely bacteria can infect the fruit.

This relates to AP Bio through the involvement of genes in protein synthesis. During protein synthesis in a cell, the first thing that happens is transcription where information on the DNA is transcribed onto mRNA. The mRNA then is sent to the Rough Endoplasmic Reticulum where it is received on the cis face. There, on the ribosomes of the rough ER, the protein is synthesized. The type of protein that is synthesized here is determined by the information of the mRNA. Then the protein is sent to the Golgi where, based on the information from the mRNA, molecules are added to determine the final location of the protein. Genes, including PH4, are sections of DNA. Therefore, the PH4 gene, in part, determines what type of proteins are produced by the cell and where they go.

Wow! It is fascinating how a gene can influence an orange’s taste. I found this research so interesting because I love oranges. I wonder how other plants’ genes influence their taste?

From Bacteria to Biotech: The Surprising Similarities in Immune Systems

Bacteria have always been considered harmful and something to be avoided, but according to a recent study by the University of Colorado Boulder, bacteria might just hold the key to unlocking novel approaches to treating various human diseases. The research reveals that bacteria and human cells possess the same core machinery required to switch immune pathways on and off, meaning that studying bacterial processes could provide valuable insights into the human body’s workings. Moreover, researchers found that bacteria use ubiquitin transferases – a cluster of enzymes – to help cGAS (cyclic GMP-AMP synthase) defend the cell from viral attack. Understanding and reprogramming this machine could pave the way for treating various human diseases such as Parkinson’s and autoimmune disorders.

CRISPR, a gene-editing tool, won the Nobel Prize in 2020 for repurposing an obscure system bacteria used to fight off their own viruses. This system’s buzz reignited scientific interest in the role proteins and enzymes play in anti-phage immune response. Aaron Whiteley, senior author and assistant professor in the Department of Biochemistry, said that the potential of this discovery is much bigger than CRISPR. The team discovered two key components, Cap2 and Cap3 (CD-NTase-associated protein 2 and 3), which serve as on and off switches for the cGAS response. Understanding how this machine works and identifying specific components could allow scientists to program the off switch to edit out problem proteins and treat diseases in humans.

CAS 4qyz

This discovery opens new avenues of research as bacteria are easier to genetically manipulate and study than human cells. Whiteley said that the more scientists understand about ubiquitin transferases and how they evolved, the better equipped the scientific community is to target these proteins therapeutically. The study provides clear evidence that the machines in the human body that are important for just maintaining the cell started out in bacteria, doing some really exciting things. The ubiquitin transferases in bacteria are a missing link in our understanding of the evolutionary history of these proteins. Thus, this research shows the importance of studying evolutionary biology, and how it can provide valuable insights into human health.

The study highlights the similarities between bacteria and human cells in terms of their immune response, specifically, describing how cGAS (cyclic GMP-AMP synthase), a protein critical for mounting a downstream defense when the cell senses a viral invader, is present in both bacteria and humans. This similarity suggests that portions of the human immune system may have originated in bacteria, a concept explored in the evolutionary biology unit. In this past unit, we discussed the origins of life, and how all life originated from a simple bacteria cell. This bacteria cell, though many many many repeated cycles of evolution and natural selection allowed for variation within its species and the formation of new species through the processes of speciation.

Exploring Multicellularity on Planet Earth

Billions of years ago, it is believed that some event—whether it be a meteor crash-landing on planet Earth, or a lightning strike creating amino acids and proteins—sparked the origin of life. From there, single celled organisms, like bacteria, made their home on our planet; and eventually, unicellularity became multicellularity. The reason behind this phenomenon, though, is what continues to be unknown. What really is the point of the majority of organisms being compiled of millions of cells, and not just one? 

Scientists at Lund University strive to answer this question. In order to do this, green algae from Swedish lakes were taken into their lab, as this specific botanic organism is extremely suitable for the goals of this experiment. For one, it is a eukaryote, which will allow researchers to gain insight on the evolution of all eukaryotes, in general. They are widely studied in the study of evolution because of their very apparent evolutionary process. There is a great amount of data to reveal that all eukaryotes have common ancestry, including the presence of double membranes, circular genomes, ribosomes, linear chromosomes, and more in all eukaryotic organisms. 

Another reason as to why green algae is such an appropriate fit for an experiment exploring the evolutionary characteristics of unicellular and multicellular organisms is that it is sometimes unicellular, other times starts off this way but then becomes multicellular, and the remaining types are always multicellular. This makes green algae the perfect candidate for an experiment such as this. Data from the environments of all these different cellularly-dense types of algae was collected and compared to one another. While doing this, scientists looked out for the adaptations promoted by the environments the algae were in, what conditions exactly promoted unicellularity or multicellularity, and why the form of life it encouraged was beneficial to the organism. 

Previously, it had been theorized by evolutionary biologists that multicellularity benefited organisms that utilized it, but the Lund University research team was shocked at the results they found from analyzing the environmental data of the algae: there were no benefits of living multicellularly for these organisms. A member of the study, Charlie Cornwallis, made the following comment on the experiment’s outcomes: “I was surprised that there were no benefits or costs to living in multicellular groups. The conditions that individual cells experience can be extremely different when swimming around on their own, to being stuck to other cells and having to coordinate activities. Imagine you were physically tied to your family members, I think it would have quite an effect on you.” 

At the conclusion of the study, Charlie Cornwallis made one final statement: “The results of this study contribute to our understanding of how complex life on Earth has evolved….The next time you walk along the shores of a lake rich in nitrogen just imagine that this fosters the evolution of multicellular life.”

Green algae under a microscope

Green algae under a microscope.

Revolutionizing Photosynthesis: The Power of Rubisco Enzyme Engineering

Enzyme engineering has the power to create several new discoveries and possibilities in the evolutionary field. Questions that were not answerable through decades of really hard biochemistry have now become accessible by integrating this evolutionary perspective. In the past, Rubisco faced many issues, such as starting to catalyze an undesired reaction, in which it mistakes O2 for CO2 and produces metabolites that are toxic to the cell. In the article by the Max Plank Society, researchers have discovered that the Rubiscos that show increased CO2 specificity recruited a novel protein component of unknown function, through resurrecting and studying billion-year-old enzymes in the lab using a combination of computational and synthetic techniques.

According to this article by Alejandra Manjarrez that analyzes that research, form I rubisco has the highest specificity for carbon dioxide and the most efficient catalytic activity. Form I Rubisco is made up of eight identical catalytic large subunits and eight identical small subunits. Researchers suspected that its enhanced ability to discriminate CO2 from chemically similar molecular oxygen could be related to the presence of these small subunits since no other forms of Rubisco have them.

1aa1

For years, research focused on changing amino acids in Rubisco itself, but new findings suggest that adding new protein components to the enzyme could be more productive. Rubisco is the most prevalent enzyme on the planet and is the key enzyme responsible for photosynthetic and chemoautotrophic carbon fixation and oxygen metabolism. It catalyzes the fixation of atmospheric CO2 to ribulose-1,5-bisphosphate (RuBP) to form two molecules of 3-phosphoglycerate (3PGA). This is the first part of the Calvin cycle which, as you learned in class, involves using atmospheric carbon dioxide, ATP, and NADPH to create G3P, which is the building block of glucose, through the processes of carbon fixation, reduction, and regeneration of the CO2 acceptor. With the new improvements in the efficiency of Rubisco and enzyme engineering as a whole, plants may be able to combat the increasing amount of carbon dioxide emissions hurting the earth through improved photosynthesis.

One Generation’s Trash is Another Generation’s Treasure: How a selected mutation during the Black Death causes dangerous illness today

The Covid-19 pandemic has certainly changed millions of lives forever, but many scientists wonder how the pandemic could affect the human genome.  In a 2022 article in US news, researchers studied the Black Death, the 14th-century pandemic that wiped out nearly 25 million Europeans, and in particular, how it affected our bodies.

According to researchers, the Black Death led our bodies to select for certain genetic traits which at the time decreased their risk of infection.  These specific genes increased the activity of the immune system to better help fight the plague, however, today these mutations are having dangerous consequences.  Researchers have noticed a connection between such genes and the risk of numerous conditions, such as Crohn’s Disease, Lupus, and Rheumatoid Arthritis.  These illnesses are known as Autoimmune Diseases, a class of illnesses that occurs when the body tricks itself into attacking its own cells.

These specific genes increased the activity of the immune system to better help fight the plague, however, today these mutations are having dangerous consequences

According to LibreTexts, this phenomenon occurs when certain pathogens have a very similar molecular structure to the antigens that our bodies produce.  Therefore, our bodies are tricked into attacking their own cells thinking that they are pathogens.  This destroys important structures in our bodies, the absence of which causes illness, such as Crohn’s disease and Rheumatoid Arthritis.

According to Dutch biologist Henrik Poinar of McMaster University, “A hyperactive immune system may have been great in the past.” This hyperactivity may have led to an increase in activity against the plague, which in turn could have increased survival rates.  This groundbreaking research suggests that even the shortest event of monumental importance can forever change our bodies.  As stated by senior researcher Luis Bareirro, “Our genome today is a reflection of our whole evolutionary history.

The obvious question here is: will our current Covid-19 pandemic affect our bodies and are our bodies evolving? Researchers say no.  According to Barreiro, Covid’s low fatality rate makes it unlikely to cause any significant genetic change.   However, Covid’s mutations are difficult to predict, and we have no way of knowing how future mutations will affect our bodies.  Furthermore, in a recent study from Stanford Medical school, researchers identified 1,000 genes linked to severe Covid infection.  It is theoretically possible for these genes to be selected for as we evolve, and it is unclear how that could affect our ancestors.

Covid’s low fatality rate makes it unlikely to cause any significant genetic change

This selection is similar to the selection we are performing on fast-growing flowers in Biology class.  Like the removal of flowers without hairs, certain human genetic traits (probably not hairs) perform more favorably in a pandemic environment and may prevail due to natural selection.

While it is impossible to know what the future will hold, it is interesting to analyze how major historical events, like the Black Death, have affected our bodies.  While there isn’t consensus around how the current pandemic will affect our ancestors, scientists agree that these events are clearly linked to our evolution as a species.  According to Barreiro, “It’s not going to stop. It’s going to keep going for sure.”

Gene Variant Saves Humans from Starvation!

A recent study in Science Advances, suggests that a variant of the growth hormone receptor gene protected humans against starvation millions of years ago. The gene protected us by limiting individuals body size during the scarcity of food. The variant, GHRd3, has been linked to characteristics such as small birth size, early sexual maturity, and other characteristics that would help a human when recourses are scarce.

The variant suddenly plummeted in number around 40,000 years ago but many people still carry it today. In order to dig deeper into what role the variant played in human evolution, Omer Gokcumen, the study’s lead author, turned mice into representations of humans millions of years ago. His team deleted part of the mice’s growth hormone receptor genes so they resembled the GHRd3 Variant.The mice all lived in the same habitat, were fed the same amount, and drank the same amount of water. The mice with the variant grew up to be smaller than their unmodified equivalents. Gokcumens’ team also found that out of 176 children today that have suffered from malnutrition, symptoms were much less severe in children with the GHRd3 variant.

Protein GH1 PDB 1a22

Researchers continue to wonder why GHRd3 has persisted for so long but these findings could help to explain! It is possible that changes in available resources could have impacted the benefits of different variants.

In my AP Biology class, we learned about receptors. Reception is the first stage of Cell signaling. It is when a signal molecule binds to a receptor protein, causing some kind of conformational change in the receptor. Growth hormone receptors are Receptor Tyrosine Kinases which means they dimerize when signaling molecules bind. The tyrosine phosphate regions are phosphorylated by ATP and trigger a relay pathway sending signals through the cell for a response.

Small But Mighty: Sea Otters And Their Leaky Mitochondria

Sea otters: they bob up and down in the water, hold hands when they are sleeping, poop together at social events, stay warm by their fur and leaky mitochondria… wait, what?

Let’s rewind.

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A Cute Sea Otter Floating On Its Back

Warm-blooded marine mammals have a thick layer of fat and oils, known as blubber, as their skin layer to insulate their body. In cold waters, blubber helps retain heat and maintain homeostasis.

But what if warm-blooded marine mammals lack blubber? Sea otters are a prime example (and the only example) of a marine mammal without a layer of blubber. Instead, they have a thick coat of dense hairs, 1000x denser than human hair–the thickest on earth. This enables sea otters to trap large amounts of air within their fur coat, acting as insulation. (This is the same reason why sea otters float: the air trapped in their fur coat makes them buoyant).

But with that said, can you stay warm in a fleece jacket? Possibly. What if you were wearing it while in the ocean? That might be somewhat difficult. Similarly, fur can’t solely protect these animals from losing too much heat. These mammals are still living in water, which transfers heat 23 times as efficiently as air. Since sea otters are the smallest aquatic mammals, they have a lot of surface area relative to their volume, making it even harder for these animals to maintain homeostasis.

So how do they do it? Researchers have already understood that sea otters have an extreme metabolism, how food gets converted to energy in cells, eating about twenty-five percent of their body mass in food every day. But the pieces were still not adding up, which prompted researcher T. Wright to investigate this question on a cellular level. He and his colleagues searched for the source of heat in otters’ muscles. Playing a pivotal role in the body’s metabolism, the skeletal muscle makes up 40 to 50 percent of the sea otters’ entire body mass. His study required the collection of tissue from 21 sea otters of different ages and then measured the muscle cells’ respiratory capacity compared to that of other animals. The sea otters’ oxygen flow rate would roughly indicate the measurement of the cells’ heat production.

Mitochondria pump protons across their cell membranes to store energy in the form of ATP, like we learned in AP Biology’s diffusion unit. From this study, T. Wright concluded that the protons are diffusing back through the membrane before being used for work, resulting in excess heat. Since some of the energy is lost as heat, sea otters need to eat more food to compensate for the lost energy. This “leak in energy” is what contributes to the sea otters’ speedy metabolism.

It’s unknown if sea otters develop leaky mitochondria by living in cold water or simply inherit it. Future research into the fascinating design of sea otters may potentially reveal intriguing insight into their evolution, behavior, and maybe someday, their cuteness.

 

 

A New Way to “Tangle” with Diseases? British Scientists Think They’ve Stumbled Upon the Future

A team of scientist from the Universities of Bath and Birmingham have made a discovery that is making noise in the world of Biology. Ironically, they had the realization while studying silent mutations in DNA. What they found is a new method of evolution. Well not a new method per say as the scientists predict this method is being used in all forms of life; however, new in the sense that it was only recently realized. What they have discovered is a trend of tangles in DNA strands. This tangling occurs in DNA strands that are not in a double helix as DNA typically is. However The DNA strands are separated during copying. This task is done by DNA polymerase enzymes. During the copying process, the enzymes are often disrupted by the tangles in the strand. The resulting skipping of genes causes specific mutations to the DNA.

DNA replication split horizontal

The scientists then tested their hypothesis by way of experiment. They did so by studying the evolution of soil bacteria called Pseudomonas fluorescens (SBW25 and Pf0-1). They began by removing the gene that give the bacteria the ability to swim. They then observed the re-evolution of the strains to regain the ability swim. Both strains evolved quickly; however, there was a clear differences in predictability. One strain (SBW25) mutated the same part of a particular gene in every trial. The other strain (Pf0-1) varied in which gene and where the mutation occurred in each trial. Upon further observation, this contrast coincided with a hair-pin shaped tangle in the SBW25 strain. As the DNA polymerase enzymes would pass this tangle they would be effected in a predictable manner that would disrupt copying of DNA and result in a mutation that allows for the bacteria to swim. The scientists tested the theory by removing the tangle. They did so using 6 silent mutations so that the DNA sequence would not have a relevant change. The trials after the change showed that both strains showed inconsistent areas being mutated.

 

DNA are the dictators of protein synthesis in the body. The DNA sequences code for the types of proteins that are created. Proteins perform many of the bodies function. This means that even the slightest change in the sequencing of DNA can have major effects on the functioning of a human body or any organism. The process of evolution was thought to be caused by random errors in DNA sequencing that coincidentally gave an organism a survival advantage. These mutations would then be tested in the concept of survival of the fittest. While this is still thought to be the most prevalent form of evolution, especially with eukaryotic organisms, the tangling of DNA strands proposes a form of evolution that would be easier to study and predict.

 

The predictability of such a phenomenon is where the intrigue in viruses arises. “If we knew where the potential mutational hotspots in bacteria or viruses were, it might help us to predict how these microbes could mutate under selective pressure.” says Dr. Tiffany Taylor, from the Milner Centre for Evolution. Mutational hotspots have already been found in cancer, and the new information on their significance is getting scientists excited about the opportunities present. The new ways to understand and predict evolution of bacteria and viruses may allow scientists to be a step ahead on vaccines and be able to anticipate and understand new variants. It’s hard not to think this information would’ve been nice before the rise of SARS-CoV-2.

Is Junk DNA Really Junk?

DNA is the base code of all living creatures. It is in every plant, animal, and single-cell organism, yet  50% of human DNA is seen to be irrelevant to bodily function. While some DNA is responsible for synthesizing materials within cells, much of it is in essence, spare genes, or ancient viruses that have become part of the human genome over time. Moreover, it has been debated whether the 50% of DNA that is not seen to be relevant is truly essential for survival. That is, can humans live without unused genetic code, or is it vital to the survival of the species?

Ácido desoxirribonucleico (DNA)

One specific element of junk DNA is transposons. Transposons are sequences of DNA that have the ability to mutate a cell or change its function as a whole. A study was conducted at the University of California, Berkley, and Washington University on transposons, as written in the So-called Junk DNA – Genetic “Dark Matter” – Is Actually Critical to Survival in Mammals, by the University of California, Berkley. The studies looked at a specific transposon in mice called MT2B2, one that controlled the growth rate of cells in a fertilized embryo, and when the embryo would implant in the uterus of the mother by initiating the short gene Cdk2ap1. When the researchers disabled the MT2B2 transposon using CRISPR-EZ, the mice created a longer version of the gene Cdk2ap2. This new version of the gene decreased cell growth and increased the period of implantation. The teams found that half of the baby mice died before birth without this transposon in their DNA. When the transposon was disabled, the mice sort randomly instead of uniformly in the uterus, and some may cause the death of a developed fetus and or the mother.

The team at Washington University researched the transposons turned on before embryos are impacted into the uterus in humans, rhesus monkeys, marmosets, mice, goats, cows, pigs, and opossums. The team used scRNA-seq, which records messenger RNA levels to indicate which genes are being used. With this technique,  the team saw that in every animal, a group of species-specific transposons was turned on. While the transposons were different for each species, the result of their use was nearly the same for all eight cases. Moreover, the gene Cdk2ap1 was expressed by all eight animals, but the amount of short and long versions of the gene expressed was unique for each one. While an animal that needs fast implantation uses more of the short version of the gene, like the mouse, animals with little to none of the shorter version of Cdk2ap1 took two weeks to longer for implantation to occur, like the cow.

Baby Mouse Rehabber

For these transposons to be promoting the expression of the Cdk2ap1 gene, at a certain point in history, a virus entered the organism and eventually part in a mutually beneficial symbiotic relationship with the organism until it evolved into the current iteration of the transposon. When viruses blend into the DNA of a species, they can be used to regulate and perform tasks that the cell could not previously perform. This can create a wide range of evolutionary options in species. Additionally, the main difference between the different genomes of species is the regulation of genes. By studying transposons, scientists can better understand differences in the genome of one species to another. With the understanding of this transposon, scientists could now begin searching further into junk DNA, as the removal of the transposon studies by the two universities proved lethal 50% of the time. Moreover, undiagnosed patients could have junk DNA mutations that lead to health problems, but those cases are currently a mystery to the medical world. Transposons are just the beginning of scientists dive into junk DNA, and who knows what wonders they will find next?

Spotlight: Sharon Strauss and Evolution of Organisms in Barren Habitats

Sharon Strauss is an evolutionary ecologist at the University of California, Davis (UC Davis) where she has been conducting research on the evolution of plants and the ways in which they interact with other species. As a woman in a STEM environment, Strauss has faced opposition due to her gender. It took her 5 years longer than the regular time trajectory to obtain a job in her field, subtle obstacles such as invitations to work with groups, and also simply not being taken seriously or personally asked to contribute to group conversations. Although she has faced challenges, Strauss has done phenomenal research on the ecology and evolution of plants and her efforts, both her research and her job as a professor, have been rewarded.

One of her largest and most well known projects was called Nowhere to run, nowhere to hide. During this project, she and her team were studying how wildlife adapted to a barren environment. During this expedition, Strauss and her team explored the possible connection between attack rates and visibility. They followed 160 seedlings of a few different species from the genus Streptanthus and observed how they grew and what their current condition was depending on the amount of bare ground and leaf coloration. Additionally, they formed small clay models of caterpillars to act as an undefended population of prey in order to measure attack rates on visible animal species. They measured this by checking the area around the caterpillars to see if there were beak or tooth marks of a predator attempting to eat it. Strauss was able to conclude that attacks on both animals and plants were connected to how apparent or visible they were in their environment. For this reason, certain plants and animals had adapted by changing their color in order to blend into their barren environment.

Since this project mainly involved studying adaption and evolution, it is not very similar to anything we have learned in class yet. However, there is a connection between evolution and genes, which we are currently learning about. Every organism that sexually reproduces passes genes down to their offspring via the sperm and the egg. The physical features of the offspring are determined by the genes they are composed of. Typically, these genes are passed down by the parents to the offspring; however, it is also possible for an error in DNA replication to occur or exposure to chemical or radiation damage that can cause a mutation. This connects to evolution since there will always be variety within a population. A certain trait could prove to be more successful in survival than another so gradually, over many generations, that trait will be passed down since the members of the population that have that gene have a higher chance at surviving and reproducing as proposed in Darwin’s Theory of Evolution.

I admire the hard work and the effort that Sharon Strauss has put into her career and passion to get where she is now and to have achieved what she has. Despite the barriers that were placed in front of her, she continued on since biology was her passion. I also have a passion for biology, specifically zoology, and as a girl, I may face similar obstacles. Even if I change my mind or find a new passion, I hope to carry the same spirit that Sharon Strauss did to push through any barriers that I may face.

The Biology of Skin Color

It’s a hot summer day and you are relaxing by the pool. Ever wonder why your skin gets darker or tanner when doing so? It’s because of melanin! 

Melanin is a skin pigment that can be found in humans, animals, and most organisms. It is responsible for making hair, skin, and eyes appear darker. Melanin exists in two forms: eumelanin and pheomelanin. Eumelanin is black or brown pigment and pheomelanin is red or yellow pigment in one’s skin tone. 

File:Influence of pigmentation on skin cancer risk.png

Different Skin Colors

When you are exposed to the sun, more melanin is produced. “In human skin, melanin pigments are synthesized in organelles called melanosomes that are found in specialized cells called melanocytes in the skin epidermis.” In order for melanocytes to produce melanin, a receptor protein called MC1R, found in the melanocyte cell membrane must be activated by melanocyte-stimulating hormone (MSH) which is secreted by the pituitary gland in response to exposure from UV light. Once MC1R is activated, it triggers the production of release of cAMP and as we learned in class, this triggers a cell signaling pathway ending with the release of eumelanin, making our skin appear darker. 

A short additional fact is that melanin protects us from skin cancer. Melanin can absorb the UV rays and block them from reaching and damaging the DNA within one’s melanocytes. In this case, melanin acts as “a protective agent in the skin” joining your first line of defense to protect you against pathogens or in this case to protect you against the damaging UV rays. There are three types of skin cancer: basal cell carcinoma, squamous cell carcinoma, and melanoma. 

A person’s skin color depends on the amount and type of melanin (eumelanin or pheomelanin) present in one’s skin. Genetically speaking, “people with naturally darkly pigmented skin have melanosomes that are large and filled with eumelanin” (biointeractive.org). As discussed above, there is a huge biological importance of melanin; without it, humans wouldn’t have a protective skin barrier against the UV rays emitted by the earth, but throughout history the importance of melanin has been placed to the side due to the idea of race or more specially racial superiority based on ones skin tone being introduced into the conversation. 

In short, while there is a biological basis of skin color, there is no biological basis or scientific explanation of race. Although it has been attempted, by Samuel Morton in the 1800s when he compared the brain sizes of the five racial groups or by Dr. Menegele during WWII when he measured facial features of the Jewish people, it is challenging to use science to support the concept of race. In fact, there are more differences within the “determined” races (African, European, Asian, Oceania, Native American) than between them! No specific amount of melanin, or any trademark alleles for that matter, specify a race. It is important to look at and understand science and evolution- looking at where people come from and why they have that skin color that they do based on melanin and weather conditions around them. It is important to take into account how we have evolved into unique humans, even though 99.6 – 99.8% of our genetic material is identical. It is important to educate ourselves about why we are the way we are and how evolution has impacted that, not how groups of people throughout history have tried to give an racist explanation for it.  

File:Map of skin hue equi.png

Skin Colors Found Around the World

 

The Evolution Of The Largest Animal On Earth

How did Blue Whales get to be as big as they are today? The answer lies in the understanding of evolution and adaptation.

In the past, Baleen whales had a diet fully consisting of plankton that rose to the ocean’s surface. About 5 million years ago, Rorqual whales started to adapt more to their environments, and were able to find that “lunge feeding” was the most efficient way to obtain their food and grow. This new finding lead their diet to change from plankton to krill and small fish. Lunge feeding and upwelling exposed them to a larger availably of food, which ultimalelty caused whales to evolve and have bigger mouths. Through wind motions, upwelling was able to occur, and rich nutrients were brought up from the depths of the ocean, which stimulated “growth and reproduction.” With their bigger mouths, came their bigger bodies, but of course it is not that simple. The evolution of whales can not be fully explained without evolutionary ecology. As whales continue to grow and evolve, their DNA gradually begins to change to continue to allow the whale to survive. The DNA begins to give it different instructions based on their new adaptations.

To get a deeper look into DNA, we can look at nucleic acids. Nucleic acids are the building blocks of DNA molecules. Phosphodiester bonds connect the phosphate and sugar groups of nucleotides, monomers of nucleic acids, to make up the double helices of DNA. A whale’s DNA is quickly evolving and forces the DNA to adjust and change the functions in the whale by changing the order of the bases, adenine, guanine, cytosine, and thymine, that it is made up of.

Whales had to adapt and conquer. The ocean is filled with competition and every animal has to do what they need to survive. Specialization comes into play when there are many animals going for the same foods. Specializing on one specific prey gives the predator an advantage against other predators. Blue Whales specialized in krill, but as whales soon came to find out, krill is not an easy prey to catch. A krill’s ideal environment is a polar ocean with upwelling zones, so in order for whales to catch their food, they must be able to be mobile and quick. Their bodies have adapted to being able to move very fluidly through the ocean and catch their prey with speed and an “element of surprise.”

With environmental problems quickly rising, whales are going to face challenges. Climate change is heating up the oceans and causing a decrease in krill and plankton. Whales’ specialization is going to play a crucial role in not letting them die out. Since they have focused their evolution on eating krill, they will have to adapt to the decrease in availability.

 

Did ants originate from zombies? This fungus will give you the answers.

There is a certain fungus that turns ants into zombies, but afterward, they explode. When ants are just walking by minding their own business they step on fungal spores. It attaches to the ant’s body and the fungal cell goes inside of the ant. The fungus feeds from within and increasingly multiples cells and it is called, Ophiocordyceps,   mainly living in the tropics. The danger about this fungus is that the ant is unaware of this whole process, it goes about its daily life, searching for food and bringing back to its nest. However, the fungus takes up half of an ant’s body mass. It undergoes a parasitic relationship where the fungus benefits, while the ant is harmed.

Once the fungus is done feeding, the ant will feel a needle-like sensation. What is happening here is that the fungus is pushing on the ant’s muscle cells. And the cell signals also get sent to the ant’s brain, then the ant will climb upwards above its nest. Ophiocordyceps does something very weird where it allows the ants to move upwards to a leaf above ground and then the ant bites down, where it locks its jaw. Then it sends out “sticky threads that glue the corpse to the leaf.” The ant’s head then bursts open, called a “fruiting body”, where it looks like horns projecting from the ant’s heads and the horns disperse more of these fungal spores onto its nest below it leaving behind a trail of spores. 

Hornlike antlers that come out of the ant’s head

There is still so much that is unknown about Ophiocordyceps because scientists don’t even know what kind of chemical gets into the ant’s brain causing it to climb. There are ants that age back to 48 million years old gripped onto leaves.  Scientists thought there was one species that zombified ants but it turns out there are at least 28 different fungal species that attack other insects as well. Dr. Araújo drew out a family tree to see what was infected by Ophiocordyceps. It became known that all Ophiocordyceps species come from a common ancestor, first infecting beetles larvae, not hemipteran.

The beetles that are affected by the larvae live in eroding logs.

“They’re mostly solitary creatures, with a very different life history,” compared to ants, she said.

It can now be inferred that possibly millions of years ago when this was happening to beetles, ants picked up the fungus if they were living in the same logs. Thus a constant cycle and more spreading of fungal spores. Even though natural selection favored keeping the ant’s host healthy and away from parasites, Ophiocordyceps had to find a way to make the ant leave the nest, not far enough from its environment, but just in the right place to send out the spore to infect whatever other ants were living around it. 

Because this behavior is so unordinary it is not possible that only one gene is responsible for all of this. They keep finding new species. Dr. Hughes and Dr. Araújo are still researching to find that there are hundreds of other species of Ophiocordyceps that are yet to be discovered.

How are ocean conditions harming its animals?

A recent article written by Rachel Nuwer discusses the dangers of ocean acidification and how the ocean environment could compromise the fishes’ ability to swim and feed. The existence of one of the world’s most threatening predators is being threatened by ocean warming and acidification. Sharks might lose their place at the top of the marine food chain due to the changing ocean environment. As carbon dioxide levels rise in the ocean, it increases the acidity of the water. As this factor starts to rise, the teeth and scales of sharks may begin to damage, which compromises their ability to swim, hunt, and feed. According to research published in Scientific Reports, acid-base adjustments have proved to be the first piece of evidence of “dentical corrosion” caused by ocean acidification conditions. After investigating the impact of hypercapnia on a specific shark species and analyzing the acid-based regulation, the team concluded that the denticle corrosion could increase denticle turnover and compromise the skin and protection of the shark species.

A close up on the denticles and scales of a wild shark

The harsh conditions placed on the sharks could cause several consequences and ultimately could affect the whole ocean community. Biologist Lutz Auerswalk states that sharks could be displaced as apex predators, which could disrupt the whole food chain. In addition, great white sharks are already endangered, and these conditions could wipe them out completely, he states. Ocean research Sarika Singh and Auerswald, while studying over beers, stumbled upon a unique idea. After realizing that the high acidity of beet and many other carbonated beverages causes human teeth to erode, they wondered what effect more acidic ocean water might have on shark teeth.

Most studies on ocean acidification examine species that specifically build shells or other calcium-based structures, including corals and shellfish. Because sharks are large and challenging to work with, only a few studies have been conducted about how acidification might impact these animals. Only one paper has examined the effect of pH on sharks’ skin denticles or scales. The study used small-spotted catsharks and exposed them to different environments and filmed their swimming patterns. After analyzing a pectoral fin skin sample, they did not find a specific impact. However, the results were possible constrained by the low carbon dioxide concentration the researches used, compared with the high levels of acidity already present in many oceans.

To begin exploring this question for themselves, Auerswald and Singh conducted an experiment and focused on puff adder shy sharks, a small species that is easy to handle. They decided to investigate the acidification effects on the bigger scales. They divided the sharks into control and experimental groups and observed the results. After a few months, the electron-microscope analysis revealed that the concentrations of calcium and phosphate in the sharks’ denticles were significantly reduced. They noticed damaged scales on many of the sharks as well. Though the corroded scales might not impact their ability to hunt, for larger species such as the great white shark, scales play an essential role in hydrodynamics. Because denticles are responsible for an increase in swimming speed, damaged denticles could slow sharks down and make it more difficult for them to catch prey. Because many animals have been wiped out, we must strive to protect all the species that are deeply impacted by this condition.

Baboons: A closer insight to understanding the Human Gut Microbiome

In a recent Northwestern University article, a new study was found that despite human’s close genetic relationship to apes, the human gut microbiome is more closely related to that of “Old World” monkeys, such as baboons than to that of apes like chimpanzees. Another article posted by Medical News Today, provided more insight on why we should specifically take a deeper look into Old world monkeys, such as baboons, to tell us more about the human microbiome. Maria Cohut, the author of the article, claims that since these baboons are closer related to humans and share 99% of their DNA with humans, they will provide clues about the human gut microbiome. 

The results also suggested that human ecology has had a stronger impact in shaping the human gut microbiome than genetic relationships. They also suggest the human gut microbiome may have unique characteristics, like an increased flexibility. In a quote by Katherine Amato,  lead author of the study and assistant professor of anthropology in the Weinberg College of Arts and Sciences at Northwestern, she explains that it is essential to understand what factors shaped the human gut microbiome over evolutionary time because it can help us understand how gut microbes may have influenced adaptation and evolution in our ancestors and how they interact with our biology and health today. She also adds that host ecology is what drives microbiome function and composition, since chimpanzees have different habitats, diets, and physiology than humans. In order to understand the human gut microbiome we must look at primates that are similar to humans since ecology is the, she also adds. Although chimpanzees are often assumed to be the best module for humans in many aspects, it is evident that this close relationship doesn’t apply when comes to analyzing the gut microbiome. 

Going forward, Amato and her team are planning on exploring which qualities of the human gut microbial functions are shared with Old World monkeys and what impact they have on human biology and physiology. The results of this study demonstrate that the human gut microbiome diverges from closely genetically related apes and converges with “cercopithecines both taxonomically and functionally.” These findings provides deep insight on the evolution of microbiomes. More importantly, the results highlight the importance of human ecology and digestive physiology in shaping the gut microbiome. Intimately exploring the relationship between baboons, or other close human related mammals, could reveal more in-depth information about the human gut microbiome and how different factors of our environment affect it. 

Does Exposure to Toxins In the Environment Affect One’s Offspring’s Immune System?

A study has recently surfaced stating that maternal exposure to industrial pollution may harm the immune system of one’s offspring and that this impairment is then passed from generation to generation, resulting in weak body defenses against viruses.

Paige Lawrence, Ph.D., with the University of Rochester Medical Center’s Department of Environmental Medicine, led the study and conducted research in mice, which have similar immune system functions as humans. Previously, studies have shown that exposure to toxins in the environment can have effects on the respiratory, reproductive, and nervous system function among generations; however, Lawrence’s research is the first study to declare that the immune system is also impacted.

“The old adage ‘you are what you eat’ is a touchstone for many aspects of human health,” said Lawrence. “But in terms of the body’s ability to fights off infections, this study suggests that, to a certain extent, you may also be what your great-grandmother ate.”

“When you are infected or receive a flu vaccine, the immune system ramps up production of specific kinds of white blood cells in response,” said Lawrence. “The larger the response, the larger the army of white blood cells, enhancing the ability of the body to successfully fight off an infection. Having a smaller size army — which we see across multiple generations of mice in this study — means that you’re at risk for not fighting the infection as effectively.”

In the study, researchers exposed pregnant mice to environmentally relevant levels of a chemical called dioxin, which is a common by-product of industrial production and wast incineration, and is also found in some consumer products. These chemicals eventually are consumed by humans as a result of them getting into the food system, mainly found in animal-based food products.

The scientists found the production and function of the mice’s white blood cells was impaired after being infected with the influenza A virus. Researchers observed the immune response in the offspring of the mice whose mothers were exposed to dioxin. Additionally, the immune response was also found in the following generations, as fas as the great-grandchildren (or great- grandmice). It was also found that this immune response was greater in female mice.  This discovery now allows researchers to have more information and evidence to be able to more accurately create a claim about this theory.

As a result of the study, researchers were able to state that the exposure to dioxin alters the transcription of genetic instructions. According to the researchers, the environmental exposure to pollutants does not trigger a genetic mutation. Instead, ones cellular machinery is changed and the immune response is passed down generation to generation. This discovery explains information that was originally unexplainable. It is obviously difficult to just avoid how much toxins you are exposed to in the environment, but it is definitely interesting to see the extent of the immune responses in subsequent generations. We can only hope that this new information, and further discoveries, help people adjust what they release into this world that results in these harmful toxins humans are exposed to, and their offsprings.

 

 

 

Gene Editing in Butterflies: What Could This Mean for Their Mating Patterns ?

The beautiful Heliconius butterflies from Central and South Africa are known for their colorful wing patterns. Some of their wing patterns mimic that of other species to protect them from their predators. There is one species of these evolutionary marvels, Heliconius cydno, that scientists have found that the activation of a single gene can determine whether the butterfly expresses white or yellow spots. To come to this conclusion scientists created a genetic map of H.cydno with both white and yellow coloring.

Through examining the genetic maps, the researchers found that the gene al1 was switched on in the white colored butterflies which would mean that al1 gene was correlated to the production of yellow pigmentation. To test this the researchers used CRISPR (a gene editing tool) to switch off the al1 gene in what was supposed to be white spotted butterfly embryo. They found that by switching off that gene the butterflies developed with yellow spots.

The researchers that carried out this experiment also looked into the evolutionary history of these butterflies since this experiment didn’t add pigmentation to the butterflies but changed an ancestrally present pigment by switching off a gene through CRISPR. They studied the al1 gene to butterflies that are closely related to the Heliconius species and found that white version of the spots is a recent development and that H.cyndo was first species to develop the white spots.

After further examination, there was evidence that the white version of the spots corresponds to matting patterns. So, the white spotted H.cydno males preferred to mate with the white spotted H.cyndo females and vise versa with the yellow spotted H.cydno males to H.cydno females. Which begs the question of what roles does the activation of al1 play in not only the coloration of these butterflies but also evolutionarily going forward? If gene activation through CRISPR continues how will that also affect the future mating patterns of these butterflies but possible of other species too?

Orangutans Observed Using Wire Tools to Retrieve Food: What’s Next?

In the natural world, orangutans have been ranked as one of the most intelligent primates.  Primates are the order that is home to apes, monkeys, and humans.  Orangutans have been observed possessing several human-like characteristics such as long-term memory the use of sophisticated tools.  Just like the other three species of great apes, orangutans have been listed as critically endangered.

In this study, orangutans were presented with a bendable wire and a box containing a treat that could only be retrieved with the use of the wire.  The orangutans consistently managed to bend the wire into a hook shape to successfully retrieve the box.

According to the scientists conducting these fascinating studies, the speed with which the apes solved this puzzle is astonishing.  It reveals just how close humans are to our relatives, the great apes.  The first evidence of homo sapiens using tools dates back to 16,000-60,000 years ago.

If you’ve seen any of the Planet of the Apes movies, these studies are probably as frightening to you as they are to me.  The ever-growing list of parallels between apes and humans is both haunting and enthralling.

To see the original article on this study click here.

Did You Know Plants Can Talk?

 

For thousands of years language has been a crucial part of cultures around the world, and a method unique to humanity of transmitting ideas, thoughts, emotions between us. Language has allowed us to work harmoniously together for our mutual improvement and survival. Recently, however, two researchers, Dr. Kim Valenta and her colleague Omar Nevo, have discovered that plants too, have developed their own unique and intricate method of conveying information to their pollinators; “the easier it is for fruit eaters to identify ripe fruits, the better the chance for both [, the plant and the fruit,] to survive.

The most vivid example of plant communication can be found in Madagascar’s Ranomafana National Park and Uganda’s Kiabale National Park where berry plants have evolved “to match each animal’s sensory capacities, [thus] signal[ing] dinner time in the jungle…” Dr. Valenta and Nevo analyzed the exact colors of each fruit with a spectrometer, and “with a model based on the visual capacities of the seed-dispersing animals, they also determined who was most likely to detect different fruit colors contrasting against an assortment of backgrounds.” The researchers concluded that “the colors of each fruit were optimized against their natural backdrops to meet the demands of the visual systems of their primary seed dispersers,” i.e. pollinators. Thus, red-green color-blind lemurs, in Madagascar were best able to detect the fruit with a blue yellow color scheme and monkeys and apes in Uganda, with tricolor vision like humans, were clearly able to distinguish red berries against a green backdrop.

Also recently discovered was that plants can communicate to their pollinators through scent. Dr. Nevo performed a scent-based study on the lemurs in Madagascar. His team collected various ripe and unripe fruits from all over the jungle of Ranomafana. “He suspected the leumur-eaten fruits would have a greater difference in odor after they ripened than the bird-eaten fruits.” To discover exactly how this scent-based communication worked, Nevo used the “semi-static headspace technique.” From this experiment it was confirmed that “fruits dispersed solely by lemurs produced more chemicals and a greater assortment of compounds upon ripening. It is now known that wild lemurs actually spend quite a lot of time smelling for the vivid difference in odor between ripe and unripe fruits in the jungle.

It is astonishing how plants have evolved over the years to be able to communicate with their pollinators for the betterment and expansion of their species. I would be interested to find out, what other organisms communicate (single cellular, multi-cellular, etc.) and what kind of information they find necessary to convey to others for their survival?

 

 

 

 

A Fintastic Discovery

Sharks have interesting biological features: a cartilage skeleton, highly developed senses, dermal denticles, and an oil-storing liver. However, these traits are difficult to identify within the huge genomes of sharks.

 

Previously, the genomes for sharks were larger than many other organisms, making it difficult for scientists to decode and understand the genetic background behind the lifestyle of sharks. However, the Japanese team at RIKEN Center for Biosystems Dynamics Research managed to decode whole genomes of two species of shark: the brown banded bamboo shark and the cloudy catshark. They also improved the genome sequences of the whale shark.

Image result for whale shark of sharks

Whale shark Photo Credit: Zac Wolf

Whale Shark

According to the RIKEN team, the large genomes in many shark species was a result of huge, repetitive insertions within the genome. Additionally, it was discovered that these shark genomes have been evolving at a slow rate, suggesting that sharks have kept some characteristics that were similar to distant ancestors.

 

Already, particular parts of the shark genome revealed certain characteristics of sharks. Using the DNA from the shark genomes, researchers discovered that the rhodopsin pigments in a whale shark can sense short wavelengths, allowing them to see at 2000 meters below the water level when they aren’t hunting on the surface. Furthermore, the team determined that there were too few olfactory genes in the shark genomes, meaning that the highly developed navigation system is not done through smell.

 

These results help fill the gaps in the genetic background in sharks while understanding the way sharks live. Keiichi Sato, deputy director of Okinawa Churaumi Aquarium, says, “Such understanding should contribute to the marine environments as well as to sustainable husbandry and exhibitions at aquariums that allow everyone to experience biodiversity up close.”

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