AP Biology – BioQuakes

Tag: AP Biology

Cracking the Code of Shigella

On October 23, 2023

In the article titled, Scientists discover the possible triggers for bacterial pathogens, opening the door for new treatment strategies, the reporter discusses how Alexander Fleming’s unintentional discovery represented a crucial turning point in medical history and sparked the creation of several additional antibiotics, saving countless lives in the process. This famous Scottish pharmacist discovered penicillin, the first antibiotic, in 1928 and since then many others have followed in his footsteps. Additionally, his discoveries led to the idea that “extraordinary appearances” should not be ignored. His famous sentiments hold true to multiple scientific discoveries; this is including a group of scientists at UNLV who are studying shigella.

In the picture above you can see Shigella in a stool sample.

Shigella is a harmful bacteria that can cause many issues in the human body such as stomach cramps, fever, diarrhea (which is frequently bloody), and can also be fatal. Shigella infection is an intestinal ailment caused by a family of bacteria called shigellosis. Shigella spreads quickly. When individuals come into touch with and ingest quantities of germs from an infected person’s feces, they get infected with shigella.

Initially I was not engaged with this topic because I had no idea how it could be relevant to my life. However, my recent work as an EMS volunteer has proved me wrong. Although I have not seen a patient who had shigella, I have observed many other patients who experienced similar bacterial diseases and am eager to find the best way to treat them.

Moreover, these scientists are focused on the proteins in shigella that are called VirB. VirB proteins act as a switch in the bacteria and bind to Shigella by interacting with Shigella’s DNA. This interaction between VirB and Shigella’s DNA is a key step in the process that activates the bacterium’s virulence genes. Essentially, the DNA is what causes disease in people. Researchers found that by interfering with the way VirB bonds to the shigella, they can minimize the effects it has on humans.

Furthermore, this research is largely important to the understanding of how proteins such as VirB are able to turn harmless bacteria into deathly ones. Moreover, this insight is also helpful in the development of treatments for other diseases such as Campylobacteriosis, E coli, and Cholera which are caused by similar proteins in different bacterias.

After studying Organic Compounds in my AP Biology class, I was able to make connections to the material we have learned such as the different protein structures which heightened my interest in this topic even more. The reason that similar proteins are able to cause so many different diseases is because of the altercation in protein shape as well as body response. All proteins have specific shapes and structures that determine how the protein will interact with the human body. Additionally, there are four main protein structures including primary, secondary, tertiary, and quaternary which all play a role in how proteins behave. Moreover, all proteins have side chains which provide characteristics and make them different from one another. The side chains in proteins give amino acids characteristics and by changing one small detail you will change the structure (shape) of the protein and thus how it interacts with the human body.

To continue, E coli is a type of bacteria frequently discovered in both the human and animal intestines. Since it aids in digestion and the creation of several vitamins, it is often safe and even advantageous. However, some E. coli strains have the potential to be dangerous and contagious.

The photo above shows a cross section illustration of an E.coli cell.

However, the most important factor in this research is a molecule known as CPT, which is short for Camptothecin. Camptothecin was first identified as a topoisomerase inhibitor in 1966. Topoisomerases are nuclear enzymes involved in DNA replication (and more). To understand its role, you can think of Camptothecin as a key part in a puzzle involving Shigella. VirB acts as a switch to turn on the bacterium’s ability to cause disease in the human body. For this switch to work correctly, it needs Camptothecin. Camptothecin is the key that enables VirB to bind to Shigella’s DNA, which then activates the disease-causing process.

The researchers are interested in interfering with this binding process. By doing so, they aim to prevent Shigella from making people sick. This line of research isn’t just about Shigella. The hope is that the knowledge gained from studying this process could be applied to finding a solution for a whole group of diseases caused by different bacteria similar to Shigella.

So… what are YOUR thoughts on the research of Camptothecin’s role in Shigella’s causing a process that could lead to the investigation of new treatment? Are you optimistic about the potential impact on the future public health?

Worms Infused with Spider Genes Spin Silk Tougher Than Kevlar

By alexoskeleton

On October 21, 2023

In Student Post

Researchers have achieved a significant milestone in biotechnology by genetically modifying silkworms to produce spider silk. Spider silk is renowned for its exceptional strength and durability, surpassing even the toughness of Kevlar. Justin Jones, a biologist specializing in engineered spider silks at Utah State University, described the material as “a truly high-performance fiber.” This breakthrough has the potential to revolutionize various industries. It could be employed in the production of lightweight yet incredibly strong structural components, thereby enhancing the fuel efficiency of planes and cars. Additionally, this innovation could lead to the development of wound dressings for faster healing and sutures for surgical procedures.

Silkworm cultivation has been practiced for thousands of years, providing raw material for textiles. However, their silks tend to be fragile. On the other hand, spiders face the opposite issue – their silks are remarkably strong and a greener alternative to synthetic fibers, which are produced by using fossil fuels. However, their silks are challenging to cultivate. Silkworms coexist peacefully, while spiders are territorial and tend to be aggressive when in close proximity.

Over the years, researchers have endeavored to genetically engineer silkworms to produce spider fibers, aiming to harness the desirable qualities of both organisms. The primary challenge has been the size of spider silk proteins, which are significantly larger. Inserting these large genes into the genomes of other animals has proven to be a complex task.

In a recent study, Junpeng Mi, a biotechnologist at Donghua University in Shanghai, China, opted to work with smaller spider silk proteins. Mi and his fellow scientists focused on MiSp, a protein found in Araneus ventricosus, an orb-weaving spider native to East Asia. They utilized CRISPR (clustered regularly interspaced short palindromic repeats), a gene editing tool, to replace the gene in silkworms responsible for their primary silk protein with MiSp. During this process, the scientists retained some silkworm sequences in their MiSp gene construct to ensure compatibility with the worm’s internal machinery.

The MiSp gene itself is 5440 base pairs in size and encodes 1766 amino acids. The protein features repetitive amino acid sequences, which contribute to the unique mechanical properties of spider silk. MiSp also possesses N and C terminal domains, which play specific roles in the assembly and characteristics of the silk protein. The protein exhibits a predominant beta-sheet structure, as opposed to an alpha-helix structure. Beta-sheets are a secondary structure in proteins, characterized by the arrangement of beta-strands connected by hydrogen bonds, resulting in a sheet-like structure.

The beta-sheet structure is a pivotal factor in the exceptional strength and toughness of spider silk. This structure facilitates the formation of crystalline regions within the silk fibers, providing both mechanical stability and properties that render spider silk one of the strongest natural materials known.

The genetically modified silkworms carrying the spider genes produced fibers with remarkable tensile strength and toughness. The resulting fibers were nearly as tough as the strongest natural spider silk and nearly six times stronger than Kevlar.

The flexibility of the MiSp-based fibers surprised the researchers. Typically, this protein produces strong but not stretchy fibers. “But it does make a flexible fiber when you put it in a silkworm,” says Jones.

Mi and his team aim to scale up the production of spider silk fibers for commercial use. This involves crossbreeding their specialized silkworms with commercially viable strains commonly used in large-scale silk farming. The resulting biodegradable fibers may initially find application in surgical sutures.

Jones raises concerns regarding safeguarding intellectual property rights during the commercialization process. This is likely to involve the distribution of transgenic silkworm eggs to numerous farmers. There is also uncertainty about whether the introduced genes will persist through subsequent generations of silkworm breeding.

The researchers plan to continue pushing the boundaries of spider silk engineering. They are currently exploring the possibility of modifying silkworms to produce spider silks with enhanced strength and elasticity. Mi and his team envision creating silk proteins that incorporate non-natural amino acids. This offers great potential for producing silks with unique properties. This could allow scientists to create silks that surpass the strength and toughness of materials like Kevlar.

When I first heard about CRISPR and the idea of genetically modifying living organisms, it raised many concerns for me. The notion of creating a material stronger than Kevlar in an organism smaller than my hand heightens my apprehensions. What if foreign countries exploit this technology for military purposes? What if it’s used as a biological weapon by enhancing the virulence or resistance of pathogens? What if terrorist organizations like Hamas employ this technology to further their destructive aims against the Israeli people?

Genetic modification prompts contemplation of numerous ethical concerns it may bring. If I were in a position of governance, I would impose stricter regulations, conduct more extensive long-term studies, and implement transparent labeling for genetically modified organisms. It is imperative to acknowledge that discussions about the ethics of genetic modification are ongoing and may evolve as the technology advances, along with society’s deepening understanding of genetics. Decisions in this realm should consider all potential applications that gene editing offers. Now, I ask you, what are your concerns with this technology? What problems do you think it brings? Personally, I am against this technology, and I believe there should be many legislative laws against it because of its potential impacts in the future.

Genetic modification is a powerful innovation with the potential to revolutionize and, potentially, disrupt our society. It is a tool that demands judicious use, taking into account its ethical and societal implications. Gene editing can be a catalyst for positive transformation in our world, cultivating a future that balances scientific progress with ethical responsibility. Spiders and silkworms represent just the beginning of this new frontier in scientific research.

Can We Alter Mammals Social Behavior Using CRISPR Gene Editing Mechanisms?

By DNAva

On April 30, 2023

In Student Post

At Georgia State University a team of researchers led by professor H. Elliott Albers and Professor Kim Huhman put gene editing mechanisms to the test to determine if it was possible to alter hamsters behaviors. The hamsters that were utilized in this experiment were Syrian hamsters. These hamsters have been extremely important in many scientific experiments that look into social behaviors, aggression and communication. Furthermore, hamsters are widely used in scientific research due to the fact that their social skills resemble most similarly to humans.

In this experiment, professor H. Elliott Albers and Professor Kim Huhman utilized CRISPR-Cas9 technology to deactivate neurochemical signaling pathways that play a major part in controlling mammalian social behaviors. The regulators of the social phenomena that controls pair bonding, cooperation, social communication, dominance and aggression are the hormone vasopressin and the receptor it acts on, Avpr1a.

After the gene editing and the observation of the hamsters were complete, the researchers were shocked by their unexpected results. As stated by Professor H. Elliott Albers, he “anticipated that if we eliminated vasopressin activity, we would reduce both aggression and social communication. But the opposite happened.”

Instead of reducing the hamsters’ aggression and social communication, the absence of the receptor that activates the vasopressin led the hamsters to demonstrate increased levels of social communication behaviors than when observed prior to the gene editing. Furthermore, it was observed that the differences in opposite sex aggression were removed. Both the male and female hamsters showed aggression towards other same-sex hamsters.

This shocking finding led the researchers to a different conclusion than foreseen. Because it is known that vasopressin correlates with the increase of social behaviors, it can be concluded that the Avpr1a receptor is inhibitory.

Moreover, confirming this study done at Georgia State University, another study published in the Proceedings of the National Academy of Sciences, finds that that eliminating the Avpr1a receptor in hamsters windes up deactivating the vasopressin’s action on the receptor, therefore changing the social behavior of the hamsters drastically in ways one would not expect.

Overall, Professor H. Elliott Albers contends that this study is of extreme value as it helps researchers understand the“neurocircuitry involved in human social behavior and our model has translational relevance for human health. Understanding the role of vasopressin in behavior is necessary to help identify potential new and more effective treatment strategies for a diverse group of neuropsychiatric disorders ranging from autism to depression.”

Connection to AP Biology 😀

This study is connected to our AP biology class as we have learned about regulation of gene expression. Without the presence of the Avpr1a receptor, the vasopressin has no way to be mediated, thus enhancing its social behavioral effects. And with the presence of the Avpr1a receptor, the vasopressin is still active, however, muted.

Back from the dead? Tech Startup attempts to bring back the Dodo bird.

By englandiffusion

On March 15, 2023

In Student Post

Perhaps the most widely known animal extinction is the famous Dodo Bird. According to Brittanica, the dodo became extinct after European settlers disrupted its native Mauritius. Extinction, as defined by National Geographic, is “the complete disappearance of a species from Earth.” However, as reported by US News, new technological innovations hope to reverse extinction and bring back the dodo bird.

According to the article, a tech startup Colossal Biosciences hopes to use gene editing technology to bring back extinct species, such as the dodo bird. According to MedlinePlus, “genome editing (also called gene editing) is a group of technologies that give scientists the ability to change an organism’s DNA.” According to Beth Shapiro, A biologist at the company stated that the company intends to edit the genes of the non-extinct Nicobar Pigeon, a close relative of the dodo, to recreate the dodo, hundreds of years after its extinction.

Despite these promising advancements, because researchers intend to use the genes of a different species, and the conditions on the island are not the same as they are today, it will be nearly impossible to revive the dodo bird exactly. For example, as reported by US News, Shapiro stated “it’s not possible to recreate a 100% identical copy of something that’s gone.”

While these advancements are exciting, as US News stated, there could be significant drawbacks to bringing back extinct speeches. As stated by ecologist Stuart Pimm of Duke University “There’s a real hazard in saying that if we destroy nature, we can just put it back together again – because we can’t.” As stated earlier, it was colonists and mistreatment of the environment that caused the extinction of the dodo bird in the 1600s, so perhaps, as reported by US News and stated by Boris Worm of the Univerity of Dahlhousie in Halifax, Nova Scotia “Preventing species from going extinct in the first place should be our priority.” Perhaps we can achieve this goal by taking better care of the environment, for according to Columbia Climate School, “The main modern causes of extinction are the loss and degradation of habitat (mainly deforestation), over exploitation, (hunting, overfishing), invasive species, climate change, and nitrogen pollution. Many of these ideas connect to what we have studied in biology class, such as the effects of genes. According to Brittanica, Gene editing technology uses enzymes to influence genetic sequences; these enzymes are called Restriction Enzymes. Additionally, according to the University of Illinois, “Restriction enzymes are essential tools for recombinant DNA technology.” As we learned in the Mitosis/Meiosis, and cellular respiration unit, recombinants are the chromosomes that occur when chromosomes “cross over” during Prophase I of meiosis, essentially creating a blend of different traits. This phenomenon is similar to what occurs in gene editing technology, where enzymes snip DNA, adding different traits, to create a sort of “mix” of traits.

Therefore, while these new technologies in gene editing are exciting, we shouldn’t be 100% convinced of their effectiveness, and we should continuously question the ethics of such practices.

BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: AP Biology

Cracking the Code of Shigella

Worms Infused with Spider Genes Spin Silk Tougher Than Kevlar

Can We Alter Mammals Social Behavior Using CRISPR Gene Editing Mechanisms?

Back from the dead? Tech Startup attempts to bring back the Dodo bird.

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