The Lumberjack



Students Serving The Cal Poly Humboldt Campus and Community Since 1929

Tag: CRISPR

  • Chopping Genes and Growing Brains

    Chopping Genes and Growing Brains

    Innovative research and a discovery in HSU’s molecular biology lab

    Biology professor John Steele guided a cell biology lab his first year at HSU wherein he wanted to teach students that cells need nutrients to survive. After 48 hours, the lab discovered quite the opposite. James Gomez, a current student in the lab, had the opportunity to research more into the groundbreaking discovery.

    “In science, you’re kinda looking for that unexpected stuff,” Gomez said. “Right after I came in, I was really excited to be a part of that. There was this thing that was happening that we particularly can’t fully explain, and I’m actually in the lab doing that science.”

    Steele’s experiment for his class involved students starving the cells of nutrients to trigger a state of autophagy, which is when the cell starts to consume itself. Steele meant to emphasize that cells needed nutrients like amino acids and lipids to survive. It was assumed that starving cells of key nutrients eventually killed them.

    • John Steele in his lab with graduate students in the background working on their research on Jan. 31. The lab specializes in molecular biology. | Photo by Collin Slavey

    Steele said the experiment was common, and was usually shut down after six to eight hours. Steele decided to run it for 48 hours instead, since that was the time between lab sections. When his class returned returned to the lab, rather than seeing a bunch of dead cells, they were decidedly more alive. The lab had made a discovery.

    Despite the cells being in autophagy in Steele’s experiment, they had stopped dividing and took on a strange morphology. Their metabolic rate was high—they were very much not dead.

    Now the lab, including Gomez, are deep in research. The lab is introducing pathway inhibitors, or drugs, to block basic cell functions, narrowing down the essential and non-essential. The project is open-ended, as students methodically look at every cellular pathway to determine the needs of cells.

    “What I love about this project is that it was born here,” Steele said. “Nobody else that I know of is working on this, outside of HSU. That’s an awesome process to be a part of, where students get hands-on training in phenotypic genetic screening and drug screening, and we get to learn about the basic biology of cells in doing this.”

    Steele encourages the students in his lab to explore the boundaries of their knowledge. CRISPR, Cas9 and stem cell cultures are unique tools available to these students, and they offer an opportunity to think outside the box and do creative science.

    Steele’s lab combines bio-technologies using unique stem cell cultures and genome editing techniques. The lab cultures stem cells—cells which can grow into any cell type—and chops up DNA using CRISPR, a revolutionary gene-clipping tool, to learn how rare neurodegenerative diseases develop in the brain.

    “There have been some really cool applications of CRISPR out there. And they’re just because somebody said, ‘I wonder if we could do that?’ and they did.”

    John Steele

    Steele’s graduate student Kyle Anthoney, on the other hand, is working on making a model of a rare disease called progressive supernucleogical palsy, which looks like a combination of Parkinson’s and Alzheimer’s diseases. The disease is a tauopathic disease because a main characteristic of the disease is a buildup of the tau protein, which blocks some necessary cell functions. To understand the finer details of the disease, Anthoney developed a new method for growing neurosphere cell types into what is, effectively, a miniature brain.

    Scientifically named 3D neural sphere cultures, these miniature brains offer a platform for researchers to study three types of brain cells at the same time. Anthoney’s method allowed him to organically grow neurons, oligodendrocytes and astrocytes, three dominant cell types in the brain, from human stem cells, so they would develop naturally like they would in a growing brain.

    Anthoney’s research is up for review in a number of scientific publications and his name is on some breakthrough scientific papers. He is contributing to research about progressive supernucleogical palsy and other tauopathic diseases. His research concentrates the tau protein in a miniature brain to simulate the symptoms of progressive supernucleogical palsy, and he is exploring how the protein and disease impact his lab-grown brain cells.

    “There have been some really cool applications of CRISPR out there,” Steele said. “And they’re just because somebody said, ‘I wonder if we could do that?’ and they did.”

  • The evolution of biology 105

    The evolution of biology 105

    Do sports drinks lie about their sugar content?

    In biology 105, HSU oceanography major Courtney Dressler and her classmates tried to answer this question.

    “We are adding dinitrosalicylic acid into solutions of Gatorade and Vitamin Water Zero,” Dressler said. “The acid helps us identify how much sugar is in these drinks.”

    Dinitrosalicylic acid, or DNS, binds to sugar molecules in a solution. When this binding occurs, the solution’s color can transform into a shade between orange and red.

    Wesley Warren, also an oceanography major at HSU, explains how these color changes are detected.

    “We put the solutions into a spectrophotometer, which tells us how much light they absorb,” Warren said.

    Orange solutions absorb a different amount of light than red solutions. By comparing the sports drinks’ light absorbance values to those of the standards, or solutions with known sugar content, the drinks’ actual sugar concentrations can be determined.

    Dr. John Steele, one of the instructors for biology 105, elaborated on how this experiment fits into the course’s schematic.

    “Biology 105 provides an introduction to topics that a cell/molecular biology, microbiology and general biology major would encounter in their undergraduate studies,” Steele said. “[The experiment] is used to teach students how to make diluted solutions from a stock solution and how to determine the concentration of [molecules] in a given solution.”

    In prior semesters, two laboratory periods were given for students to complete the experiment and learn these essential techniques. Now, students are allowed three periods to conduct the experiment.

    A few other labs in biology 105 were also modified to include more time.

    Video by Linh Pham and Surya Gopalan.

    Dr. Brigitte Blackman, who teaches a section of biology 105, explained the factor that prompted these changes.

    “We try to take feedback from students every semester and change the course based on their comments,” Blackman said. “In past semesters, some students have felt the labs were too long and covered too much in one period.”

    “By spreading out the labs, we hope that students will be able to better understand the principles covered in lab and apply these principles to test a scientific hypothesis,” Steele said.

    For Marjani Ellison, an environmental science major who’s retaking biology 105, the order in which the experiments are conducted also seemed to change.

    “Last semester, the labs and lectures materials did not coordinate. I felt as if the two were separate classes,” Ellison said. “This semester, the labs follow the lectures. I feel that I’m actually learning this time.”

    In addition to student feedback, current trends and issues in biology also determine the necessary changes for the class.

    “Last semester, we incorporated the Small World Initiative into our laboratory curriculum,” Blackman said. “The initiative was introduced to the course by [professor] Mark Wilson. As part of this initiative, students sampled and grew bacteria from the local environment, such as the Arcata Marsh, then searched for bacteria that were producing antibiotics.”

    This semester, biology 105 replaced the Small World Initiative with gene-editing using CRISPR as the current topic in biotechnology.

    “CRISPR is a gene editing system made by two scientists named Jennifer Doudna and Emmanuelle Chapentier. To use this tool, all you need to know is the DNA sequence where you would like to make an edit,” Steele said. “Because of its versatility and popularity in biotechnology, bio 105 students need to learn the basics of this tool and the first step of building it.”

    Learning CRISPR at the introductory biology level could increase the horizon of opportunities for HSU students.

    “This topic has grown from being a sentence in a textbook to a paragraph, and soon, probably full sections of a chapter,” Steele said. “Biotech companies are looking for people who know how to use CRISPR and gene editing technologies. Learning this technique early could really put HSU students ahead of the competition.”

    Steele also claimed a selfish reason for teaching students CRISPR.

    “If more students know how to use this tool, then more students will be able to work for my lab,” Steele said. “My lab uses this tool everyday!”