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  • Writer's pictureVedant Parikh

Lab Notes on: Dr. Daniel Shain

Updated: Aug 11, 2023

Rebecca Zhang's notes on Dr. Daniel Shain, a zoology professor at Rutgers University.

 

Dr. Daniel Shain is a professor of zoology at Rutgers University. He attended college at the University of New Hampshire and earned his Ph.D at Colorado State University, where he originally was on a neurobiology path. However, Dr. Shain soon discovered that he did not enjoy working with model organisms commonly used in the field such as mice and frogs. Not only would they have to be killed, but these types of model organisms are also quite genetically redundant—if one gene is replaced, it is possible that the function the gene coded for will still be completed due to other genes compensating. This obstacle often makes it difficult to study biological processes at a fundamental level. Instead, Dr. Shain developed a deep fascination in working with a more unusual model organism: leeches.


Though not as commonly studied as mice, frogs, fruit flies, or the nematode C. elegans, leeches offer many research advantages: they are more genetically basic, have larger embryos, and are easier to work with. In addition, leech research has a smaller community and is rather unique—a perfect fit for Dr. Shain, who explained, “I’m not that comfortable being in the mainstream. I’d rather be an outlier.” So when he stumbled upon a leech lab at UC Berkeley while searching for a post-doc experience, he immediately knew he needed to go.

California was kind to Dr. Shain; he thoroughly enjoyed the dynamic learning environment UC Berkeley offered and, uniquely, life on a boat. Though he eventually moved into a house, he fondly recalls watching the nighttime California traffic from his boat and spending time on the water. Even after moving to and staying in New Jersey, Dr. Shain noted that he enjoyed working and still collaborates with his advisor in his UC Berkeley lab.


In his current lab, Dr. Shain continues his exploration in worm biology. He frequently incorporates molecular biology in his experiments, such as identifying genes important in development and testing their functions by manipulating their expression. This requires the use of different genetic engineering techniques, like PCR. Abbreviated from polymerase chain reaction, PCR is essentially synthetic DNA replication. The DNA of interest is placed into a thermocycler machine that replicates the DNA using a thermostable DNA polymerase I from a special bacteria, Thermus aquaticus. Though it possesses the same function as human DNA polymerase, Taq polymerase can withstand the high temperatures the three steps of PCR are completed under:

  1. Denaturation: separate the two strands of DNA (94-96℃)

  2. Hybridization/Annealing: bind the DNA primer to the 3’ ends of each DNA strand (55-65℃)

  3. Extension/Elongation: replicate the DNA with Taq polymerase (70-75℃)


Using this and other procedures, Dr. Shain focuses on understanding the fundamental processes of biology and investigating new findings. For example, Dr. Shain has recently aided in the discovery of various ice animals living in glaciers, an extreme environment in which only worms were thought to reside in. Currently, genomics is being used to sequence the DNA of the animals, compare the ice animals’ genomes to those of non-ice animals, and find similarities and differences in the DNA. The results can then be studied to identify unique genes of interest to isolate and test.


Another focus of Dr. Shain’s research is determining the genetic requirements for embryonic stem cell (ESC) genesis in leeches. Stem cells are special, undifferentiated cells that can transform into specific cells (like a nerve or red blood cell), and different kinds of stem cells can differentiate into varying amounts and types of cells. ESCs are considered ideal in that they can become any type of cell. Dr. Shain aims to identify the underlying mechanisms behind ESC formation, and leeches are an incredible way to study this because, as mentioned before, leeches have remarkably large embryos that can be dissected with fine needles. Using RNA sequencing (RNA-seq) technology, Dr. Shain is able to explore detailed questions regarding ESC formation in leeches.


Dr. Shain has conducted many other projects, and all enjoy his affections, but perhaps his best contribution was on the mechanisms ice worms use to survive cold glacier environments¹. The normal trend in biology is that higher temperatures lead to higher levels of energy. However, in the ice worms Dr. Shain studied, intracellular ATP (energy) levels increase as an inverse function of temperature: if temperature decreases, energy produced increases and vice versa. This phenomenon seems to be a key factor in the ice worm’s ability to function efficiently in such cold conditions. In the future, Dr. Shain would like to further explore the specific mechanisms involved in this adaptation. He mentioned two key enzymes: one silenced and the other modified. This modified enzyme causes ATP production to surge by attaching to its site of synthesis. Understanding this process will allow Dr. Shain to dive deeper and target specific molecules involved.


There is an underlying reason for Dr. Shain’s extensive research: a love for learning new things. His favorite part of the process is the discovery—finding something never known before and making progress in the scientific community. He highlights the importance of taking steps forward in your work, however small, every day. But even while persistency and consistency are key, knowing your limits is too. Push forward when there are still possibilities to look into, but also acknowledge when the possibilities have been exhausted. Trust yourself and stay motivated, for research is all but a simple process. Becoming discouraged is inevitable, but there is always a way.



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