Richard Harland, Professor

Closed (1) Tadpole from head to tail: Establishment of the AP axis and formation of the nervous system, in Xenopus

Applications for fall 2021 are now closed for this project.

The focus of the lab is to understand development; that is, the molecular mechanisms that orchestrate how a single cell (the egg) transforms into an adult animal with a multitude of functioning organs, following a specific body plan. The first milestone in the establishment of the body plan is to define the three main axes: anterior-posterior, dorso-ventral and left-right. The arrangement of the cells and specification of the territories requires 1. cell populations and tissue movements where mechanical forces are generated, and 2. gene expression which gives identity to those regions. The important processes that generate the vertebrate body plan are gastrulation (literally- formation of the gut), and neurulation (formation of the hollow dorsal nerve cord). The engine of gastrulation, the dorsal mesoderm (the future spine and muscles), acquires a mixture of invasive, pushing and migratory abilities. Subsequently, the tissues cause the neural tube to roll up and extend to elongate the body axis. At a genetic level, during development, the processes are controlled at three levels: transcription factors, which regulate the expression of other genes, members of the signaling pathways which take part in cell communication, and the gene products that execute the individual cells’ migrations and shape changes. Hence, in order to understand the architecture of body plans, we must understand how these factors and pathways are regulated, talk to each other and interact. In particular, this project will focus on formation of the anterior-posterior axis, that we can divide in head, trunk and tail, and genes involved in patterning the developing neural tissue that give rise to the future brain and spinal cord. We will search for genes that control cellular behavior, and study how they are turned on by the signaling pathways and transcription factors, and what those products do in the process of gastrulation and neurulation.

Cloning in-situ probes and performing in-situ hybridization to visualize potential genes involved in neural patterning.
Specific techniques: Molecular biology methods such as polymerase chain reaction (PCR), and subsequent cloning techniques. As the project progresses, additional different methods (i.e. in situ hybridization, microscopy, etc.) might be used to visualize different transcripts. When more expertise and higher understanding are acquired, other techniques can be performed (microinjections, embryos culture, drug treatments, surgeries…) in order to achieve more complex experiments and make interesting discoveries.

Day-to-day supervisor for this project: Marta Truchado, Post-Doc

Qualifications: Undergraduates seeking to apply should be highly motivated, perseverant, with low tendency to give up, engaged and with a proactive attitude without being afraid of making mistakes or being wrong. Innate curiosity is 100% required; ability to ask questions and willing to learn, both techniques and scientific attitude. Recommended for those interested in molecular biology especially as it pertains to development and genetics. Although previous research experience is valuable, no previous research experience is necessary, but real passion for research and this topic is required. Students should be able to devote AT LEAST 14 hours/week to laboratory experiments and discussion. We prefer to recruit Sophomores or Juniors, with the expectation that they will work towards an honors thesis in their senior year; but we could consider seniors with experience. We also prefer to recruit those who plan to take MCB 140 (Genetics) and MCB C100A, (Biophysical Chemistry: Physical Principles and the Molecules of Life).

Weekly Hours: 12 or more hours

Closed (2) Improving Animal Research Welfare

Applications for fall 2021 are now closed for this project.

To perform high quality research, animals need to be healthy. However, animal health and welfare is not just a requirement for performing research, but a right of those.

Tasks proper from animal care, and constant follow up of the animals. Data recollection, analysis and protocol optimization.

Day-to-day supervisor for this project: Marta Truchado

Qualifications: This project is directed to pre-vet students with interest in lab research animals. The lab works with frogs: Xenopus laevis and Xenopus tropicalis. No experience in these animals is necessary, though high standards of animal welfare are essential.

Weekly Hours: 6-8 hrs

Closed (3) A screen for genes that control shape change in the embryo

Applications for fall 2021 are now closed for this project.

We will isolate DNAs encoding cytoskeletal regulators, describe their expression, and knock-out or add back functions to determine whether they are active in controlling cell behaviors.
Amphibian embryos have been valuable models to examine the behaviors of cells that contribute to the shape changes of the embryo. The embryos develop outside the mother, so they are accessible for experiments and observation at all stages.
We will screen for genes that are expressed in the Xenopus embryo, and focus further on genes specifically expressed in cells undergoing shape changes or rearrangements. We will focus on neural tube closure, and the movements of gastrulation- formation of the three-layered embryo with ectoderm, mesoderm and endoderm, which provides the raw material for making the tadpole. Once we identify interesting activities we will test them for their function by gain and loss of function.

This is also a pilot lab to determine the feasibility of scaling up this project as a capstone lab experience for undergraduates who may not have been able to get other lab research experience. It is a highly cooperative project, which led to interesting results this last academic year.

Day-to-day supervisor for this project: Marta Truchado, Post-Doc

Qualifications: No specific qualifications are required, but it is mainly indicated to sophomores.

Weekly Hours: 12 or more hours

Closed (4) Determining the possible functions of sleep in the jellyfish Cassiopea

Applications for fall 2021 are now closed for this project.

Though sleep is pervasive across animals, the core function of this deeply conserved behavior remains unknown. Sleep has been hypothesized to serve many roles, from the replenishing of molecules consumed during periods of activity, to the facilitation of learning and the formation of long term memories. Recently, colleagues and I discovered that the upside-down jellyfish, Cassiopea, displays the key behavioral characteristics of a sleep-like state. This is the first animal without a centralized nervous system to have a defined sleep-like state. Cassiopea are also members of the phylum Cnidaria, one of the earliest branching metazoan lineages. Together, the presence of sleep within this ancient phylum supports the hypothesis that sleep is an ancestral behavior and emphasizes its functional importance. However, we still do not know what role sleep is playing in these relatively simple animals.

We will be investigating several questions that relate to the possible functions of sleep in Cassiopea. Is the sleep behavior affected by age? Is metabolic rebalancing impacted by sleep? Does sleep help them recover after injury? Do their neurons display cycles in activity as seen in the sleep states of other animals? Answering these questions, and others, would be significant progress towards understanding the role of sleep in Cassiopea, and give us insights into its function across animals.

This apprenticeship will involve assisting in the use and development of software to track Cassiopea activity over several days and nights under different experimental conditions. Additionally, projects may involve animal husbandry, data analysis, dissections, immunohistochemical and in vivo staining, gene expression studies, microscopic imaging, electrophysiology and considerable creativity.

Day-to-day supervisor for this project: Michael Abrams

Qualifications: Applicants should be self-motivated and possess good communication skills. Experience in python programming or neuroscience is a plus - although no specific undergraduate course work is required. Creativity and a willingness to get your hands wet is essential. A long-term interest is desired so preference will be given to sophomores and juniors.

Weekly Hours: to be negotiated