Richard Harland, Professor

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

Closed. This professor is continuing with Spring 2018 apprentices on this project; no new apprentices needed for Fall 2018.

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. Students should be able to devote a 9-12 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. 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: to be negotiated

Closed (2) Biological Sciences - Breakthroughs Research Assistant

Closed. This professor is continuing with Spring 2018 apprentices on this project; no new apprentices needed for Fall 2018.

Are you interested in scientific journalism or science communications (including photography/videography) covering a wide range of biological topics?

This project is open to a wide range of students, from biology majors with a love of writing to English or history majors who love science -- all are encouraged to apply. Cultivate that budding inner journalist and learn about biosciences research at Cal!

Unearth breakthrough science in the Letters and Science, Biological Sciences at Berkeley -- news stories from Integrative Biology, Molecular and Cell Biology, the Physical Education Program, and the Biology Scholars Program. Interview faculty, researchers, and students to document their discoveries and experiences. In light of Berkeley’s 150th anniversary, this project may also involve historical/archival research. In this project, you'll interview experts and perform independent online and library research to create engaging content that may be used in the Letters and Science website, social media, and/or newsletters. If you not only love science, but also love communications, this is the project for you.

There's definitely room to get creative -- we’re particularly interested in students that have skills in writing, photography, cartooning, creating podcasts, online videos, or working with social media.

Under the supervision of Monica Albe and Dr. Richard Harland, the student will investigate UC Berkeley bioscience research, people, events, and programs. Content will be created highlighting individuals and projects -- work may not only highlight the biological sciences, but also people who have “crossover” skills like scientists who are artists, historians who study biologists, etc. Student may be asked to attend lectures or meetings, or set up one-on-one interviews with some of our world-renowned researchers.

Depending on student’s skill set -- graphic arts, photography, social media, or other creative pursuits may also be included in this project.

Day-to-day supervisor for this project: Monica Albe

Qualifications: Required Qualifications: Student must have excellent written and communication skills. Student must be able to work with strict deadlines, be self-motivated, and be able to work independently on projects. Student should have an interest in science journalism or science communications. Students with past writing/communication/journalism experience are preferred. Desirable but not essential are applicants who are knowledgeable in one or more of the following: Adobe Photoshop, Powerpoint, video editing. Please be aware: the essay part of the URAP application will be treated as a writing sample.

Weekly Hours: to be negotiated

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

Applications for Fall 2018 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.

Weekly Hours: to be negotiated

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

Applications for Fall 2018 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, Post-Doc

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