Michael Shapira, Professor

Closed (1) The role of environmentally-acquired gut microbes in host adaptation to environmental stress

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

All animals harbor extensive gut microbial communities that contribute to their health and fitness. The human colon harbors as many bacteria as there are cells in the entire body, and the number of bacterial genes is estimated to be 100-fold greater than genes in the human genome. Bacterial genes are thus a potential source for genetic variation that could contribute to host adaptation. On top of that, exchange of microbes with the environment could further expand this genetic variation. In a particularly interesting demonstration of such microbe-assisted adaptation, bean bugs, pests of soybean, were found to become resistant to pesticides by acquiring pesticide-hydrolyzing bacteria from fields, where spraying selected for bacteria that could utilize the toxicant as carbon source. The project aims to evaluate the prevalence of such contributions and their long-term consequences using the worm C. elegans as a model host, raising it in soil microcosms in the presence of different environmental toxins.

Students will take part in analysing toxin-induced changes in microbiota composition, the proportion of toxin-metabolizing microbes following toxin exposure, and their contributions to host resistance and fitness. Experiments will be carried out examining host adaptation within one generation as well as during multi-generational passaging of worms and microbes under toxin exposure. Work will involve assessing host fitness. During this work, students will learn how to design experiments, select appropriate controls, organize and analyze data, and present results. Technically, students will learn to use aseptic techniques culturing and analysing various bacteria, work with C. elegans, and handling DNA in order to perform analyses such as sequencing and qPCR.

Day-to-day supervisor for this project: Samuel Slowinski, Post-Doc

Qualifications: Pre-requisites: Bio1A/Bio1B; students should be able and willing to read and understand scientific literature (especially research articles) to a level that will allow them to understand the general concepts described in the project description. Sophomores or Juniors.

Weekly Hours: 12 or more hours

Related website: http://ib.berkeley.edu/labs/shapira/

Closed (2) Age-dependent interactions between C. elegans stress signaling and a regulator of longevity

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

Previous results from our lab showed that the stress MAP kinase KGB-1 had age-dependent contributions: while its activation in developing larvae provided protection from heavy metals and from protein folding stress, its activation in adults sensitized worms to the same types of stress and further shortened lifespan (Twumasi-Boateng 2012). This age-dependent switch was associated with antagonistic regulation of the transcription factor DAF-16/FOXO, an evolutionary conserved regulator of stress resistance and longevity. KGB-1 activation in larvae promoted DAF-16 nuclear localization, while activation in adults attenuated localization. The current project seeks to characterize a recently identified mechanism that links KGB-1 activation and DAF-16 regulation.

The student chosen for this project will work under Cyrus Ruediger an experienced specialist, and with a second undergraduate student to conduct experiments aiming to understand the role of a microRNA found to regulate the function of the insulin signaling pathway, which regulates DAF-16. The student will carry out lifespan experiments, measurements of the expression of fluorescent gene reporters and quantitative RT-PCR measurements to elucidate the role of this microRNA, Staff Researcher

Qualifications: We seek candidates who are interested in basic science. They should have solid understanding of molecular biology (gene expression, PCR, and the like) but also an interest in evolutionary biology. pre-requisite courses are Bio1A and Bio1B, but good understanding of topics covered by these courses obtained from other sources will be fine (provided that the knowledge is there, not just the credentials). Students are also expected to be able to read from the primary scientific literature - to understand the overall gist of a scientific paper and to be able to seek (by asking, or in any other way) more information about the topic and methods.

Weekly Hours: 12 or more hours

Related website: http://ib.berkeley.edu/labs/shapira/