Nipam Patel, Ph.D. - US grants

A gene, Odysseus (Ods), which contributes to reproductive isolation in Drosophila species was recently cloned in this laboratory. Introgression of an appropriate D. maturitiana chromosomal region containing the Ods locus causes male sterility in D. simulans. Preliminary evidence suggests that Ods is a homeodomain-containing gene but an unusual one in that the homeodomain has experienced extremely rapid amino acid substitution in Drosophila species. It is suggested that its rapid evolution coupled with its unusual expression in the male germline is expressed as hybrid male sterility. The specific objectives are 1) to prove that the cloned gene Ods is the molecular basis for hybrid male sterility by germline transformations 2) to study the expression pattern of Ods by in situ antibody staining and 3) to investigate the molecular basis of Ods divergence by exon swapping and germline transformation. The correlation between expression in male germ cells and the rapid sequence evolution of the homeodomain will be explored. Speciation can be the result of reproductive isolation. Although that has been an accepted dogma of biology for several decades, little progress has been made in understanding the molecular genetic basis for speciation. The recent studies which have identified several genetic elements responsible for reproductive isolation between two species of Drosophila has resulted in the cloning of one of the suspected responsible genes, Odysseus (Ods). This work will continue the characterization of the Ods gene and collect supporting evidence for its role in speciation.

Nipam H. Patel
Proposal # IOS-0829295
Integrating Evolution, Development, and Genomics (IEDG 2008) Meeting

"Integrating Evolution, Development, and Genomics 2008 (IEDG 2008)" is a graduate student-organized biology meeting to be held at the University of California, Berkeley from May 28-30th, 2008. It will highlight innovative research from diverse branches of biological science, ranging from embryo development to dinosaur paleontology to genomics, with the aim of understanding the mechanisms that have generated the great diversity of life we see on Earth today. The goals of the meeting are to promote collaborations between specialists from different but complementary research fields, encourage the exchange of their creative methods, and communicate a breadth of exciting research to all participants. Seventeen researchers from around the world have been invited to speak at IEDG 2008. Of these, 35% are young scientists, 29% are women, and 23% are from international institutions. Their research interests are diverse and their research subjects include plants, animals, and fungi. The attendees of IEDG 2008 will be limited to 200 graduate students, postdoctoral fellows, and other researchers who will attend talks and participate in formal and informal workshops and fieldtrips. This uniquely intimate meeting format will encourage all participants (especially graduate students and postdoctoral researchers) to learn from one-on-one discussions with other scientists and promote links between traditional and newer fields of biology. Funds from this award will be used, in part, to subsidize travel for graduate student participants. This meeting will also publicize the value of innovative and integrated biological research and the need for its continued progress and expansion.

A major challenge in evolutionary biology is to understand the molecular basis of diversification. This project applies recent advances in comparative genomics, including genome-wide sequence scanning, linkage mapping, and candidate genes, to address the evolution of diverse color patterns in the exuberantly patterned Hawaiian happy face spider. The happy face spider has a balanced genetic color polymorphism for which the mode of inheritance differs between islands in the Hawaiian chain. Accordingly, despite similar sets and frequencies of color forms across islands, the color diversity has arisen independently on different islands. This research will identify the genomic basis for the differences between islands, and hence the mechanism through which color diversity has been recreated.
The research will provide insights into the molecular origins of diversity during evolutionary history and also will produce the first genome sequence and expressed gene data for any spider. The visible and genetically controlled color polymorphism of spiders provides a compelling context for teaching complex concepts in genetics and molecular evolution. Parallel systems to that of the Hawaiian happy face spider occur elsewhere (including California) and will be used to support the development of teaching tools using local spiders in collaboration with an on-going science education project.

1338139
Hosemann

Technical Abstract:

The acquisition of the ORION Nanofab, a Multi-beam (Ga, Ne, He,) Ion Microscope for Nanomaterials Modification and Investigation, will significantly upgrade the capabilities at the University of Californian Berkeley campus and to outside users interested in ion microscopy. The instrument will be housed at a multiuser facility on campus as a multi-user device. The three ion beams Ga, Ne and He will allow for not just high resolution ion imaging but also virtually damage-free nanofabrication and ion patterning while also enabling direct He or Ne implantation studies. This instrument combines fast ion milling using the Ga beam with a precise fine milling utilizing either Ne or the He beam while being usable as helium ion microscope (HIM) for high resolution imaging. The instrument will be used for patterning in polymers, imaging of biomaterials, fabrication of optical antennas, imaging cell structures, modifying grapheme structures, enabling nano-scale heat transfer studies, quantitative characterization of near-field energy transfer, in-situ He implantation, or for the manufacturing of damage-free and site-specific TEM (transmission electron microscopy), APT (atom probe tomography) and nanoscale specimens for further investigation. The device marks a new generation of nanofabrication tools with wide applicability and unprecedented resolution and accuracy. The novelty of this device will also have a substantial impact on teaching at U.C. Berkeley as well as cutting-edge demonstrations for students and outside interested personnel.


Non-Technical Abstract:

This Major Research Instrumentation (MRI) Program grant supports the acquisition of a Multi-beam (Ga, Ne, He,) Microscope for Nanomaterials Modification and Investigation at the University of California at Berkeley. This tool will allow for advanced characterization of nanoscale structures ranging from Biology, Chemistry, Geoscience, Materials Science, Physics and Mechanical, Electrical, Mining and Nuclear Engineering. In addition, the instrument will allow for materials modification at the nanoscale with unprecedented precision and little damage to the material. The instrument utilizes three different beams of ions allowing the user to select the right beam for the right application and material. The instrument has extremely wide applicability and will be installed as a multi-user tool incorporated into a UC Berkeley user center accessible to scientists, engineers and interested personnel nationwide. This instrument marks a new generation of ion beam microscopes and nanofabrication tools allowing for the investigation and modification of matter at the smallest scales. The tool will also be used to demonstrate to the general public cutting-edge applications of nanoscale science and technology using a "seeing is believing" approach. This instrument will also have be used in teaching to students in the areas mentioned above by incorporation of real life examples and demonstrations.

Most animals, including humans, display an obvious organization of specific body parts and organs along the anterior to posterior axis (A-P axis, head to toe for humans), and over the past several decades scientists have discovered a set of genes, known as homeotic genes, which control the placement of organs and appendages along the A-P axis. While these genes were first discovered in fruit flies, they were subsequently identified in all animals and found to play a common role in controlling the development of such varied species as flies, mice, humans, and worms. While the overall functions of these genes are well conserved, changes in where and when these genes are activated can create remarkable changes in body organization. The aim of this research is to understand the role that these genes have played in the evolutionary processes that have generated animal biodiversity. To do this, the investigators will focus on a group of animals that shows the greatest diversity in the organization of their appendages, the crustaceans, which include shrimp, crabs, lobsters, and an emerging model system called Parhyale. Using modern genetic approaches, the investigators will determine the specific roles of individual homeotic genes in Parhyale, and then use comparative methods to determine if changes in the patterns of homeotic gene expression are responsible for the differences between appendage organization in the various species. The research is expected to reveal the specific types of developmental and evolutionary changes that can be mediated by these genes. This research will train students in the laboratory and will be used to illustrate evolutionary principles to K-12 students and local community college students. Broader outreach to the general public will include public lectures and media presentations.

A major goal in biology is to understand the biological basis of traits that mediate an organism's interactions with its environment. Color mediates organismal success in diverse ways, including camouflage and signaling to other organisms. While pigments such as melanin are one familiar source of coloration, many organisms also employ structural coloration. Structural color is caused by interference of light as it interacts with nanometer-sized physical structures near the surface of an organism. Organisms use structural mechanisms to display colors for which they lack pigments (frequently blue) or to create optical effects like iridescence. Structural coloration is a pervasive and adaptive phenomenon, and is highly relevant for the bio-inspired synthesis of optical materials and devices. This project investigates the biological basis of structural color (e.g. how genes and developmental processes sculpt the underlying nanostructures, as well as how the shapes of nanostructures evolve). The researchers are also involved in outreach to K-12 teachers in rural Nevada.

This study will focus on a single species, the Buckeye butterfly, to explore the biological basis of blue structural color. Although wild buckeyes are predominantly brown, a population that was artificially selected to be a pronounced blue, through structural mechanisms, is recently available. In this study, blue and brown buckeyes will be interbred to generate variably colored offspring. These progeny will be statistically analyzed to correlate extent of blueness with the genetic information carried by each individual, thus identifying genetic loci that regulate structural color. This study will also analyze the nanostructures of six related species to track the evolution of structural color within a phylogenetic context.