Direct Support of Research
The Foundation provides support in selected areas or sub-areas of research that are of scientific significance and
where its support can make a difference. This usually means that there are no major government funders when Sloan support begins.
Areas in this program include the indoor environment, molecular evolution, theoretical neurobiology, computational molecular biology,
astrophysics (Sloan Sky Survey), limits to knowledge (The Known, Unknown, Unknowable), and marine science
(Census of Marine Life).
Indoor Environment
Paula J. Olsiewski, Program Director
The goal of this program is to understand the human indoor environment at the microbial level. We believe that this understanding may ultimately help us make this artificial environment more hospitable to human life or resistant to biological attacks.
Our plan has three parts. First, we want to establish a basic understanding of the indoor microbial environment. Second, we want to help develop tools for understanding and probing the indoor environment. And lastly, we want to apply the knowledge and tools to various human indoor environments, such as hospitals.
Very little is known about what microbes exist in the air. The little that is known is based on the ability of scientists to get the microorganisms to grow in the laboratory. But the vast majority (>90%) cannot be grown in the laboratory and bacteria lack morphologically distinct characteristics that allow species to be differentiated visually. Because of this, microorganisms are the least well understood groups of species on the planet, especially outside the human body. But they matter enormously.
We have made a number of important grants in this area. Our first ($2.5MM in the fall of 2004) was to the J. Craig Venter Institute to study the genome of indoor and outdoor air samples from a NYC skyscraper. While that work will provide important new information about the microbial world, the method used in this work, DNA sequencing is still very expensive and we need to find other approaches. In October 2005 we awarded $385,000 to support a project at Rockefeller University to design and examine new growth media to culture bacteria that were known to be living or viable but could not be grown using conventional growth media and conditions. In December 2005 we awarded $1.152MM to the University of Colorado at Boulder to start examining and cataloging the indoor microbial world using highly conserved ribosomal RNA (rRNA), the genetic information used to construct a universal phylogenetic tree. The resulting inventory of micro-organisms in our daily environment will provide an essential baseline reference.
We are open to other methods for exploration. In 2007, we provided a grant to the University of South Carolina to examine the microbial world of occupied and unoccupied schoolrooms using proteomics. This work will generate a catalog of microbes based on protein sequence information.
We are interested in understanding how the built environment influences the indoor microbial world. In December 2007, we awarded a grant to Yale University to explore the microbial ecology of the built environment. The Yale researchers are collaborating with environment engineers at the Unversity of California at Berkeley and the work will integrate physical aerosol processes with molecular biology-based tools to describe the dynamics and sources of biological aerosols in indoor environments.
In March 2007, we awarded a grant to the Marine Biological Laboratory to develop a novel combinatorial technology for imaging and distinguishing between members of a microbial community. If this project is successful, it will provide new tools to visualize the microbial world and the capabilities to assess relative abundance, organization, and function of particular microbes. In June 2007, we awarded another grant to the Marine Biological Laboratory to develop a prototype tool for describing and comparing microbial communities, VAMPS, Visualization and Analysis of Microbial Population Structures (http://vamps.mbl.edu/). The VAMPS tools will allow microbial ecologists to integrate population structure information with geochemical, physical, and other contextual data at sites of interest.
Exploring the indoor microbial world has been challenging. Several of our grantees are collecting air samples – which turns out to be really difficult – using techniques to deposit the microbes into aqueous media and then extracting and analyzing the genetic material from the samples. The preliminary results are promising, but the microbes are broken up and the results reveal what genes are in the sample. These “metagenomic” studies are identifying previously unknown genes, but it is not yet possible to assemble the DNA sequence data into complete genomes. Another issue that arises from analyzing samples of cells rather than individual cells is that we don’t know if the DNA was from dead microbes floating by or from microbes that are alive, either living in the room/building or else passing on the way to an environment where they can grow. And, since air, unlike water, is merely a transport medium, not a growth medium, we need to start sampling other places in the indoor environment. It would be a real breakthrough if we could collect samples from many different locations, separate the individual cells, and then analyze each cellIn May 2007, we awarded a grant to the University of Illinois at Chicago to develop a microfluidic sieve to isolate and analyze individual microbes. In September 2007, we sponsored a workshop at the Bigelow Laboratory for Ocean Sciences: Single Cell Alternatives to Metagenomics in Environmental Microbiology, http://www.bigelow.org/ssg/. The purpose of the workshop was two –fold: 1. gather representatives from the different groups who are developing and applying microbial single cell genomics methodology, exchange information, and thereby enable the field to make faster progress and 2. examine the dominant science questions that are best addressed by this powerful new tool. Later in 2007, we awarded a grant to the J, Craig Venter Institute to study microbial genomics in hospital and office environments using the first robotic pipeline dedicated to high throughput DNA amplification from single cells. We expect that this ambitious project will generate numerous key insights into the indoor microbial world. It will generate an in-depth understanding of the taxonomic composition of microbial communities found in four important indoor environments: office air, office surfaces, hospital air and hospital surfaces. The project will also provide for the first time, a detailed understanding of the individual microbes that have previously been identified only by their taxonomy from ribosomal RNA analysis. Single cell analysis will reveal population members and the distribution of virulence factors, antibiotic resistance, and other important functional genes within each of the key environments. Our expectation is that the technology will be broadly applicable to microbial studies of natural environments (e.g., water, air, soil), manmade environments (e.g., indoor air and surfaces) and clinical samples (e.g., human GI or respiratory tracts), and could usher in a new era in microbial research.
Theoretical Neurobiology
Paula J. Olsiewski, Program Director
The foundation is no longer funding new work in this area. The goal of this program was to accelerate the development of theory in neurobiology. The plan had been to bring young theoreticians from the physical, mathematical and computer sciences into neurobiology. Major grants in 1994 supported creation of five research centers in theoretical neurobiology at Brandeis University, California Institute of Technology, New York University, Salk Institute, and University of California, San Francisco. The young scientists, pre-docs, post-docs, and in a few cases new assistant professors, learned experimental methods and worked with senior neurobiologists. The program attracted strong participants and new scientific results have been emerging. Across the Centers scientific themes are appearing including topics such as gain fields and gain control in nerve circuits, neural coding and information theory, neural population coding and response, natural scene analysis, and short-term memory. Those that have completed post-doc appointments - 59 in all - are finding positions in neuroscience departments including Baylor, Carnegie Mellon, University of Washington, Cold Spring Harbor, Irvine, UCLA, Rutgers, University of Pennsylvania, Georgetown, UCSF and many others. There are still others in the pipeline so that the total number of new theoreticians coming into the field in the next three years will be over 90 plus an additional number of new Ph.D.s who will move into post-doc positions.
The Centers received three-year renewal grants in 1997. In 2000 the Centers' funding was renewed again by the Sloan Foundation, this time joined by the Swartz Foundation (see www.theswartzfoundation.org for further information on the program of the Swartz Foundation).In addition to support of the Centers, the Foundation also supported summer meetings of the Centers which have included guest speakers from various subfields of the neurosciences and theoreticians. Workshops on some of the topics listed above have also been funded. Although Sloan Center funding has been completed in 2003, the Foundation may continue to give workshop grants from time to time. The Swartz Foundation has begun its own program of support of the Centers.
For further information on the activities at each of the Centers:
Salk InstituteComputational Molecular Biology
Brandeis
Caltech
NYU
UCSF
Michael Teitelbaum, Vice President
The goal of this program was to produce scientists who can link the powerful theoretical and practical tools of molecular biology with the power of modern computational techniques. In a joint program initiated in 1995 with the U.S. Department of Energy, up to ten two-year postdoctoral awards were made each year to facilitate the transition of young mathematicians, physicists, and other quantitative scientists into computational molecular biology. The final awards in this program were made in 2003. Since 2000, support has been provided for the development of new professional science master's degrees in bioinformatics/computational molecular biology. (For additional information, click here: Professional Master's Degrees in Bioinformatics/Computational Molecular Biology.)
Hiring Patterns Experienced by Students Enrolled in Bioinformatics/Computational Biology Programs
Sloan
Digital Sky Survey (SDSS)
Hirsh G. Cohen, Consultant
The goal of this project is to understand the evolution and structure of the universe by providing the largest uniform, detailed archive of objects in the skies that has ever existed. The original plan to build and operate a specially designed telescope and conduct a five-year observation period is now close to completion. The success of that phase has led to a three-year extension. Funding for this final phase was supplied by the Sloan Foundation, the National Science Foundation, and the collaborating universities. The Sloan Foundation has now contributed a total of $25.4million to SDSS. The Astrophysical Research Consortium, a group of universities and national labs, has carried out the work.
The Survey archive has now recorded the spectra of close to one million galaxies and 100,000 quasars located in three-dimensional space. There are also image data on over 25 million galaxies with preliminary spectral data. This vast collection of data is providing an increasingly accurate picture of the structure of the universe, one of the original scientific objectives of SDSS. The Survey, together with the Wilkinson Cosmic Microwave experiment, corroborated the presence of a new force in the universe, dark energy. In addition it has shown that only 30% of the universe is matter; the rest is dark energy. The survey has also established (1) that the universe is flat (non-zero curvature would imply eventual recollapse or infinite expansion) and (2) that the inflationary version of the Big Bang, which predicts zero curvature, best fits the data. Further information on these and other scientific findings will be found at the SDSS website (www.SDSS.org).
Large releases of the Survey’s data to the astronomical and general public have been made in several forms so that both professional astronomers and amateurs can download from the internet. A fifth release of data will be made in the summer of 2006. This large volume of data, the largest ever made available, can be reached at several web sites whose addresses can be found on the SDSS web site.
The Known,
Unknown, and Unknowable
Jesse H. Ausubel, Program
Director
The goal of this program is the exploration of what is known, unknown,
and unknowable in a variety of fields. It is very valuable to know what
you do not know and why. Research has been funded on limits to knowledge
in a broad spectrum of academic areas. Grants have supported such studies
in plant molecular biology and genetics, ecology, computational economics,
history of science, and prehistoric linguistics. Some of the work was
summarized at an October 2000 conference at Columbia University. (for
details, see http://www1.cs.columbia.edu/~traub.sloan/)
A project begun in 2002 addresses predictability of weather and climate.
We seek during 2003 to add to the viewpoint of producers of knowledge
the viewpoint of consumers. We would like to explore limits to knowledge
in fields with obvious practical implications, such as health or finance,
where it is important for knowledge consumers, such as regulators or investors,
to know what you can or cannot know about therapies or market movements.
Proposals should be organized around conferences
involving both producers and consumers of knowledge.
An Essay by Ralph E.
Gomory, from Scientific American, June 1995
Census of
Marine Life
Jesse H. Ausubel, Program
Director
The goal of this project is to advance a major new international observational
program to be completed by 2010 to assess and explain the diversity, distribution,
and abundance of marine life. During 1997-1998 our plan was to understand
the technical and institutional feasibility of a marine census. Favorable
technical and institutional signals led us during 1999 to adopt the ambitious
goal of trying to make the Census happen. An international Scientific
Steering Committee and Secretariat based at the Consortium for Oceanographic
Research and Education in Washington DC now guide the program. Grant-making
occurs in conjunction with the National Ocean Partnership Program. One
round of grants focused on creation of the Ocean Biogeographical Information
System (OBIS), the framework for assimilation of data for the Census.
In addition, support has been provided to plan initial field projects
and to develop information on the history of marine animal populations.
A periodic newsletter www.coreocean.org
reports "What's New" with the Census.
During 2006 we plan to continue to support the institutional framework
for the Census. We will also consider efforts to address particular,
indispensable scientific needs on which the success of the Census will
rest. Also, we seek opportunities to work with the institutions and
media that can build public interest and with maritime industries and
environmentalists to assure their meaningful participation.
The
Census of Marine Life website.