Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.21
Invited Talk
Center for Earth Observations and Applications
Advisory Committee
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
La Jolla, CA
The increase in resolution and taxon sampling of algal phylogenies resulting from the various algal tree of life projects and other initiatives worldwide opens tremendous opportunity to learn more about the evolution of all aspects of algal biology. Using evolutionary modeling techniques in a phylogenetic context, hypotheses about the evolution of particular traits and their interaction with speciation-extinction dynamics become testable. I will illustrate this with three case studies. First, I will investigate the evolution of the thermal niche of seaweeds, showing how it affects latitudinal diversity patterns. Second, I will test the hypothesis that the evolution of cellular trace element requirements (stoichiometry) is dominated by endosymbiosis events. Third, I will investigate the evolution of morphological traits typically used in species-level systematics, focusing on its implications for the prevalence of cryptic diversity. These case studies show the potential and limitations of the approach, and offer new insights in algal evolution from the very recent to the very ancient, and across the various subdisciplines of algal biology.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.21
Invited Talk
Center for Earth Observations and Applications
Advisory Committee
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
La Jolla, CA
The increase in resolution and taxon sampling of algal phylogenies resulting from the various algal tree of life projects and other initiatives worldwide opens tremendous opportunity to learn more about the evolution of all aspects of algal biology. Using evolutionary modeling techniques in a phylogenetic context, hypotheses about the evolution of particular traits and their interaction with speciation-extinction dynamics become testable. I will illustrate this with three case studies. First, I will investigate the evolution of the thermal niche of seaweeds, showing how it affects latitudinal diversity patterns. Second, I will test the hypothesis that the evolution of cellular trace element requirements (stoichiometry) is dominated by endosymbiosis events. Third, I will investigate the evolution of morphological traits typically used in species-level systematics, focusing on its implications for the prevalence of cryptic diversity. These case studies show the potential and limitations of the approach, and offer new insights in algal evolution from the very recent to the very ancient, and across the various subdisciplines of algal biology.
Seminar abstract: I will be talking about two ongoing research projects in my laboratory: (1) evolution of thermal niches in seaweeds, (2) biodiversity of endolithic algae in coral skeletons and its relationship with the environment. Using evolutionary models in an explicit phylogenetic framework, patterns of evolution in environmental traits such as the sea surface temperature (SST) affinities of species can be studied. Based on case studies in the green algae Codium and Halimeda, it is shown that lineages behave differently when it comes to their evolution of SST affinities, and that there is a strong correlation between the evolution of SST affinities and rates of species diversification. For the second part of the talk, I will focus on our recent work on environmental sequencing of coral skeletons. These feature unexpectedly high biodiversity of limestone-boring algae as well as many unknown inhabitants. Our first results indicate that the diversity of algal endoliths may be linked to environmental conditions, but this hypothesis needs further testing.
Sleeping Beauty Transposon: Awakening a new approach to cancer treatmentJulie Kendrick
13 million years in the making, Perry Hackett’s Sleeping Beauty transposon has far-reaching implications for identifying causes of disease, use in gene therapy and more. His Sleeping Beauty (SB) transposon, reconstructed from a fish DNA sequence that went extinct 13 million years ago, proved to be a gamechanger in non-viral cancer gene therapy.
Research done by Mahendra Trivedi - Effect of a Biofield Treatment on Plant G...Abby Keif
Research on Trivedi Effect - The present experiments found an enhanced and significant impact of the biofield treatment on adaptive micropropagation response and callus induction of two plant species, Withania somnifera and Amaranthus dubius. For details, visit: http://works.bepress.com/mahendra_trivedi/23/
Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analys...Larry Smarr
06.04.26
Invited Talk
CONNECT Board Meeting
Title: Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)
La Jolla, CA
Mapping the Human Gut Microbiome in Health and Disease Using Sequencing, Supe...Larry Smarr
Invited Talk Delivered by Mehrdad Yazdani, Calit2 Ayasdi Sponsored Lunch & Learn American Society of Human Genetics (ASHG) San Diego Convention Center October 19, 2014
The Microbiome: Sorting the Hype from the Hope DrBonnie360
Content and Visual Design by Tiffany Simms
Cambridge Healthtech Institute's 23rd International Molecular-Med Tri-Con presents a short course on the Microbiome.
DrBonnie360 brings together two rising stars of the Sonnenburg Lab and the Knight Lab, and four microbiome companies, Second Genome, Osel Inc, AOBiome, and WholeBiome, to discuss the importance of the microbiome and how we can harness its power.
The course took place Sunday, March 6, 2016 in San Francisco.
Last spring, University of Minnesota undergrads formed a team to participate in iGEM, an international competition to design and develop modular molecular building blocks known as BioBricks and assemble them to create microorganism-based systems for manufacturing useful products. Here's what happened.
Seminar abstract: I will be talking about two ongoing research projects in my laboratory: (1) evolution of thermal niches in seaweeds, (2) biodiversity of endolithic algae in coral skeletons and its relationship with the environment. Using evolutionary models in an explicit phylogenetic framework, patterns of evolution in environmental traits such as the sea surface temperature (SST) affinities of species can be studied. Based on case studies in the green algae Codium and Halimeda, it is shown that lineages behave differently when it comes to their evolution of SST affinities, and that there is a strong correlation between the evolution of SST affinities and rates of species diversification. For the second part of the talk, I will focus on our recent work on environmental sequencing of coral skeletons. These feature unexpectedly high biodiversity of limestone-boring algae as well as many unknown inhabitants. Our first results indicate that the diversity of algal endoliths may be linked to environmental conditions, but this hypothesis needs further testing.
Sleeping Beauty Transposon: Awakening a new approach to cancer treatmentJulie Kendrick
13 million years in the making, Perry Hackett’s Sleeping Beauty transposon has far-reaching implications for identifying causes of disease, use in gene therapy and more. His Sleeping Beauty (SB) transposon, reconstructed from a fish DNA sequence that went extinct 13 million years ago, proved to be a gamechanger in non-viral cancer gene therapy.
Research done by Mahendra Trivedi - Effect of a Biofield Treatment on Plant G...Abby Keif
Research on Trivedi Effect - The present experiments found an enhanced and significant impact of the biofield treatment on adaptive micropropagation response and callus induction of two plant species, Withania somnifera and Amaranthus dubius. For details, visit: http://works.bepress.com/mahendra_trivedi/23/
Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analys...Larry Smarr
06.04.26
Invited Talk
CONNECT Board Meeting
Title: Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)
La Jolla, CA
Mapping the Human Gut Microbiome in Health and Disease Using Sequencing, Supe...Larry Smarr
Invited Talk Delivered by Mehrdad Yazdani, Calit2 Ayasdi Sponsored Lunch & Learn American Society of Human Genetics (ASHG) San Diego Convention Center October 19, 2014
The Microbiome: Sorting the Hype from the Hope DrBonnie360
Content and Visual Design by Tiffany Simms
Cambridge Healthtech Institute's 23rd International Molecular-Med Tri-Con presents a short course on the Microbiome.
DrBonnie360 brings together two rising stars of the Sonnenburg Lab and the Knight Lab, and four microbiome companies, Second Genome, Osel Inc, AOBiome, and WholeBiome, to discuss the importance of the microbiome and how we can harness its power.
The course took place Sunday, March 6, 2016 in San Francisco.
Last spring, University of Minnesota undergrads formed a team to participate in iGEM, an international competition to design and develop modular molecular building blocks known as BioBricks and assemble them to create microorganism-based systems for manufacturing useful products. Here's what happened.
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
07.06.07
Director's Colloquium
Los Alamos National Laboratory
Title: Using Supercomputers and Supernetworks to Explore the Ocean of Life
Los Alamos, NM
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
Synthetic biology is the designing of new biological systems or the modification of the existing ones that do not occur naturally. Synthetic or artificial cells organisms with minimal genomes have uses in molecular medicine, vaccines, environmental chemistry and bio-sensors. Creation of synthetic cells involve in-vitro synthesis of unitary DNA fragments of one-kilo base pairs (1kb). These unitary fragments are ligated to make ten kilo base pair (10kb) fragments, followed by tethering 10 fragments to form one hundred kilo base pair (100kb) fragments. Each step involves transformation and sequencing procedures in E. coli host cells. Ultimately, eleven of these hundred kilo base pair fragments are joined to create a “Synthetic Genome” which is maintained in yeast cells, as maximum limit of DNA transplant acceptance of E. coli is 100kb. By this approach, synthetic chromosomes can be maintained, manipulated and transplanted to an acceptor organism to create a synthetic cell. Applications of the technology include semi-synthetic approach of Artemisinic acid, which can be used to chemically synthesize anti-malarial drug Atremisinin and its therapeutically important derivatives. Second application of synthetic biology is production of meningitis vaccine against poorly immunogenic Neisseria meningitidis serogroup-B, by preparing synthetic vesicles. Third application includes disease mechanism identification of a rare-primary immunodeficiency disease “Agamaglobinemia” using reconstruction of mutant B-cell receptor components in synthetic membranes to validate a point mutation. Fourth application include environmental fixation of carbon di-oxide to produce methane by using minimal genome containing synthetic cells of Metahnococcous sp. Fifth application is production of novel biosensors which can be toggled ON and OFF using “Visible Light” as modulator. These “Gene switches” are also able to operate in mammalian cells. With potential applications and wide research domains, synthetic biology is also under ethical and religious criticism. Future of this new dimension of biological science requires scrutiny from regulatory authorities, and monetary input from funding agencies.
1. Characterizing microbiological gradients within an in-vessel aerobic composter
Partnering the Research First Initiative with ILSE
STME2903-03 Students: Alyssa Bellomo1
, Bruce Galdos2
, Anastasia Giordano1
, Victor Suarez1
and Linda Yarfi2
with Suzanne Kupiec3
, Raul Cano4
, John Pace4
and Marshall Hayes1
1
New Jersey Center for Science Technology & Mathematics (NJCSTM), Kean University, 1000 Morris Ave., NJ 07083
2
College of Natural, Applied and Health Sciences, Kean University, 1000 Morris Ave., NJ 07083
3
Food Scraps Composting Laboratory, Kean University, 1000 Morris Ave., NJ 07083
4
ATCC Center for Translational Microbiology, 1000 Morris Ave., NJ 07083
From L to R: Bruce, Victor, Anastasia (Stacey), Alyssa and Linda
Enabled by a collaboration between the NJCSTM and
the ILSE-sponsored ATCC Center for Translational
Microbiology (CTM), Kean undergraduates enrolled in
STME 2903-03, the Microbes and Microbiomes stream
of the Research First Initiative, are using both culture-
based and high-throughput sequencing approaches to
assess the diversity and composition of the bacterial
community within our campus in-vessel aerobic
composter. The goal of this research experience is to
understand compost production as a vital component of
campus waste handling and an essential strategy for
realizing sustainability initiatives in general.
Our Research GroupThe Opportunity
Since 2010, Kean has operated a composter capable of
processing ~1000 lbs. of pre- and post-consumer food
scraps per day. This facility is the cornerstone of an
innovative farm-to-table-to-farm model for managing
campus waste. The FSCL is located in close proximity to
several campus eateries such as the Cougars’ Den (Fig.
A). In 5 days, mixtures of food scraps (Fig. B) and wood
shavings are converted within the vessel (Fig. C) into
rich compost (Fig. D). Our research group has made
initial strides in characterizing the microbial dynamics
of the composting process and other factors that may
influence the optimal functioning of our campus facility.
The Food Scraps Composting Lab (FSCL)
Preliminary Results Research Activities
• Sanger sequencing of select thermophilic (>50 °C) bacteria isolated from fresh compost
• 16S rRNA gene sequencing of compost DNA using the CTM’s Illumina MiSeq platform
Acknowledgements
We thank: Dean Bostian and Dean Tocci for implementing the RFI; Nan Perigo, Judy April, Marianne Gass, Michele Smalls and Noemy Gaitan for providing logistical
support from the NJCSTM; and Jess Schuyler and Ron McMillan for offering technical assistance from the ATCC-CTM. We are also indebted to the entire staff of the
FSCL: Head Compost Technician Farzan Ahmed; Student workers Steve Mondelus, Raisa Mateo, Naomi Horowitz and Nicholas Allen; and Student intern Malcolm Edeen.
• Kean compost supports ~106
bacterial colony-forming units per gram of compost.
• Selective and differential culture indicates that Gram-negative spp. comprise ~10% of the
community, and ~10% of this Gram-negative population are lactose fermenters.
• Absolute bacterial numbers are highly variable (50-80%) from experiment to experiment.
• Tetracycline-resistant bacteria are present and viable in compost.
A. B. C. D.