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Massachusetts Institute of Technology Department of Biology

Overview
Works: 171 works in 180 publications in 1 language and 215 library holdings
Genres: Bibliography  Periodicals  Abstracts 
Classifications: QH324.M41,
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Publications about Massachusetts Institute of Technology Publications about Massachusetts Institute of Technology
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Most widely held works about Massachusetts Institute of Technology
 
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Most widely held works by Massachusetts Institute of Technology
A Report for the year ... of the Department of Biology at the Massachusetts Institute of Technology by Massachusetts Institute of Technology ( )
in English and held by 15 WorldCat member libraries worldwide
Fast fundamental transfer processes in aqueous biomolecular systems; abstracts and references, seminar lecture series, spring term, 1960 by Massachusetts Institute of Technology ( Book )
2 editions published in 1960 in English and held by 12 WorldCat member libraries worldwide
Report by Massachusetts Institute of Technology ( Book )
5 editions published in 1983 in English and held by 5 WorldCat member libraries worldwide
Analysis and distribution of integrins in chicken embryos by Lisa Andrea Urry ( )
1 edition published in 1990 in English and held by 3 WorldCat member libraries worldwide
Integrating bioenergetics and foraging behavior : the physiological ecology of larval cod (Gadus morhua) by James Joseph Ruzicka ( Book )
1 edition published in 2004 in English and held by 2 WorldCat member libraries worldwide
(Cont.) Small larvae (5mm) can survive on typical mean Georges Bank prey densities in mildly turbulent conditions. Larger larvae (>6mm) can survive even at high turbulence levels. Simulated alternative foraging strategies predict that when predator-prey contact rates are high, the greatest net energy gain is realized with short pause durations. When predator-prey contact rates are low, larvae should achieve greater net energy gains by remaining at rest for extended periods. Larvae observed foraging in the absence of prey do not change behavior as much as the simulation model predicts, suggesting that they use a prey encounter maximization strategy rather than an energy conservation strategy
Prochlorococcus genetic transformation and genomics of nitrogen metabolism by Andrew Carl Tolonen ( Book )
1 edition published in 2005 in English and held by 2 WorldCat member libraries worldwide
Prochlorococcus, a unicellular cyanobacterium, is the most abundant phytoplankton in the oligotrophic, oceanic gyres where major plant nutrients such as nitrogen (N) and phosphorus (P) are at nanomolar concentrations. Nitrogen availability controls primary productivity in many of these regions. The cellular mechanisms that Prochlorococcus uses to acquire and metabolize nitrogen are thus central to its ecology. One of the goals of this thesis was to investigate how two Prochlorococcus strains responded on a physiological and genetic level to changes in ambient nitrogen. We characterized the N-starvation response of Prochlorococcus MED4 and MIT9313 by quantifying changes in global mRNA expression, chlorophyll fluorescence, and Fv/Fm along a time-series of increasing N starvation. In addition to efficiently scavenging ambient nitrogen, Prochlorococcus strains are hypothesized to niche-partition the water column by utilizing different N sources. We thus studied the global mRNA expression profiles of these two Prochlorococcus strains on different N sources. The recent sequencing of a number of Prochlorococcus genomes has revealed that nearly half of Prochlorococcus genes are of unknown function
Inhibition of IFN-[gamma] promoter function by site-specific methylation by Brendan T Jones ( Book )
1 edition published in 2006 in English and held by 2 WorldCat member libraries worldwide
When they become activated, naive helper T cells are able to polarize into either THI cells or TH2 cells. Development of naive CD4+ T cells into TH1 cells is characterized by the expression of IFN-y and the silencing of IL-4, while development into TH2 cells is characterized by expression of IL-4 and silencing of IFN-y. Naive helper T cells are hypomethylated at the IFN-y proximal promoter and hypermethylated at the contiguous transcribed region. During THI polarization, the promoter remains hypomethylated, while the transcribed region becomes demethylated. During TH2 polarization, the promoter undergoes progressive de novo methylation while the transcribed region remains hypermethylated. Notably, TH2 de novo methylation occurs at different rates at different CpG positions, with methylation occurring fastest at the CpG located at the -53 position relative to the transcription start site. Methylation at this position inhibits c-Jun, ATF2 and CREB binding in vitro. Consistently, the same factors bind to the unmethylated promoter in a TH1 cell line, but not the methylated promoter in a TH2 cell line. Furthermore, methylation of the proximal promoter at the -53 position alone is sufficient to inhibit promoter activity in transient transfection assays
Form, function and flow in the plankton : jet propulsion and filtration by pelagic tunicates by Kelly Rakow Sutherland ( Book )
2 editions published in 2010 in English and held by 2 WorldCat member libraries worldwide
Trade-offs between filtration rate and swimming performance among several salp species with distinct morphologies and swimming styles were compared. Small-scale particle encounter at the salp filtering apparatus was also explored. Observations and experiments were conducted at the Liquid Jungle Lab, off the pacific coast of Panama in January 2006 through 2009. First, time-varying body volume was calculated by digitizing salp outlines from in situ video sequences. The resulting volume flow rates were higher than previous measurements, setting an upper limit on filtration capacity. Though each species possessed a unique combination of body kinematics, normalized filtration rates were comparable across species, with the exception of significantly higher rates in Weelia cylindrica aggregates, suggesting a tendency towards a flow optimum. Secondly, a combination of in situ dye visualization and particle image velocimetry (PIV) measurements were used to describe properties of the jet wake and swimming performance variables including thrust, drag and propulsive efficiency. All species investigated swam via vortex ring propulsion. Though Weelia cylindrica was the fastest swimmer, Pegea confoederata was the most efficient, producing the highest weight-specific thrust and wholecycle propulsive efficiency. Weak swimming performance parameters in Cyclosalpa afinis, including low weight-specific thrust and low propulsive efficiency, may be compensated by comparatively low energetic requirements
Fluorescent dye probe of ionic transport in liposomes by Brian William Tokar ( )
1 edition published in 1976 in English and held by 2 WorldCat member libraries worldwide
Inception by Hugh Blumenfeld ( )
1 edition published in 1980 in English and held by 2 WorldCat member libraries worldwide
Biology and potential biogeochemical impacts of novel predatory flavobacteria by Erin C Banning ( Book )
2 editions published in 2010 in English and held by 2 WorldCat member libraries worldwide
Predatory bacteria are ubiquitous in aquatic environments and may be important players in the ecology and biogeochemistry of microbial communities. Three novel strains belonging to two genera of marine flavobacteria, Olleya and Tenacibaculum, were cultured from coastal sediments and found to be predatory on other bacteria on surfaces. Two published species of the genus Tenacibaculum were also observed to grow by lysis of prey bacteria, raising the possibility that predation may be a widespread lifestyle amongst marine flavobacteria, which are diverse and abundant in a variety of marine environments. The marine flavobacterial clade is known to include species capable of photoheterotrophy, scavenging of polymeric organic substances, pathogenesis on animals, the degradation and lysis of phytoplankton blooms and, now, predation on bacterial communities. Strains from the two genera were found to exhibit divergent prey specificities and growth yields when growing predatorily. Olleya sp. predatory cells accumulated to an order of magnitude greater cell densities than Tenacibaculum sp. cells on equivalent prey cell densities. Experiments were conducted to constrain the potential of the novel isolates to affect prey communities under more environmentally relevant conditions. An investigation of the minimum number of predatory cells needed to generate clearings of prey cells found that the inoculation of individual predatory flavobacteria cells can ultimately result in dense lytic swarms. In some cases, the susceptibility of particular prey species to lysis by a flavobacterial predator was found to vary based on the growth state of the prey cells or the presence of their spent growth media. A novel methodology for the experimental study of biofilms was used to assess the impact of exposure to predatory marine flavobacteria on the release of macronutrients from prey biofilms. The Olleya sp. predator had a stimulative effect on macronutrient release while the Tenacibaculum sp. did not, further suggesting the two groups of predators are adapted to different ecological niches
Biophysical coupling between turbulence, veliger behavior, and larval supply by Heidi L Fuchs ( Book )
1 edition published in 2005 in English and held by 2 WorldCat member libraries worldwide
The goals of this thesis were to quantify the behavior of gastropod larvae (mud snails Ilyanassa obsoleta) in turbulence, and to investigate how that behavior affects larval supply in a turbulent coastal inlet. Gastropod larvae retract their velums and sink rapidly in strong turbulence. Turbulence-induced sinking would be an adaptive behavior if it resulted in increased larval supply and enhanced settlement in suitable coastal habitats. In laboratory experiments, mud snail larvae were found to have three behavioral modes: swimming, hovering, and sinking. The proportion of sinking larvae increased exponentially with the turbulence dissipation rate over a range comparable to turbulence in a tidal inlet, and the mean larval vertical velocity shifted from upward to downward in turbulence resembling energetic nearshore areas. The larval response to turbulence was incorporated in a vertical advection-diffusion model to characterize the effects of this behavior on larval supply and settlement in a tidal channel. Compared to passive larvae, larvae that sink in turbulence have higher near-bed concentrations throughout flood and ebb tides
Meiotic regulation of cyclin-dependent kinases by Matthew P Miller ( Book )
1 edition published in 2013 in English and held by 1 WorldCat member library worldwide
During meiosis, a single round of DNA replication is followed by two consecutive rounds of nuclear divisions called meiosis I and meiosis II. In meiosis I, homologous chromosomes segregate, while sister chromatids remain together. Determining how this unusual chromosome segregation behavior is established is central to understanding germ cell development. Here we show that preventing microtubule-kinetochore interactions during premeiotic S phase and prophase I is essential for establishing the meiosis I chromosome segregation pattern. Premature interactions of kinetochores with microtubules transform meiosis I into a mitosis-like division by disrupting two key meiosis I events: coorientation of sister kinetochores and protection of centromeric cohesin removal from chromosomes. Furthermore we find that restricting outer kinetochore assembly contributes to preventing premature engagement of microtubules with kinetochores. We propose that inhibition of microtubule-kinetochore interactions during premeiotic S phase and prophase I is central to establishing the unique meiosis I chromosome segregation pattern
Flow cytometry quantitation of dopamine receptor D2 loss as a sensitive measure of Huntington's Disease progression in mouse neurons by Zachary R Crook ( )
1 edition published in 2013 in English and held by 1 WorldCat member library worldwide
Mouse models of Huntington's Disease (HD) are often used for testing potential therapeutic compounds. These experiments require substantial investments in time and resources, and have yet to produce any intervention that has made a significant impact on disease progression in the clinic. In evaluating potential therapeutics, there is an unmet need for a rapid, highly quantitative measure of disease progression in the HD mouse model brain. Such an assay would help make preclinical trials more efficient. To address this need, I have developed a novel technique for measuring the progression of transcriptional dysregulation, a phenotype with substantial similarities between mouse models and patients. Specifically, utilizing mice that drive GFP expression under the control of one such dysregulated gene (Drd2), I have improved on previous protocols for the isolation and characterization of adult neurons by flow cytometry. Drd2 is a well-studied marker of a particularly vulnerable population in HD patients, the indirect medium spiny neurons of the striatum. Using this technique, I have demonstrated the ability to accurately and rapidly quantitate Drd2 transcript levels, as measured by Drd2 GFP (D2GFP) fluorescence, in several strains of HD model mice. This D2GFP loss is particularly robust, with sufficient power to allow subtle, statistically significant alterations to be observed with very small cohorts. Furthermore, the introduction of this D2GFP transgene does not alter the classic HD pathology in these mice. Finally, I show that D2GFP dysregulation can be either induced or ameliorated genetically by delivering transgenes via adeno associated viral vectors, and that a small molecule with only subtle transcriptional effects (cystamine) fails to rescue D2GFP loss. I hope that this system can be of great utility in the validation of effective therapeutic interventions for HD
Functional analysis of the histone variant H2A.Z during lineage commitment by Lauren E Surface ( )
1 edition published in 2014 in English and held by 1 WorldCat member library worldwide
remained enigmatic. In this thesis, we dissect the role of H2A.Z during lineage commitment. In particular, we focused on the Polycomb-mediated mono-ubiquitylation of H2A.Z. We found that this modification regulates the differentiation potential of mouse embryonic stem cells (mESCs). Loss of H2A.Z ubiquitylation leads to a disrupted chromatin state and derepression of key developmental regulators in mESCs. Furthermore, we show that H2A.Zub is a crucial component required for regulating canonical Wnt signaling, a key pathway in early embryogenesis. Consistent with hyperactivation of Wnt signaling, ESCs lacking H2A.Zub fail to differentiate into neuronal lineages. Therefore, we suggest that modification of H2A.Z is crucial for the response to stimuli. Using quantitative proteomics, we uncovered a role for H2A.Z ubiquitylation in modulating the protein interaction landscape of H2A.Z. H2A.Zub impacts a specific subset of protein interactions. By investigating several of these differential interactions, we revealed a role for H2A.Zub in regulation of DNA methylation, the deposition of repressive histone modifications, as well as a potential connection between H2A.Zub and DNA damage. Therefore, ubiquitin may serve as a binding platform for subsequent recruitment of chromatin-associated factors. These data suggest a mechanism by which post-translation modification of H2A.Z can allow for rapid changes in cell state in a context dependent manner. On a broader level, our work contributes mechanistic insights into the essential requirement of H2A.Z across eukaryotes. Collectively, this work sets the stage for understanding how post-translation modifications can contribute to further specialization of H2A.Z in a context-dependent manner
Theses submitted to the Department of Biology during 1963 by Massachusetts Institute of Technology ( Book )
1 edition published in 1963 in English and held by 1 WorldCat member library worldwide
Elucidating the role of effector caspases in immune development using lentiviral RNAi by Christopher P Dillon ( Book )
1 edition published in 2006 in English and held by 1 WorldCat member library worldwide
Caspases play an important role in apoptosis, or programmed cell death. In particular, three highly related effector caspases, caspases-3, -6, and -7, translate upstream death signals into the physical manifestations of apoptosis by proteolytically cleaving structural and enzymatic targets. However, it is not clear what specific role each individual caspase plays in apoptosis or whether interaction between them is important. We used RNA interference (RNAi) to examine their roles in immune cells. RNAi has revolutionized the field of mammalian genetics by expediting the interrogation of gene function. Endogenous genes are targeted for silencing by the introduction of double stranded RNAs, known as short interfering RNAs (siRNAs), through a mechanism that is well conserved across many species. While this technique has been used successfully in tissue culture experiments, our studies focused on extending the use of RNAi into immune cells. Our initial experiments demonstrated that primary T cells were capable of RNAi-based gene silencing, but were difficult to introduce siRNAs into. Therefore, more robust techniques for the stable and efficient introduction of siRNAs into primary immune cells and animal models were required
Annual report ( )
in English and held by 1 WorldCat member library worldwide
Oscillatory behaviour in cellular control processes; final report, by Brian C. Goodwin by Massachusetts Institute of Technology ( Book )
1 edition published in 1964 in English and held by 1 WorldCat member library worldwide
Research summaries, biographies and recent publications of the faculty ( )
in English and held by 1 WorldCat member library worldwide
 
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English (49)