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Massachusetts Institute of Technology Department of Biology

Works: 281 works in 290 publications in 1 language and 327 library holdings
Genres: Bibliography  Periodicals  Abstracts 
Classifications: QH324.M41,
Publication Timeline
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 13 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

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
Inhibition of IFN-[gamma] promoter function by site-specific methylation by Brendan T Jones( )

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
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
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
Inception by Hugh Blumenfeld( )

1 edition published in 1980 in English and held by 2 WorldCat member libraries worldwide

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

Side chain mobility and hydration in homeodomain-DNA recognition by Ernest Samuel Benjamin Fraenkel( Book )

1 edition published in 1998 in English and held by 1 WorldCat member library worldwide

Discovery and biochemical characterization of RNA interference in budding yeast by David E Weinberg( )

1 edition published in 2013 in English and held by 1 WorldCat member library worldwide

RNA interference (RNAi) is a eukaryotic pathway for the post-transcriptional regulation of gene expression. In the simplest form of RNAi, a double-stranded RNA (dsRNA) trigger is converted into small-RNA duplexes by the Dicer enzyme. These duplexes are then loaded into the effector protein Argonaute to guide the cleavage of target transcripts. RNAi and related RNA-silencing pathways are found in plants, animals, fungi, and protists, suggesting origins in an early eukaryotic ancestor and selective pressures to maintain the pathway. A prominent exception to this widespread conservation of RNAi is the budding yeast Saccharomyces cerevisiae, which lacks homologs of Dicer and Argonaute. Indeed, RNAi had been presumed lost in all budding yeasts. Motivated by the presence of Argonaute homologs in some budding-yeast species, we examined whether these species contain a functional RNAi pathway. High-throughput sequencing led to the identification of endogenous small RNAs that are generated by a novel Dicer enzyme. In Saccharomyces castellii, these Argonaute-bound small RNAs serve as guides to repress mRNA targets, which are predominantly repetitive elements. RNAi can be restored to S. cerevisiae by introducing the genes encoding S. castellii Dicer and Argonaute, and the reconstituted pathway silences endogenous transposons. Budding-yeast Dicer has a different domain architecture than canonical Dicer yet generates siRNAs of a similar length. In contrast to canonical Dicer, which successively removes small-RNA duplexes from the dsRNA termini, budding-yeast Dicer molecules bind cooperatively to the interior of dsRNA substrates, with the distance between adjacent active sites determining product length. These distinct mechanisms impart corresponding substrate preferences and product characteristics that are important for Dicer function. Structural studies of budding-yeast Argonaute yielded a crystal structure of the functional Argonaute-guide complex. Eukaryotic Argonaute makes extensive sequence-independent interactions with the guide RNA to maintain the seed region in a helical conformation with the base edges accessible for target binding. An invariant glutamate residue, which is only positioned in the catalytic pocket after guide-RNA binding, constitutes the previously missing component of a ribonuclease H-like active site
An in vivo evaluation of aneuploid hematopoietic stem cell fitness by Sarah Jeanne Pfau( )

1 edition published in 2016 in English and held by 1 WorldCat member library worldwide

Aneuploidy is an unbalanced cell state associated with developmental conditions such as Down syndrome (DS) as well as cancer, a disease of rapid proliferation. Studies of yeast, mouse and human cells harboring one extra chromosome have demonstrated that aneuploid cells show a number of common phenotypes in vitro, notably decreased proliferation. However, the precise role of aneuploidy in cancer has yet to be elucidated, in part due to lack of systematic in vivo model systems. Furthermore, evaluation of aneuploidy-associated phenotypes in vivo has been difficult because autosomal trisomy is generally embryonic lethal in mice. Here, I have evaluated hematopoietic stem cells (HSCs) derived from three aneuploid mouse models in vivo, two models of autosomal trisomy and one model of chromosome instability. By performing hematopoietic reconstitutions, I found that aneuploid HSCs have a range of fitness in vivo that correlates with the amount of extra DNA in each line. My results demonstrate that aneuploidy-associated cellular phenotypes are observed in vivo and in the context of a euploid organism. Additionally, I found that aneuploidy is well tolerated in the hematopoietic lineage under normal conditions in two of the three mouse models analyzed. However, even these relatively fit aneuploid cells begin to show more severe phenotypes upon repeated proliferative challenge. In humans, DS is associated with perturbations in the hematopoietic system, often resulting in childhood leukemia. Trisomy is also frequently observed in non-DS leukemias. Establishment of this model system enables future systematic dissection of the source of aneuploidy-associated fitness defects in vivo both in hematopoiesis and in the context of cancer
Elucidating the role of effector caspases in immune development using lentiviral RNAi by Christopher P Dillon( )

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
Blood coagulation; final report, 6/15/61 to 3/31/61 by Massachusetts Institute of Technology( Book )

1 edition published in 1961 in English and held by 1 WorldCat member library worldwide

Meiotic regulation of cyclin-dependent kinases by Matthew P Miller( )

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
Lipopolysaccharide, K antigen, and other components of the bacterial cell surface important for S. meliloti-alfalfa symbiosis by Gordon R. O Campbell( Book )

1 edition published in 2001 in English and held by 1 WorldCat member library worldwide

Sinorhizobium meliloti can form a symbiotic relationship with alfalfa plants in which the bacteria fix atmospheric nitrogen into ammonia for the plant in exchange for nutrients. During this symbiosis, the bacteria live in organs called nodules that develop in the roots of the plant. This thesis explores a range of bacterial components necessary for an effective symbiosis. One overarching theme to these components is that most of them are involved with the bacterial cell surface. Chapter 2 is a study of the lpsB389 mutant, which codes for a predicted glycosyl transferase involved with LPS core synthesis. Bacteria carrying the lpsB389 mutation are capable of carrying out the first steps of nodule invasion on alfalfa plants. However, they display dramatic abnormalities upon entry into plant cells. In Chapter 3, I identified four new classes of mutants involved in K antigen synthesis. Finally, in Chapters 4 and 5, I made use of the newly sequenced S. meliloti genome to determine the locations of the insertions in 43 mutants identified by having an effect on the cell surf ace. Most of these mutants also have symbiotic defects. Chapter 4 examines a series of mutations that affect either LPS or other factors involved in membrane integrity. In contrast to a previous report, I found·that most of these mutants have symbiotic defects. In addition, this study has identified genes coding for proteins not previously recognized as being involved with the integrity of the cell surface or as being required for symbiosis including: GreA, and a protein with a Sua5/Yci0/YrdC family signature domain. Chapter 5 implicates many new genes and processes in symbiosis including: the vitamin B12 , or cobalamin; QxtA, a predicted terminal oxidase of respiration; a predicted magnesium and cobalt transporter; and the process of carbon fixation. Undoubtedly the genes, factors, and metabolic processes identified in these studies will lead to a greater understanding of the complex interaction between S. meliloti and alfalfa during symbiosis. Furthermore, since S. meliloti is closely related to a number of mammaljan and plant pathogens, these discoveries may also contribute to our understanding of how pathogens infect their hosts
Behavioral responses of invertebrate larvae to water column cues by Jeanette Danielle Wheeler( )

1 edition published in 2016 in English and held by 1 WorldCat member library worldwide

Many benthic marine invertebrates have two-phase life histories, relying on planktonic larval stages for dispersal and exchange of individuals between adult populations. Historically, larvae were considered passive drifters in prevailing ocean currents. More recently, however, the paradigm has shifted toward active larval behavior mediating transport in the water column. Larvae in the plankton encounter a variety of physical, chemical, and biological cues, and their behavioral responses to these cues may directly impact transport, survival, settlement, and successful recruitment. In this thesis, I investigated the effects of turbulence, light, and conspecific adult exudates on larval swimming behavior. I focused on two invertebrate species of distinct morphologies: the purple urchin Arbacia punctulata, which was studied in pre-settlement planktonic stages, and the Eastern oyster Crassostrea virginica, which was studied in the competent-to-settle larval stage. From this work, I developed a conceptual framework within which larval behavior is understood as being driven simultaneously by external environmental cues and by larval age. As no a priori theory for larval behavior is derivable from first principles, it is only through experimental work that we are able to access behaviors and tie them back to specific environmental triggers. In this work, I studied the behavioral responses of larvae at the individual level, but those dynamics are likely playing out at larger scales in the ocean, impacting population connectivity, community structure, and resilience. In this way, my work represents progress in understanding how the ocean environment and larval behavior couple to influence marine ecological processes
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
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English (49)