Nantucket Shellfish Management Plan

Nantucket’s shellfisheries are significant both locally and nationally. Locally, commercial and recreational shellfishing are critical to the Island’s history, culture, and economy. Nationally, the Island’s largest commercial shellfishery — the Nantucket bay scallop fishery is one of the last wild-harvest bay scallop fisheries in the country, but there is growing concern over the health of the overall population and the sustainability of the fishery. Given the importance of the shellfisheries on Nantucket and the drastic decline of bay scallop populations elsewhere along the Atlantic coast, there is a compelling interest in ensuring that the Town’s shellfish are managed to sustain both the shellfishing industry and the resources. This is the first official management plan for commercially and recreationally harvested shellfish in Nantucket waters. The Plan addresses bay scallops, quahogs, oysters, mussels, soft‐shell clams, and conchs

From nanoliter to large-scale bioreactors: How integrated technologies bring antibody treatments to patients faster

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The Potential and Challenges of Nanopore Sequencing

A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of ‘third generation’ instruments that will sequence a diploid mammalian genome for ~$1,000 in ~24 h.Molecular and Cellular BiologyPhysic

Genotyping by nanopore force spectroscopy : method development and evaluation for clinical diagnostics

Clinical diagnostic genotyping has the potential to predict an individual’s response to a prescribed drug, and could thus dramatically improve drug efficacy and reduce adverse drug interactions. However, widespread implementation of clinical diagnostic genotyping is currently prevented by a lack of fast, simple clinical genotyping platforms. This thesis describes the development of a new genotyping technique based on nanopore force spectroscopy (NFS) which may fulfill this need, and serves as a feasibility study for further development towards a commercial instrument. The thesis begins by describing NFS, which is a novel, general technique used to detect bio-molecules and characterize their physical interactions with one another. NFS is applied to base-calling by forming a duplex between an engineered single-stranded DNA probe and a DNA sample, and then measuring the dissociation rate under an applied force. The dissociation rate is shown to be extremely sensitive to duplex sequence homology: tests using purified synthetic DNA fourteen bases long demonstrate that even a single base mismatch can increase the dissociation rate over 100-fold. This high specificity, combined with the sensitivity of nanopore detection, allows a base-call to be made from as few as 100 single molecule dissociation events involving the target. Based on these results, it is estimated that with further development, NFS genotyping could be possible from purified, unlabeled genomic DNA in less than 1 hour, without requiring PCR amplification. These characteristics would make NFS extremely attractive as a clinical diagnostic genotyping technology. Further development is still required to produce an instrument capable of testing genomic DNA. However, based on the success of tests so far, this thesis concludes that further development of such an instrument is clearly warranted, especially given its potential impact on human health.Medicine, Faculty ofBiochemistry and Molecular Biology, Department ofGraduat

Long Dwell-Time Passage of DNA through Nanometer-Scale Pores: Kinetics and Sequence Dependence of Motion

A detailed understanding of the kinetics of DNA motion though nanometer-scale pores is important for the successful development of many of the proposed next-generation rapid DNA sequencing and analysis methods. Many of these approaches require DNA motion through nanopores to be slowed by several orders of magnitude from its native translocation velocity so that the translocation times for individual nucleotides fall within practical timescales for detection. With the increased dwell time of DNA in the pore, DNA-pore interactions begin to play an increasingly important role in translocation kinetics. In previous work, we and others observed that when the DNA dwell time in the pore is substantial (>1 ms), DNA motion in α-hemolysin (α-HL) pores leads to nonexponential kinetics in the escape of DNA out of the pore. Here we show that a three-state model for DNA escape, involving stochastic binding interactions of DNA with the pore, accurately reproduces the experimental data. In addition, we investigate the sequence dependence of the DNA escape process and show that the interaction strength of adenine with α-HL is substantially lower relative to cytosine. Our results indicate a difference in the process by which DNA moves through an α-HL nanopore when the motion is fast (microsecond timescale) as compared with when it is slow (millisecond timescale) and strongly influenced by DNA-pore interactions of the kind reported here. We also show the ability of wild-type α-HL to detect and distinguish between 5-methylcytosine and cytosine based on differences in the absolute ionic current through the pore in the presence of these two nucleotides. The results we present here regarding sequence-dependent (and dwell-time-dependent) DNA-pore interaction kinetics will have important implications for the design of methods for DNA analysis through reduced-velocity motion in nanopores

Teaching the Environmental Humanities: International Perspectives and Practices

This article provides the first international overview and detailed discussion of teaching in the environmental humanities (EH). It is divided into three parts. The first offers a series of regional overviews: where, when, and how EH teaching is taking place. This part highlights some key regional variability in the uptake of teaching in this area, emphasizing important differences in cultural and pedagogical contexts. The second part is a critical engagement with some of the key challenges and opportunities that are emerging in EH teaching, centering on how the field is being defined, shared concepts and ideas, interdisciplinary pedagogies, and the centrality of experimental and public-facing approaches to teaching. The final part of the article offers six brief summaries of experimental pedagogies from our authorship team that aim to give a concrete sense of EH teaching in practice.publishedVersio