The distribution of cirripeds and gastropods on plain vertical rock surfaces in the upper intertidal and splash zones

This is a student paper done for a University of California Berkeley Zoology class. Since UCB didn't have its own marine lab at the time, it rented space at Hopkins Marine Station where this work was done. Cadet Hand earned his Ph.D. from Berkeley and went on to become Director of the Bodega Marine Laboratory. Donald Putnam Abbott also earned his Ph.D. from Berkeley and later became a Stanford professor at Hopkins Marine Station. (PDF contains 26 pages)

A Synoptic View of a Coastal Plain Estuary.

During October, 1972 the Patuxent River Estuary was monitored intensively and synoptically over two tidal cycles to determine the spatial and temporal patterns of various hydrodynamic, chemical and biological features. Forty-one depths at eleven stations along nine transects were sampled simultaneously at hourly intervals for salinity, temperature, dissolved oxygen, chlorohyll a, particulate nitrogen, nitrate, nitrite, total kjeldahl nitrogen, ammonia, particulate carbohydrate, dissolved organic carbon, total hydrolizable phosphorous, dissolved inorganic phosphorous, suspended sediment, particle size distribution, and zooplankton. Tidal velocity was continuously monitored at each depth by recording current meters. Riverine input and meteorological conditions were relatively stable for two weeks preceeding the deployment. This communication describes the calculation of the intrinsic rates of change of the observed variables from their measured distributions in the Estuary. The steady-state, one-dimensional equation of species continuity is employed to separate the advection and tidal dispersion of a hydrodynamically passive substance frbm its intrinsic rate of change at point. A new spatial transform is introduced for the purpose of interpolation and extrapolation of data.The intrinsic rate of change profiles reveal a region of heavy bloom activity in the upper estuary and a secondary bloom near the point in the River that most of the suspended material settles out. The changes in ammonia and nitrates are highly correlated to the productivity patterns. Phosphorous rates are less closely correlated to productivity. The perturbations that the Chalk Point steam electric power plant have on the heat and oxygen balances are easily discernible.

Temperature-and pH-Sensitive Nanohydrogels of Poly(N-Isopropylacrylamide) for Food Packaging Applications: Modelling the Swelling-Collapse Behaviour

Temperature-sensitive poly(N-isopropylacrylamide) (PNIPA) nanohydrogels were synthesized by nanoemulsion polymerization in water-in-oil systems. Several cross-linking degrees and the incorporation of acrylic acid as comonomer at different concentrations were tested to produce nanohydrogels with a wide range of properties. The physicochemical properties of PNIPA nanohydrogels, and their relationship with the swelling-collapse behaviour, were studied to evaluate the suitability of PNIPA nanoparticles as smart delivery systems (for active packaging). The swelling-collapse transition was analyzed by the change in the optical properties of PNIPA nanohydrogels using ultraviolet-visible spectroscopy. The thermodynamic parameters associated with the nanohydrogels collapse were calculated using a mathematical approach based on the van't Hoff analysis, assuming a two-state equilibrium (swollen to collapsed). A mathematical model is proposed to predict both the thermally induced collapse, and the collapse induced by the simultaneous action of two factors (temperature and pH, or temperature and organic solvent concentration). Finally, van't Hoff analysis was compared with differential scanning calorimetry. The results obtained allow us to solve the problem of determining the molecular weight of the structural repeating unit in cross-linked NIPA polymers, which, as we show, can be estimated from the ratio of the molar heat capacity (obtained from the van't Hoff analysis) to the specific heat capacity (obtained from calorimetric measurements).

On the contact width in generalized plain strain JKR model for isotropic solids

Adhesive contact model between an elastic cylinder and an elastic half space is studied in the present paper, in which an external pulling force is acted on the above cylinder with an arbitrary direction and the contact width is assumed to be asymmetric with respect to the structure. Solutions to the asymmetric model are obtained and the effect of the asymmetric contact width on the whole pulling process is mainly discussed. It is found that the smaller the absolute value of Dundurs' parameter beta or the larger the pulling angle theta, the more reasonable the symmetric model would be to approximate the asymmetric one.

Promoting innovative stormwater solutions for coastal plain communities

In 2008, the Center for Watershed Protection (CWP) surveyed seventy-three coastal plain communities to determine their current practices and need for watershed planning and low impact development (LID). The survey found that communities had varying watershed planning effectiveness and need better stormwater management, land use planning, and watershed management communication. While technical capacity is improving, stormwater programs are under staffed and innovative site designs may be prohibited under current regulations. In addition, the unique site constraints (e.g., sandy soils, low relief, tidal influence, vulnerability to coastal hazards, etc.) and lack of local examples are common LID obstacles along the coast (Vandiver and Hernandez, 2009). LID stormwater practices are an innovative approach to stormwater management that provide an alternative to structural stormwater practices, reduce runoff, and maintain or restores hydrology. The term LID is typically used to refer to the systematic application of small, distributed practices that replicate pre-development hydrologic functions. Examples of LID practices include: downspout disconnection, rain gardens, bioretention areas, dry wells, and vegetated filter strips. In coastal communities, LID practices have not yet become widely accepted or applied. The geographic focus for the project is the Atlantic and Gulf coastal plain province which includes nearly 250,000 square miles in portions of fifteen states from New Jersey to Texas (Figure 1). This project builds on CWP’s “Coastal Plain Watershed Network: Adapting, Testing, and Transferring Effective Tools to Protect Coastal Plain Watersheds” that developed a coastal land cover model, conducted a coastal plain community needs survey (results are online here: http://www.cwp.org/#survey), created a coastal watershed Network, and adapted the 8 Tools for Watershed Protection Framework for coastal areas. (PDF contains 4 pages)

Biophysics of V(D)J recombination and Genome Packaging: In singulo studies on RAG, HMGB1, and TFAM

The recombination-activating gene products, RAG1 and RAG2, initiate V(D)J recombination during lymphocyte development by cleaving DNA adjacent to conserved recombination signal sequences (RSSs). The reaction involves DNA binding, synapsis, and cleavage at two RSSs located on the same DNA molecule and results in the assembly of antigen receptor genes. Since their discovery full-length, RAG1 and RAG2 have been difficult to purify, and core derivatives are shown to be most active when purified from adherent 293-T cells. However, the protein yield from adherent 293-T cells is limited. Here we develop a human suspension cell purification and change the expression vector to boost RAG production 6-fold. We use these purified RAG proteins to investigate V(D)J recombination on a mechanistic single molecule level. As a result, we are able to measure the binding statistics (dwell times and binding energies) of the initial RAG binding events with or without its co-factor high mobility group box protein 1 (HMGB1), and to characterize synapse formation at the single-molecule level yielding insights into the distribution of dwell times in the paired complex and the propensity for cleavage upon forming the synapse. We then go on to investigate HMGB1 further by measuring it compact single DNA molecules. We observed concentration dependent DNA compaction, differential DNA compaction depending on the divalent cation type, and found that at a particular HMGB1 concentration the percentage of DNA compacted is conserved across DNA lengths. Lastly, we investigate another HMGB protein called TFAM, which is essential for packaging the mitochondrial genome. We present crystal structures of TFAM bound to the heavy strand promoter 1 (HSP1) and to nonspecific DNA. We show TFAM dimerization is dispensable for DNA bending and transcriptional activation, but is required for mtDNA compaction. We propose that TFAM dimerization enhances mtDNA compaction by promoting looping of mtDNA.

Temperature-and pH-Sensitive Nanohydrogels of Poly(N-Isopropylacrylamide) for Food Packaging Applications: Modelling the Swelling-Collapse Behaviour

Temperature-sensitive poly(N-isopropylacrylamide) (PNIPA) nanohydrogels were synthesized by nanoemulsion polymerization in water-in-oil systems. Several cross-linking degrees and the incorporation of acrylic acid as comonomer at different concentrations were tested to produce nanohydrogels with a wide range of properties. The physicochemical properties of PNIPA nanohydrogels, and their relationship with the swelling-collapse behaviour, were studied to evaluate the suitability of PNIPA nanoparticles as smart delivery systems (for active packaging). The swelling-collapse transition was analyzed by the change in the optical properties of PNIPA nanohydrogels using ultraviolet-visible spectroscopy. The thermodynamic parameters associated with the nanohydrogels collapse were calculated using a mathematical approach based on the van't Hoff analysis, assuming a two-state equilibrium (swollen to collapsed). A mathematical model is proposed to predict both the thermally induced collapse, and the collapse induced by the simultaneous action of two factors (temperature and pH, or temperature and organic solvent concentration). Finally, van't Hoff analysis was compared with differential scanning calorimetry. The results obtained allow us to solve the problem of determining the molecular weight of the structural repeating unit in cross-linked NIPA polymers, which, as we show, can be estimated from the ratio of the molar heat capacity (obtained from the van't Hoff analysis) to the specific heat capacity (obtained from calorimetric measurements).

Assessment of agrobiodiversity resources in the Borotse flood plain, Zambia

Concerns about perceived loss of indigenous materials emerged from multiple stakeholders during consultations to plan and design the CGIAR Research Program on Aquatic Agricultural Systems for the Borotse hub in Zambia’s Western Province. To come to grips with and address the concerns, the AAS Borotse hub program of work included an assessment of agrobiodiversity to inform community-level and program initiatives and actions. The agrobiodiversity assessment comprised three components: key informant and expert surveys complemented by review of grey and published literature, focus group discussions in the communities, and individual household surveys. This working paper reports the findings from assessments of agrobiodiversity resources in the Borotse hub by key informants and local experts working in government ministries, departments and agencies, and non-governmental organizations operating in the communities. This working paper covers the following topics: agriculture in the Borotse flood plain; major agricultural land types in the Borotse flood plain; soils and their uses; production systems; crops, including the seed sector and ex-situ resources; indigenous materials collected from the wild, including non-perennial and perennial plants, aquatic plants, and forest biodiversity; fish resources, including both capture fisheries and aquaculture; livestock resources; dietary diversity; and indigenous and local knowledge on management systems.