MathSBML: a package for manipulating SBML-based biological models

Summary: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). Math-SBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity. Availability: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml. Supplementary information: Extensive online documentation is available at http://www.sbml.org/mathsbml.html. Additional examples are provided at http://www.sbml.org/software/mathsbml/bioinformatics-application-not

An Oceanographic Perspective on Early Human Migrations to the Americas

Early migrants to the Americas were likely seaworthy. Many archaeologists now agree that the first humans who traveled to the Americas more than 15,000 years before present (yr BP) used a coastal North Pacific route. Their initial migration was from northeastern Asia to Beringia where they settled for thousands to more than ten thousand years. Oceanographic conditions during the Last Glacial Maximum (18,000-24,000 yr BP) would have enhanced their boat journeys along the route from Beringia to the Pacific Northwest because the influx of freshwater that drives the opposing Alaska Coastal Current was small, global sea level was at least 120 m lower than at present, and necessary refugia existed. The onset of the Bølling- Allerød warming period, between 15,000 yr BP and 14,000 yr BP, accelerated the melting of the Cordilleran Ice Sheet. Rapid increases in freshwater influx would have hindered travel along the coast of Alaska and British Columbia as global sea levels rose 14-18 m in 340 years, submerging refugia that had been used as haul-out locations. The northward- flowing Alaska Coastal Current accelerated, making southward movement along the coast less likely. An increase in the challenges to migration beginning with the Bølling-Allerød until the Younger Dryas (12,800-11,600 yr BP) likely occurred and could have resulted in a migration hiatus

Evaluating Evidence for Historical Anadromous Salmon Runs in Eklutna Lake, Alaska

We assessed historical presence of sockeye salmon in Eklutna Lake, Alaska, prior to construction of a diversion dam on the downstream Eklutna River in 1929, using nitrogen stable isotopes measured in a lacustrine core 93 cm long. Sediments in the core were dated using varve counts, verified by 210Pb and 137Cs measurements. The basal date of the core was AD 1859, and varves became slightly thinner and less distinct after 1929. Sediments were primarily clastic with carbon content below 1%. Nitrogen isotope values were generally low and stable throughout the core, ranging from 1.5‰ to 2.5‰. There is no statistical evidence for a change in isotopic composition after emplacement of the dam. In light of published evidence from oral history, cultural records, and habitat relationships that suggest sockeye salmon could have been present in the lake before 1929, we conducted a simple sensitivity test to assess the possibility that a small salmon run may have gone undetected by our technique. We found that a salmon run of up to 1000/year, and potentially as many as 15 000/year, would be possible without noticeably altering the measured isotopic composition of the sediments in Eklutna Lake. Our results provide no evidence that such runs occurred, but do not preclude the possible existence of a relatively small sockeye fishery in Eklutna Lake before 1929.Nous avons évalué la présence historique du saumon rouge dans le lac Eklutna, en Alaska, avant la construction d’un barrage de dérivation sur la rivière Eklutna en aval en 1929, à l’aide d’isotopes stables de l’azote mesurés dans un noyau lacustre de 93 cm de longueur. Les sédiments du noyau ont été datés au moyen du dénombrement des varves et vérifiés avec les mesures du plomb 210 et du césium 137. La date de base du noyau était de 1859 A.D., et les varves devenaient un peu plus minces et moins distinctes après 1929. Les sédiments étaient principalement clastiques, leur teneur en carbone étant inférieure à 1 %. Les valeurs des isotopes d’azote étaient généralement faibles et stables dans l’ensemble du noyau, variant ainsi entre 1,5 ‰ et 2,5 ‰. Il n’existe pas de preuve statistique de changement de composition isotopique après l’aménagement du barrage. À la lumière de la preuve publiée à partir de l’histoire orale, des dossiers culturels et des relations avec l’habitat qui suggèrent que le saumon rouge aurait pu être présent dans le lac avant 1929, nous avons réalisé un simple test de sensibilité afin d’évaluer la possibilité qu’une petite montaison de saumon n’ait pas été détectée au moyen de notre technique. Nous avons constaté qu’une montaison pouvant atteindre 1 000 saumons par année, voire 15 000 par année, serait possible sans pour autant altérer considérablement la composition isotopique mesurée des sédiments du lac Eklutna. Nos résultats ne fournissent aucune preuve de telles montaisons, sans toutefois exclure l’existence possible d’une pêche relativement petite de saumon rouge dans le lac Eklutna avant 1929

Holocene Thermokarst Lake Dynamics in Northern Interior Alaska: The Interplay of Climate, Fire, and Subsurface Hydrology

The current state of permafrost in Alaska and meaningful expectations for its future evolution are informed by long-term perspectives on previous permafrost degradation. Thermokarst processes in permafrost landscapes often lead to widespread lake formation and the spatial and temporal evolution of thermokarst lake landscapes reflects the combined effects of climate, ground conditions, vegetation, and fire. This study provides detailed analyses of thermokarst lake sediments of Holocene age from the southern loess uplands of the Yukon Flats, including bathymetry and sediment core analyses across a water depth transect. The sediment core results, dated by radiocarbon and 210Pb, indicate the permanent onset of finely laminated lacustrine sedimentation by ∼8,000 cal yr BP, which followed basin development through inferred thermokarst processes. Thermokarst expansion to modern shoreline configurations continued until ∼5000 cal yr BP and may have been influenced by increased fire. Between ∼5000 and 2000 cal yr BP, the preservation of fine laminations at intermediate and deep-water depths indicate higher lake levels than present. At that time, the lake likely overflowed into an over-deepened gully system that is no longer occupied by perennial streams. By ∼2000 cal yr BP, a shift to massive sedimentation at intermediate water depths indicates that lake levels lowered, which is interpreted to reflect a response to drier conditions based on correspondence with Yukon Flats regional fire and local paleoclimate reconstructions. Consideration of additional contributing mechanisms include the possible influence of catastrophic lake drainages on down-gradient base-flow levels that may have enhanced subsurface water loss, although this mechanism is untested. The overall consistency between the millennial lake-level trends documented here with regional paleoclimate trends indicates that after thermokarst lakes formed, their size and depth has been affected by North Pacific atmospheric circulation in addition to the evolution of permafrost, ground ice, and subsurface hydrology. As the first detailed study of a Holocene thermokarst basin that links expansion, stabilization and subsequent climate-driven lake level variations in a loess upland, these results provide a framework for future investigations of paleoclimatic signals from similar lake systems that characterize large regions of Alaska and Siberia

Mixed Integer Programming Models for Water Resources Management

A regional water quality control model is developed by linking a steady-state water quality simulation model with an optimization model. The water quality simulation model can be applied to complex river systems with both point and nonpoint loads using multiple interdependent pollution parameters described by either linear or nonlinear equations. Twelve water quality parameters can be modeled simultaneously: four non conservative constituents (or conservative constituents if the decay rate is set equal to zero); coliform bacteria (MPN); phosphorus; biochemical oxygen demand (BOD); ammonia (NH3); nitrate (NO3); dissolved oxygen (DO); temperature (°C); and algae. The water quality model is used to generate constraint equation for the optimization model. The optimization model is formulated as an integer programming problem in which the integer decision variables are wastewater treatment levels or diffuse source management practices to be determined for each load. The model considers the addition or upgrading of wastewater treatment with structural and nonstructural schemes for both point and diffuse pollution sources. A least cost solution is found subject to water quality standards at surveillance points. Additional constraints can include uniform and zoned uniform treatment. Low flow augmentation and bypass piping can be considered with slight water quality simulation model modification. A simulation model-optimization model iteration procedure is used to find an optimum solution. The regional water quality model is applied to two problems, a hypothetical problem and the Jordan River in Utah. The hypothetical consists of four pollution discharge points, at which seven possible treatment levels are available for six quality constituents: phosphorus; biochemical oxygen demands; ammonia; nitrate; dissolved oxygen; and algae. Water quality standards for three constituents are imposed at five surveillance points along the river. The portion of the Jordan River examined consists of seven pollution discharge points, at which seven treatment levels are available for the same six quality constituents as in the hypothetical problem. Water quality standards for two constituents are imposed at three surveillance points. The cost minimization problem for the Jordan River (1975 flows) required tertiary sand filters at all point loads at an increase from current costs of $1,75,881 per year to meet stream water quality standards. To assist in gaining familiarity with the linked simulation optimization model, several sensitivity studies are performed. The sensitivity of the optimal solution to two model input parameters is investigated. These parameters are the water quality equation coefficients and the water quality stream standards. Substantial reductions in treatment costs were possible by making minor changes in some of the input parameters. In the hypothetical problem, 10 percent increase in the ammonia decay rate or a 15 percent increase in the maximum specific algae growth rate would result in a 16 percent reduction in the minimum system treatment cost. A 10 percent relaxation of the stream standards at all surveillance points would result in a 54 percent reduction in the minimum system treatment costs. The optimal solution’s sensitivity to changes in headwater and point discharge flow is also investigated. The optimal treatment scheme for the projected 1995 flows in the Jordan River was the same as for the 1975 flows. The increase from current costs for the 1995 flows was$2,407,092 per year

Diatom and stable isotope records of late-Holocene lake ontogeny at Indrepollen, Lofoten, NW Norway: a response to glacio-isostasy and Neoglacial cooling

Borg Indrepollen is a coastal lake on the island of Vestvågøy, Lofoten, NW Norway. A sedimentary sequence spanning the last 4500 cal. yr BP was analysed for diatom, C/N and stable isotopes (δ13C and δ15 N). The record provides clear evidence of glacio-isostatic rebound in the Lofoten region. Five distinct lithostratigraphic-geochemical zones (I—V) and four major diatom zones (A—D) were identified. The early record (I—III, A—Biii; 4500—550 cal. yr BP) contains coarse sedimentary material and diatoms indicative of more marine conditions. The correlation between the isotopic data (high δ13C and low C/N) and trends in the biological data (marine/brackish flora) suggest the marine influence on the Indrepollen basin is a controlling factor of the source of organic material. The latter part of the record (IV, C; 550 cal. yr 550—226) indicates a transitional phase from marine-dominated diatom to brackish taxa and is coincident with a section of microlaminations in the core. The youngest zone (V, D; 226 cal. yr BP—present) is indicative of an isolated basin, with the deposition of fine sediments; freshwater diatom taxa dominate the biological record and δ13C are indicative of freshwater conditions. C/N suggests a shift to a terrestrial source of organic matter. The proxies show a transition from full marine conditions, when Indrepollen was a submerged fjord, to more freshwater, lacustrine conditions in the last 200 years. The record of land uplift from Borg Indrepollen mirrors changes in sedimentary records from across Northern Norway and relative sea-level curves for the region

The Northeast Pacific GLOBEC Program: Coastal Gulf of Alaska

(First Paragraph) The Gulf of Alaska (GOA) continental shelf encompasses approximately 370,000 km2, or about 13% of the U.S. continental shell and supports a rich and diverse marine ecosystem including some of the largest commercial fisheries in the U.S. Exclusive Economic Zone. Of particular economic importance is the salmon fishery, which was worth on the order of $170 million (landed value) in 2000 accrued from a catch of over 100 million fish. However, there is considerable variability on both interannual and longer time scales in harvest and recruitment success to this and other GOA fisheries. Of recent interest are compelling indications that abundances of salmon, other fish species, and zooplankton vary on decadal scales in association with North Pacific basin-scale climate changes (Beamish, 1995; Mantua et al., 1997; Roemmich and McGowan, 1995; Brodeur et al., 1996; Francis et al., 1998; Anderson and Piatt, 1999; Hollowed et al., 2001)

A 2000 year varve-based climate record from the central Brooks Range, Alaska

Varved minerogenic sediments from glacial-fed Blue Lake, northern Alaska, are used to investigate late Holocene climate variability. Varve-thickness measurements track summer temperature recorded at Atigun Pass, located 41 km east at a similar elevation (r2 = 0.31, P = 0.08). Results indicate that climate in the Brooks Range from 10 to 730 AD (varve year) was warm with precipitation inferred to be higher than during the twentieth century. The varve-temperature relationship for this period was likely compromised and not used in our temperature reconstruction because the glacier was greatly reduced, or absent, exposing sub-glacial sediments to erosion from enhanced precipitation. Varve-inferred summer temperatures and precipitation decreased after 730 AD, averaging 0.4°C above the last millennial average (LMA = 4.2°C) from 730 to 850 AD, and 0.1°C above the LMA from 850 to 980 AD. Cooling culminated between 980 and 1030 AD with temperatures 0.7°C below the LMA. Varve-inferred summer temperatures increased between 1030 and 1620 AD to the LMA, though the period between 1260 and 1350 AD was 0.2°C below the LMA. Although there is no equivalent to the European Medieval Warm Period in the Blue Lake record, two warm intervals occurred from 1350 to 1450 AD and 1500 to 1620 AD (0.4 and 0.3°C above the LMA, respectively). During the Little Ice Age (LIA; 1620 to 1880 AD), inferred summer temperature averaged 0.2°C below the LMA. After 1880 AD, inferred summer temperature increased to 0.8°C above the LMA, glaciers retreated, but aridity persisted based on a number of regional paleoclimate records. Despite warming and glacial retreat, varve thicknesses have not achieved pre-730 AD levels. This reflects limited sediment availability and transport due to a less extensive retreat compared to the first millennium, and continued relative aridity. Overall, the Blue Lake record is similar to varve records from the eastern Canadian Arctic that document a cool LIA and twentieth century warming. However, the occurrence and timing of events, such as the LIA and Medieval Warm Period, varies considerably among records, suggesting heterogeneous climatic patterns across the North American Arctic

Late-Holocene Indian summer monsoon variability revealed from a 3300-year-long lake sediment record from Nir’pa Co, southeastern Tibet

Sedimentological and geochemical results from Nir’pa Co, an alpine lake on the southeastern Tibetan Plateau, detail late-Holocene Indian summer monsoon (ISM) hydroclimate during the last 3300 years. Constrained by modern calibration, elevated silt and lithics and low sand and clay between 3.3 and 2.4 ka and 1.3 ka and the present indicate two pluvial phases with lake levels near their current overflow elevation. Between 2.4 and 1.3 ka, a sharp increase in sand and corresponding decrease in lithics and silt suggest drier conditions and lower lake levels at Nir’pa Co. Hydroclimate expressions in the sedimentological proxies during the Medieval Climate Anomaly (MCA) and ‘Little Ice Age’ (LIA) are not statistically significant, suggesting that these events were minor compared to the millennial scale variability on which they were superimposed. However, decreasing sand and increasing lithics and silt during the MCA between 950 and 800 cal. yr BP may suggest briefly wetter conditions, while increasing sand and reduced lithics and silt from 500 to 200 cal. yr BP suggest potentially drier conditions during the LIA. Similarities with regional records from lake sediment and ice cores and speleothem records from the central and eastern Tibetan Plateau, India, and the Arabian Sea, suggest generally coherent late-Holocene ISM variability in these regions. Increased late-Holocene ISM intensity occurred during times when Tibetan Plateau surface air temperatures were warmer, Indo-Pacific sea surface temperatures were elevated, and the tropical Pacific was in a La Niña–like mean state. Conversely, aridity between 2.4 and 1.3 ka occurred in concert with cooling on the Tibetan Plateau and in the Indo-Pacific with more El Niño–like conditions in the tropical Pacific. Differences with western Tibetan records may reflect a weakened ISM and stronger westerlies in this region during the late-Holocene

Late-Holocene floodplain development, land-use, and hydroclimate–flood relationships on the lower Ohio River, US

Floodplain development, land-use, and flooding on the lower Ohio River are investigated with a 3100-year-long sediment archive from Avery Lake, a swale lake on the Black Bottom floodplain in southern Illinois, US. In all, 12 radiocarbon dates show that Avery Lake formed at 1130 BCE (3100 cal. yr BP), almost 3000 years later than previously thought, indicating that the Black Bottom floodplain is younger and more dynamic than previously estimated. Three subsequent periods of extensive land clearance were identified by changes in pollen composition, corresponding to Native American occupations before 1500 CE and the current Euro-American occupation beginning in the 18th century. Sedimentation rates prior to 1820 CE changed independently of land clearance events, suggesting natural as opposed to land-use controls. Comparison with high-resolution paleoclimate data from Martin Lake, IN, indicates that lower Ohio River flooding was frequent when cold-season precipitation originating from the Pacific/Arctic predominated when atmospheric circulation resembled positive Pacific North American (PNA) conditions and the Pacific Decadal Oscillation (PDO) was in a positive mean state (1130 BCE to 350 CE and 1150–1820 CE). Conversely, Ohio River flooding was less frequent when warm-season precipitation from the Gulf of Mexico prevailed during negative PDO- and PNA-like mean states (350 and 1150 CE). This flood dynamic appears to have been fundamentally altered after 1820 CE. We suggest that extensive land clearance in the Ohio River watershed increased runoff and landscape erosion by reducing interception, infiltration, and evapotranspiration, thereby increasing flooding despite a shift to negative PDO- and PNA-like mean states. Predicted increases in average precipitation and extreme rainfall events across the mid-continental US are likely to perpetuate current trends toward more frequent flood events, because anthropogenic modifications have made the landscape less resilient to changing hydroclimatic conditions