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Biochemistry


Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms. Biochemistry governs all living organisms and living processes. By controlling information flow through biochemical signalling and the flow of chemical energy through metabolism, biochemical processes give rise to the incredible complexity of life. Much of biochemistry deals with the structures and functions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules although increasingly processes rather than individual molecules are the main focus.

 
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A Simplified Gross Primary Production and Evapotranspiration Model...

By: M. Peltoniemi; A. Lohila; S. Launiainen; F. Minunno; I. Mammarella; M. Aurela; A. Mäkelä; A. Lindroth; K. Minkkinen

Description: Department of Forest Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland. The problem of model complexity has been lively debated in environmental sciences as well as in the forest modelling community. Simple models are less input demanding and their calibration involves a lower number of parameters, but they might be suitable only at local scale.

In this work we calibrated a simplified ecosystem process model (PRELES...

Amiro, B. D., Orchansky, A. L., Barr, A. G., Black, T. A., Chambers, S. D., Chapin III, F. S., Goulden, M. L., Litvak, M., Liu, H. P., McCaughey, J. H., McMillan, A., and Randerson, J. T.: The effect of post-fire stand age on the boreal forest energy balance, Agr. Forest Meteorol., 140, 41–50, 2006.; Aubinet, M., Vesala, T., and Papale, D.: Eddy Covariance: a Practical Guide to Measurement and Data Analysis, Springer Science & Business Media, 460 pp., London, UK, 2012.; ...

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A Simplified Gross Primary Production and Evapotranspiration Model...

By: M. Peltoniemi; A. Lohila; S. Launiainen; F. Minunno; I. Mammarella; M. Aurela; A. Mäkelä; A. Lindroth; K. Minkkinen

Description: Department of Forest Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland. The problem of model complexity has been lively debated in environmental sciences as well as in the forest modelling community. Simple models are less input demanding and their calibration involves a lower number of parameters, but they might be suitable only at local scale.

In this work we calibrated a simplified ecosystem process model (PRELES...

Amiro, B. D., Orchansky, A. L., Barr, A. G., Black, T. A., Chambers, S. D., Chapin III, F. S., Goulden, M. L., Litvak, M., Liu, H. P., McCaughey, J. H., McMillan, A., and Randerson, J. T.: The effect of post-fire stand age on the boreal forest energy balance, Agr. Forest Meteorol., 140, 41–50, 2006.; Aubinet, M., Vesala, T., and Papale, D.: Eddy Covariance: a Practical Guide to Measurement and Data Analysis, Springer Science & Business Media, 460 pp., London, UK, 2012.; ...

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Empower-1.0: an Efficient Model of Planktonic Ecosystems Written i...

By: A. Yool; W. C. Gentleman; T. R. Anderson

Description: National Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK. Modelling marine ecosystems requires insight and judgement when it comes to deciding upon appropriate model structure, equations and parameterisation. Many processes are relatively poorly understood and tough decisions must be made as to how to mathematically simplify the real world. Here, we present an efficient plankton modelling te...

Anderson, T. R.: Relating C : N ratios in zooplankton food and faecal pellets using a biochemical model, J. Exp. Mar. Biol. Ecol., 184, 183–199, 1994.; Anderson, T. R.: Plankton functional type modelling: running before we can walk?, J. Plankton Res., 27, 1073–1081, 2005.; Anderson, T. R.: A spectrally averaged model of light penetration and photosynthesis, Limnol. Oceanogr., 38, 1403–1419, 1993.; Anderson, T. R.: Progress in marine ecosystem modelling and the unreasonab...

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A Stochastic, Lagrangian Model of Sinking Biogenic Aggregates in t...

By: T. Jokulsdottir; D. Archer

Description: University of Chicago, Chicago, IL 60637, USA. We present a new mechanistic model, Stochastic Lagrangian Aggregate Model of Sinking particles (SLAMS) for the biological pump in the ocean, which tracks the evolution of individual particles as they aggregate, disaggregate, sink, and are altered by chemical and biological processes. SLAMS considers the impacts of ballasting by mineral phases, binding of aggregates by transparent exopolymer particles (TEP), zoop...

Alldredge, A. and Gotschalk, C.: In situ settling behavior of marine snow, Limnol. Oceanogr., 33, 339–351, 1988.; Alldredge, A. and McGillivary, P.: The attachment probabilities of marine snow and their implications for particle coagulation in the ocean, Deep-Sea Res., 38, 431–443, 1991.; Alldredge, A. and Silver, M. W.: Characteristics, dynamics and significance of marine snow, Prog. Oceanogr., 20, 41–82, 1988.; Alldredge, A., Granata, G. C., Gotschalk, C. C., and Dicke...

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Vegetation Dynamics and Soil Water Balance in a Water-limited Medi...

By: J. D. Albertson; M. Mancini; N. Montaldo

Description: Dipartimento di Ingegneria del Territorio, Università di Cagliari, Cagliari, Italy. Mediterranean ecosystems are commonly heterogeneous savanna-like ecosystems, with contrasting plant functional types (PFTs, e.g. grass and woody vegetation) competing for water. Mediterranean ecosystems are also commonly characterized by strong inter-annual rainfall variability, which influences the distributions of PFTs that vary spatially and temporally. An extensive f...

Aber, J. D. and Melillo, J. M.: Terrestrial ecosystems, Academic press, 556~pp., 2001.; Albertson, J. D. and Kiely, G.: On the structure of soil moisture time series in the context of Land Surface Models, J. Hydrol., 243(1–2), 101–119, 2001.; Amthor, J. S.: The role of maintenance respiration in plant growth, Plant Cell Environ., 7, 561–569, 1984.; Arora, V.: Modeling vegetation as a dynamic component in soil-vegetation-atmosphere transfer schemes and hydrological models...

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Accurate Lai Retrieval Method Based on Proba/Chris Data : Volume 1...

By: X. C. Liu; B. Y. Yan; Y. K. Cui; W. J. Fan; X. R. Xu

Description: Institute of Remote Sensing and GIS, Peking University, Beijing, China. Leaf area index (LAI) is one of the key structural variables in terrestrial vegetation ecosystems. Remote sensing offers an opportunity to accurately derive LAI at regional scales. The anisotropy of canopy reflectance, variations in background characteristics, and variability in atmospheric conditions constitute three factors that can strongly constrain the accuracy of retrieved LAI...

Brown, L., Chen, J. M., Leblanc, S. G., and Cihlar, J. A.: shortwave infrared modification to the simple ration for LAI retrieval in boreal forest: An image and model analysis, Remote Sens. Environ., 71, 16–25, 2000.; Badhwar, G. D., MacDonald, R. B., and Metha, N. C.: Satellite-derived leaf-area-index and vegetation maps as input to global carbon cycle models – a hierarchical approach, Int. J. Remote Sens., 7, 265–281, 1986.; Baret, F. and Guyot, G.: Potentials and limi...

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Domestic Wells Have High Probability of Pumping Septic Tank Leacha...

By: J. E. Bremer; T. Harter

Description: Department of Land, Air, and Water Resources, University of California, Davis, CA 95616-8629, USA. Onsite wastewater treatment systems are common in rural and semi-rural areas around the world; in the US, about 25–30% of households are served by a septic (onsite) wastewater treatment system, and many property owners also operate their own domestic well nearby. Site-specific conditions and local groundwater flow are often ignored when installing septic sy...

Ahmed, W., Neller, R., and Katouli, M.: Evidence of septic system failure determined by a bacterial biochemical fingerprinting method, J. Appl. Microbiol., 98, 910–920, doi:10.1111/j.1365-2672.2004.02522.x, 2005.; Alhajjar, B., Stramer, S., Cliver, D., and Harkin, J.: Transport modelling of biological tracers from septic systems, Water Res., 22, 907–915, ...

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Thermodynamic Constraints on Effective Energy and Mass Transfer an...

By: C. Rasmussen

Description: Department of Soil, Water and Environmental Science, The University of Arizona, 1177 E. Fourth Street, P.O. Box 210038, Tucson, AZ 85721, USA. Understanding how water, energy and carbon are partitioned to primary production and effective precipitation is central to quantifying the limits on critical zone evolution. Recent work suggests quantifying energetic transfers to the critical zone in the form of effective precipitation and primary production provi...

Berry, S. L., Farquhar, G. D., and Roderick, M. L.: Co-evolution of climate, vegetation, soil and air, in: Encyclopedia of Hydrological Sciences, edited by: Bloschl, G. and Sivapalan, M., John Wiley and Sons, Ltd., Chichester, UK, 177–192, 2005.; Black, P. E.: Revisiting the Thornthwaite and Mather Water Balance1, J. Am. Water Resour. Assoc., 43, 1604–1605, 2007.; Hamon, W. R.: Estimating potential evapotranspiration, Proc. Am. Soc. Civil Eng., 87, 107–120, 1961.; Amunds...

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Quantifying the Uncertainty in Estimates of Surface–atmosphere Flu...

By: A. Verhoef; C. Van Der Tol; W. Verhoef; J. Timmermans; Z. Su

Description: University of Twente, Faculty for Geoinformation Sciences and Earth Observation (ITC), the Netherlands. Accurate estimation of global evapotranspiration is considered to be of great importance due to its key role in the terrestrial and atmospheric water budget. Global estimation of evapotranspiration on the basis of observational data can only be achieved by using remote sensing. Several algorithms have been developed that are capable of estimating the d...

Bastiaanssen, W. G. M., Menenti, M., Feddes, R. A., and Holtslag, A. A. M.: A remote sensing surface energy balance algorithm for land (SEBAL). 1. Formulation, J. Hydrol., 212–213, 198–212, 1998.; Bosveld, F., Holtslag, A. A. M., and Van Den Hurk, B. J. J. M.: Interpretation of Crown Radiation Temperatures of a Dense Douglas fir Forest with Similarity Theory, Bound.-Layer Meteor., 92, 429–451, doi:10.1023/a:1002087526720<...

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Effects of Extreme Drought on Agriculture Soil and Sustainability ...

By: B. S. Weng; D. H. Yan; T. X. Zhang; W. Gang; Z. B. Zhang; S. M. Geng

Description: College of Civil and Hydraulic Engineering, Tsinghua University, Beijing, 100084, China. Content of microbial biomass carbon was selected as indicator for identifying effects of extreme drought on agriculture soil ecosystem. Through a series of prototype observation experiments, changing tendencies of microbial biomass carbon content and the proportion of microbial biomass carbon in soil organic carbon were identified. The optimum mass water conten...

Christ, M. J. and David, M. B.: Temperature and moisture effects the production of dissolved organic carbon in a podosol, Soil Biol. Biochem., 28, 1191–1199, 1996.; Balser, T. C. and Firestone, M. K.: Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest, Biogeochemistry, 73, 395–415, 2005.; Bastida, F., Moreno, J. L., Hernández, T., and García, C.: Microbiological activity in a soil 15 years after its devege...

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The Normalized Difference Infrared Index (Ndii) as a Proxy for Soi...

By: H. H. G. Savenije; H. Gao; E. Maekan; S. Thianpopirug; N. Sriwongsitanon; S. Saengsawang

Description: Department of Water Resources Engineering, Faculty of Engineering, Kasetsart University, Bangkok, Thailand. With remote sensing we can readily observe the Earth's surface, but looking under the surface into the root zone of vegetation is still a major challenge. Yet knowledge on the dynamics of soil moisture in the root zone is essential for agriculture, land–atmosphere interaction and hydrological modelling, alike. In this paper we develop a novel appro...

Albergel, C., Rüdiger, C., Pellarin, T., Calvet, J.-C., Fritz, N., Froissard, F., Suquia, D., Petitpa, A., Piguet, B., and Martin, E.: From near-surface to root-zone soil moisture using an exponential filter: an assessment of the method based on in-situ observations and model simulations, Hydrol. Earth Syst. Sci., 12, 1323–1337, doi:10.5194/hess-12-1323-2008, 2008.; Ceccato, P., Flasse, S., Tarantola, S., Jacquemoud...

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Domestic Wells Have High Probability of Pumping Septic Tank Leacha...

By: J. E. Horn; T. Harter

Description: Department of Land, Air, and Water Resources, University of California, Davis, CA 95616-8629, USA. Onsite wastewater treatment systems such as septic systems are common in rural and semi-rural areas around the world; in the US, about 25–30 % of households are served by a septic system and a private drinking water well. Site-specific conditions and local groundwater flow are often ignored when installing septic systems and wells. Particularly in areas wit...

US EPA: The Report to Congress: Waste Disposal Practices and Their Effects on Groundwater. EPA 570/9-77-002, 1998{a}.; Ahmed, W., Neller, R., and Katouli, M.: Evidence of septic system failure determined by a bacterial biochemical fingerprinting method, J. Appl. Microbiol., 98, 910–920, doi:10.1111/j.1365-2672.2004.02522.x, 2005.; Alhajjar, B., Stramer, S., Cliver, D., and Harkin, J.: Transport modelling of b...

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Inter-comparison of Two Land-surface Schemes Applied on Different ...

By: W. Mauser; T. Marke; C. Wastl; F. Zabel; G. Zängl; A. Pfeiffer

Description: Department of Geography, Ludwig-Maximilians-Universität, Munich, Germany. Feedback effects between the land surface and the atmosphere are an important issue in modelling the climate system. Therefore, in order to take land surface heterogeneity adequately into account, a representation of the land surface in sufficient spatial resolution is necessary. In order to analyze the impact of different land surface models on the atmosphere, we analyzed the dif...

Bach, H. and Verhoef, W.: Sensitivity studies on the effect of surface soil moisture on canopy reflectance using the radiative transfer model GeoSAIL, Igarss 2003: Ieee International Geoscience and Remote Sensing Symposium, Vols I–Vii, Proceedings, 1679–1681, 2003.; Baldocchi, D. D., Hicks, B. B., and Camara, P.: A canopy stomatal resistance model for gaseous deposition to vegetated surfaces, Atmospheric Environment (1967), 21, 91–101,

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Thermodynamic Constraints on Effective Energy and Mass Transfer an...

By: C. Rasmussen

Description: Department of Soil, Water and Environmental Science, The University of Arizona, 1177 E. Fourth Street, P.O. Box 210038, Tucson, AZ 85721, USA. Understanding how water, energy and carbon are partitioned to primary production and effective precipitation is central to quantifying the limits on critical zone evolution. Recent work suggests quantifying energetic transfers to the critical zone in the form of effective precipitation and primary production provi...

Amundson, R., Richter, D. D., Humphreys, G. S., Jobbagy, E. G., and Gaillardet, J.: Coupling between biota and earth materials in the critical zone, Elements, 3, 327–332, 2007.; Anderson, G. M.: Thermodynamics of natural systems, 2nd ed., Cambridge University Press, Cambridge, UK, 2005.; Aphalo, P. J. and Jarvis, P. G.: Do stomata respond to relative-humidity, Plant Cell and Environment, 14, 127–132, 1991.; Bejan, A.: Advanced engineering thermodynamics, 3rd ed ed., John...

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Application of a Hybrid Enkf-oi to Ocean Forecasting : Volume 5, I...

By: P. Sakov; L. Bertino; F. Counillon

Description: Mohn Sverdrup Center/Nansen Environmental and Remote Sensing Center Thormøhlensgate 47 , Bergen, Norway. Data assimilation methods often use an ensemble to represent the background error covariance. Two approaches are commonly used; a simple one with a static ensemble, or a more advanced one with a dynamic ensemble. The latter is often non-practical due to its high computational requirements. Some recent studies suggested using a hybrid covariance, which...

Bentsen, M., Evensen, G. Drange, H. and Jenkins, A. D.: Coordinate transformation on a sphere using conformal mapping, Mon.\ Weather Rev.\/, 127\/, 2733–2740, 1999.; Bishop, C. H., Etherton, B. J., and Majumdar, S. J.: Adaptive sampling with the ensemble transform Kalman filter. Part I: Theoretical aspects, Mon.\ Weather Rev.\/, 129\/, 420–436, 2001.; Browning, G. L. and Kreiss, H. O.: Initialization of the shallow water equations with open boundaries by the bounded deri...

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Surface Circulation in the Eastern Mediterranean Using Drifters (2...

By: C. Millot; I. Taupier-letage; P.-m. Poulain; C. Sammari; S. Ben Ismail; R. Gerin

Description: Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Borgo Grotta Gigante, 42/c, 34010 Sgonico, Trieste, Italy. Within the framework of the EGITTO/EGYPT programs, the spatial structure and the temporal variability of the surface circulation in the eastern basin of the Mediterranean Sea was studied with satellite-tracked drifters. A total of 97 drifters drogued to 15-m nominal depth were released between September 2005 and March 2007, reg...

Emery, W. J. and Thomson, R. E.: Data Analysis Methods in Physical Oceanography, Elsevier, Amsterdam, 638 pp., 2004.; Alhammoud, B., Béranger, K., Mortier, L., Crépon, M., and Dekeyser, I.: Surface circulation of the Levantine Basin: comparison of model results with observations, Prog. Oceanogr., 66(2–4), 299–320, 2005.; Beranger, K., Taupier-Letage, I., Alhammoud, B., Lellouche, J. M., Emelianov, M., Mortier, L., and Millot, C.: Analysis of two mesoscale eddies in the s...

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Assimilating Globcolour Ocean Colour Data Into a Pre-operational P...

By: R. M. Barciela; D. Lea; K. P. Edwards; M. J. Martin; D. A. Ford; J. Demaria

Description: Met Office, FitzRoy Road, Exeter, EX1 3PB, UK. As part of the GlobColour project, daily chlorophyll a observations, derived using remotely sensed ocean colour data from the MERIS, MODIS and SeaWiFS sensors, are produced. The ability of these products to be assimilated into a pre-operational global coupled physical-biogeochemical model has been tested, on both a hindcast and near-real-time basis, and the impact on the system assessed. The assimila...

Allen, J. I., Eknes, M., and Evensen, G.: An Ensemble Kalman Filter with a complex marine ecosystem model: hindcasting phytoplankton in the Cretan Sea, Ann. Geophys., 21, 399–411, doi:10.5194/angeo-21-399-2003, 2003.; Anderson, L. A., Robinson, A. R., and Lozano, C. J.: Physical and biological modeling in the Gulf Stream region – Part 1: Data assimilation methodology, Deep-Sea Res. Pt. I, 47, 1787–1827, 2000.; Ander...

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The Mediterranean Ocean Colour Observing System – System Developme...

By: V. Forneris; C. Tronconi; S. Colella; G. Volpe; R. Santoleri

Description: Istituto di Scienze dell'Atmosfera e del Clima, Via Fosso del Cavaliere 100, 00133 Rome, Italy. This paper presents the Mediterranean Ocean Colour Observing System in the framework of the growing demand of near real-time data emerging within the operational oceanography international context. The main issues related to the satellite operational oceanography are tied to the following: (1) the near real-time ability to track data flow uncertainty sources; ...

Le Traon, P. Y.: Satellites and Operational Oceanography, in: Operational Oceanography in the 21st Century, edited by: Schiller, A., and Brassington, G., Springer Dordrecht Heidelberg London New York, 29–54, 2011.; McClain, C. R., Arrigo, K. R., Esaias, W., Darzi, M., Patt, F. S., Evans, R. H., Brown, C. W., Brown, J. W., Barnes, R. A., and Kumar, L.: SeaWiFS Quality Control Masks and Flags: Initial Algorithms and Implementation Strategy, SeaWiFS Technical Report Series,...

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Toward a Multivariate Reanalysis of the North Atlantic Ocean Bioge...

By: J.-m. Brankart; P. Brasseur; C. Fontana

Description: Université Pierre Marie Curie, Laboratoire d'Océanographie de Villefranche – UMR 7093, Villefranche sur mer, France. Today, the routine assimilation of satellite data into operational models of ocean circulation is mature enough to enable the production of global reanalyses describing the ocean circulation variability during the past decades. The expansion of the reanalysis concept from ocean physics to biogeochemistry is a timely challenge that motivate...

Brasseur, P. and Verron, J.: The SEEK filter method for data assimilation in oceanography: a synthesis, Ocean Dynam., 56, 650–661, 2006.; Bertino, L., Evensen, G., and Wackernagel, H.: Sequential Data Assimilation Techniques in Oceanography, Int. Stat. Rev., 71, 223–241, doi:10.1111/j.1751-5823.2003.tb00194.x, 2003.; Bocquet, M., Pires, C. A., and Wu, L.: Beyond Gaussian Statistical Modeling in Geophysical ...

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Nemo on the Shelf: Assessment of the Iberia-biscay-ireland Configu...

By: B. Levier; J. Chanut; P. Marsaleix; F. Lyard; E. A. Fanjul; S. Cailleau; G. Reffray; P. De Mey; N. Ayoub; M. Drévillon; M. G. Sotillo; C. Maraldi

Description: Laboratoire d'études en géophysique et océanographie spatiales (LEGOS), UMR 5566, CNRS – Université de Toulouse, 14 Avenue Edouard Belin, 31400 Toulouse, France. The Iberia-Biscay-Ireland (IBI) system serves one of the 7 MyOcean Monitoring and Forecasting Centres. A high resolution simulation covering the IBI region is set-up over July 2007–February 2009. The NEMO (Nucleus for European Modelling of the Ocean) model is used with a 1/36° horizontal resolut...

Adcroft, A. and Campin, J.-M.: Rescaled height coordinates for accurate representation of free-surface flows in ocean circulation models, Ocean Model., 7, 269–284, 2004.; Alvarez, M., Perez, F. F., Bryden, H. L., and Rios, A. F.: Physical and biochemical transports structure in the North Atlantic subpolar gyre, J. Geophys. Res., 109, C03027, doi:10.1029/2003JC002015, 2004.; Arbic, B. K., Wallcraft, A. J., and Metzger, E....

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