bluuebunny/crossref_metadata_2025 huggingface dataset:
Parvalbumin
Authors: Nakayama Susumu , Kawasaki Hiroshi , Kretsinger Robert H
Published: April 2006

Parvalbumin was the first EF‐hand protein to have been characterized and to have its crystal structure determined. This prototype consists of an α‐helix E (extended forefinger of a clenched right hand), loop around the Ca2+ion (clenched middle finger), and α‐helix F (extended thumb). Parvalbumin has provided a reference point for the analyses of 76 other subfamilies of proteins that contain 2 to 12 EF‐hands. Most, but not all, EF‐hands bind calcium. The Ca2+ion is almost always coordinated by seven oxygen atoms arranged in an approximate pentagonal bipyramid; usually one of the ligands is a carboxylate group that coordinates calcium with both its oxygen atoms. The affinities of EF‐hands for calcium range from pKd(Ca2+) 6 to 8. The dissociation constant of parvalbumin for calcium (Kd ∼ 10−8 M) reflects one of the highest affinities of all the EF‐hand proteins. All, or most, of the EF‐hand proteins bind calcium ∼104.0more strongly than they bind the six‐coordinate magnesium. Most of this difference in affinity derives from the ∼103.4greateronrate for calcium, which in turn derives from its faster dehydration rate. Parvalbumin functions in fast, white, skeletal muscle to soak up messenger calcium following a stimulus, thereby facilitating rapid relaxation. Whether it has an analogous function in neurons, thymus, or other tissues remains to be demonstrated. Most EF‐hand proteins change conformation upon binding calcium, thereby transducing the information content of a pulse of cytosolic messenger Ca2+ions. Although the binding of calcium to the two EF‐hands of monomeric parvalbumin is not (or only very weakly) cooperative, as is the case for other EF‐hand proteins, the interaction of a pair of EF‐hands is essential for the stability of these proteins. The angle between the two helices (E and F) of a single EF‐hand as well as the contact between the pair of EF‐hands is usually moreopenfollowing binding of calcium, thereby exposing hydrophobic side chains. However, a survey of the known structures of all known EF‐hands proteins does not reveal a bimodalclosed, openset of conformations reflecting either binding of calcium and/or binding of targets for those EF‐hand proteins involved in information transduction.
Membrane Binding
C
2‐Like Domains
Authors: Verdaguer Nuria , Corbalán‐García Senena , Ochoa Wendy F , Gómez‐Fernández Juan Carmelo , Fita Ignacio
Published: April 2006

C2‐domains are independently folded modules, of about 130 residues, found in a large and diverse set of eukaryotic proteins. Many of the best‐characterized C2‐domains are found in proteins involved in membrane trafficking and fusion, such as synaptotagmins or rabphilin, and in signal transduction, such as phospholipases A2 (cPLA2) and C (PLC) or the protein kinase C isoforms (PKCs). All C2‐domains share a common overall fold: a single compact Greek‐key motif organized as an eight‐stranded antiparallel β‐sandwich consisting of a pair of four‐stranded β‐sheets – the A and B sheets – with a long axis of about 50 Å. Connections between β‐strands emerge from the top and bottom of the domain according to the two distinct topologies of C2‐domains. In topology I (the S family), the first β‐strand occupies the same structural position as the eighth β‐strand of topology II (the P family), which shifts in a circular permutation the order of homologous strands in the primary structure. The structural information defines adjacent calcium binding sites within a broad acidic cleft that contains highly conserved acidic residues. These provide most of the oxygen atoms that coordinate with the calcium ions. The present work will focus on the wealth of functional and structural information, which is being obtained at an exponential pace, on the membrane‐binding C2‐domains that require calcium.
Cytochrome

c

553
Authors: Nakagawa Atsushi
Published: April 2006

Cytochrome
c
553
in sulfate‐reducing bacteria,
Desulfovibrio vulgaris
, receives electrons from formate dehydrogenase and lactate dehydrogenase, and then transfers them to cytochrome
c
3
. Cytochrome
c
553
is a monoheme
c
‐type cytochrome with an absorption band at 553 nm in the reduced form and is the smallest
c
‐type cytochrome with a molecular weight of 9000. Its three‐dimensional structure has been determined by both x‐ray crystallography and NMR.
Nine‐Heme Cytochrome

c
Authors: Arménia Carrondo Maria , Soares Cláudio M , Matias Pedro M
Published: April 2006

Nine heme cytochrome c (9Hcc) is a monomeric multi‐heme cytochrome c found in the sulfate‐reducing bacteria of

Desulfovibrio desulfuricans

(Dd) ATCC 27774 and

Desulfovibrio desulfuricans

Essex 6. The polypeptide chain comprises 296 residues and wraps around nine hemes of type‐c that bind the polypeptide chain through thioether bridges to cysteine residues. This represents the first known structure of a multi‐heme cytochrome where copies of a tetra‐heme cytochrome
c
3
‐like fold are present in the same polypeptide chain.

The high homology between 9Hcc and the C‐terminal region of

Desulfovibrio vulgaris

Hildenborough (DvH) Hmc, as well as the presence of the
9Hcc
gene within an operon similar to that of the DvH Hmc, strongly support the proposal that 9Hcc is the high‐molecular‐weight cytochrome of Dd. Several
in vitro
studies, as well as our crystallographic and modeling studies suggest that cytochrome
c
3
is the mediator between the [NiFe] hydrogenase and 9Hcc in Dd.
b‐Type Cytochrome Electron Carriers: Cytochromesb562andb5, and Flavocytochromeb2
Authors: Mathews F Scott
Published: April 2006

b‐Type cytochromes form a class of proteins that contain a heme (iron‐protoporphorin IX) bound non‐covalently to its polypeptide chain with two of its side chains coordinated to the iron. One of these side chains is always histidine and the other can be histidine or methionine. Cytochromes b5and b562are simple mono‐domain proteins that contain heme as the only prosthetic group and histidine and methionine, respectively, as the second heme ligand. Flavocytochrome b2also contains histidine as the second heme ligand, but contains a second prosthetic group, flavin mononucleotide (FMN), that resides in a separate domain. Cytochromes b5and b562each mediate intracellular electron transfer between redox partners, the former within the endoplasmic reticulum of mammalian cells and the latter within bacteria. Flavocytochrome b2catalyzes the oxidation of lactic acid within yeast mitochondria, with the cytochrome domain mediating electron transfer from substrate‐reduced FMN to exogenous cytochrome c. The structural, electrochemical, and catalytic properties of these three proteins are presented, along with the results of mutagenesis.
Prostaglandin EndoperoxideH2Synthases‐1 and ‐2
Authors: Michael Garavito R
Published: April 2006

The prostaglandin endoperoxide H2synthase (PGHS) isozymes 1 and 2 are membrane bound, heme‐dependent enzymes that catalyze the committed step in the conversion of polyunsaturated fatty acids to prostanoids and thromboxanes. The PGHS isozymes, which are also known as cyclooxygenases, produce prostaglandin H2in two sequential enzymatic steps – a bis‐oxygenase (cyclooxygenase) reaction generates prostaglandin G2from arachidonic acid and a hydroperoxidase reaction creates the final product, prostaglandin H2. The PGHS isozymes are also the primary targets of nonsteroidal anti‐inflammatory drugs (NSAIDs), such as aspirin and ibuprofen, and recent pharmacological research efforts have led to the development of isoform selective drugs like Celebrex® and Vioxx®. In this chapter, we discuss the biochemistry, enzymology, and the structural biology of the PGHS isozymes and their relevance to prostanoid physiology and NSAID pharmacology.
Succinate:Quinone Oxidoreductases
Authors: Lancaster C Roy D
Published: April 2006

Succinate:quinone oxidoreductases encompass the succinate:quinone reductase (SQR) enzymes of aerobic respiration (respiratory complex II) and the quinol:fumarate reductase (QFR) enzymes of anaerobic respiration. These enzymes couple the two‐electron oxidation of succinate to fumarate to the two‐electron reduction of quinone to hydroquinone (quinol), and also catalyse the reverse reaction, the reduction of fumarate by quinol. Members of the superfamily are composed of two hydrophilic subunits, a large flavoprotein subunit A and a smaller subunit B containing three iron–sulfur centers, and one large subunit C or two small subunits C and D hydrophobic polypeptides that are integral membrane proteins and bind two, one, or no hemebgroups. On the basis of the available crystal structures of members of the superfamily, structural and functional aspects of succinate:quinone oxidoreductases are comprehensively discussed.
Cytochromecd1Nitrite Reductase
Authors: Allen James WA , Ferguson Stuart J , Fülöp Vilmos
Published: April 2006

Cytochromecd1catalyzes the one‐electron reduction of nitrite (NO2−) to nitric oxide and water. It is isolated from many bacteria, which respire by the process of denitrification.In vitro,cd1is also an oxidase and a hydroxylamine reductase. Each monomer of the dimeric enzyme contains onec‐type cytochrome center, which accepts electrons from donor proteins, and oned1heme, which is the active site and is unique to this class of enzymes. High‐resolution X‐ray structures have shown that in the oxidized forms, when isolated, the axial coordination of the hemes differs between the best‐studied cytochromescd1, the enzymes fromParacoccus pantotrophusandPseudomonas aeruginosa. Upon reduction, theP. pantotrophusenzyme undergoes a major and unprecedented conformational change and adopts the same heme coordinations as that of the reducedP. aeruginosacd1. The structural differences between the enzymes from these two sources are reflected in their biochemical, electron transfer, and spectroscopic properties.
Cytochrome

c

Nitrite Reductase
Authors: Einsle Oliver
Published: April 2006

Nitrite (NO
2
–
) is a central intermediate for various metabolic pathways within the biogeochemical nitrogen cycle. In dissimilatory nitrate ammonification, NO
2
–
is reduced to ammonia in a remarkable six‐electron reaction, catalyzed by the multiheme enzyme cytochrome
c
NO
2
–
reductase. The protein is a homodimer with a monomer mass of 58 kDa and five covalently attached heme cofactors, one of which features a free coordination site at the distal axial position of its central iron atom and an unusual and unique lysine ligand on the opposing, proximal axial position. The substrate NO
2
−
binds to this iron atom through the free electron pair on the nitrogen atom and is then reduced consecutively to ammonia, without any detectable release of reaction intermediates or by‐products. In the bacterial cell, many NO
2
−
reductases form a membrane‐associated complex with a small protein, NrfH, which is able to couple the oxidation of menaquinone from within the membrane to electron transfer to the catalytically active NO
2
−
reductase. A proton gradient is generated in a Q‐loop mechanism on NrfH, making NO
2
−
reduction an effective energy metabolism in anaerobic environments.
Ferredoxins Containing One [4Fe–4S] Center
Authors: Fukuyama Keiichi
Published: April 2006

Ferredoxins (Fds) are iron–sulfur proteins that function as electron carriers in diverse metabolic pathways. Generally, Fds are acidic proteins with a low molecular weight and have very low redox potentials. Although historically the name of Fd was given to electron carrier proteins containing iron–sulfur clusters in bacteria, plants and algae, and animals, they differ not only in the foldings of the polypeptide chains but also in the structures of the active centers; the canonical bacterial Fds have one or two [4Fe–4S] (or [3Fe–4S]) centers whereas the plant‐type and animal‐type Fds have one [2Fe–2S] cluster. Bacterial Fds are evolutionally related whether they have one or two [4Fe–4S] (or [3Fe–4S]) clusters, but are distinct from high potential iron–sulfur proteins that also have one [4Fe–4S] cluster. Fds containing one [4Fe–4S] cluster, on which this article is focussed, are one of several distinct classes of bacterial Fds with low redox potentials.
2,3‐Dihydroxybiphenyl 1,2‐Dioxygenase
Authors: Bolin Jeffrey T , Eltis Lindsay D
Published: April 2006

2,3‐Dihydroxybiphenyl 1,2‐dioxygenase (DHBD) is an Fe
2+
‐dependent extradiol dioxygenase. DHBD catalyzes the extradiol cleavage of 2,3‐dihydroxybiphenyl (DHB) to 2‐hydroxy‐6‐oxo‐6‐phenylhexa‐2,4‐dienoate (HOPDA) incorporating both atoms of dioxygen into the product HOPDA. DHBDs are found in a range of Gram‐negative and Gram‐positive bacteria that aerobically assimilate biphenyl. Amino acid sequences are available for over 50 bacterial extradiol dioxygenases that are evolutionarily related to DHBDs (i.e. type I enzymes); all are involved in the degradation of aromatic compounds. The type I bacterial enzymes may have large (∼33 kDa) or small (∼21 kDa) monomers. DHBD catalyzes the third reaction of the upper
bph
pathway, which catabolizes biphenyl to benzoate and 2‐hydroxypentadienoate. This pathway also transforms some polychlorinated biphenyls (PCBs). DHBDs can be best expressed heterologously in pseudomonads like
Burkholderia
sp. strain LB400 or
Pseudomonas
sp. strain KKS102. Mössbauer and EPR spectroscopies demonstrated the presence of high spin Fe
2+
in purified active preparations of
Pseudomonas putida
mt‐2 (C23O).

High‐resolution crystal structures of the active ferrous form of DHBD from
Burkholderia
sp. strain LB400 and
Pseudomonas
sp. strain KKS102 were determined. These octameric DHBDs have 422 point group symmetry. The monomer has an α + ß fold that may be subdivided into superimposable barrel‐like N‐ and C‐terminal half‐molecules. The active site Fe and the substrate binding sites are located in the cavity of the C‐terminal half. The ferrous Fe is bound by five ligands in square pyramidal geometry. The axial ligand is a conserved histidine, and the basal ligands are a second conserved histidine, a conserved monodentate glutamic acid, and two water molecules. X‐ray structures of DHBD in complex with DHB and 3‐methyl catechol are known for both the ferric and ferrous forms. Spectroscopic, mechanistic, and X‐ray structural studies were used to elaborate a plausible reaction mechanism for DHBDs.
Hemerythrin
Authors: Stenkamp Ronald E
Published: April 2006

Hemerythrin is a non‐heme iron protein that serves as an oxygen transfer or storage protein in several marine invertebrate phyla (sipunculids, brachiopods, priapulids and annelids). Each protein subunit (13 500 kD) binds two iron atoms by histidine, aspartic acid, and glutamic acid side‐chains. The protein carboxylates and a μ‐oxygen atom bridge the iron atoms in a prototypic FeOFe complex that has been extensively studied. One iron binds exogenous ligands including dioxygen and small anions. The protein functions by reversibly adding dioxygen to a deoxy form containing ferrous iron to produce an oxy form containing ferric iron and a peroxo anion.
Aldehyde Oxidoreductase (
MOP
)
Authors: João Romão Maria , Moura José JG
Published: April 2006

The aldehyde oxido‐reductase from

Desulfovibrio gigas

(MOP) is a member of the xanthine oxidase family but simpler since it lacks the flavin–adenine dinucleotide (FAD) domain. It is composed of a single polypeptide chain of 907 amino acids and contains one molybdenum atom bound to a molybdopterin cytosine dinucleotide (MCD) cofactor, as well as two spectroscopically distinguishable [2Fe2S] clusters involved in electron transfer. The Mo atom is pentacoordinated by the two sulfurs of the
cis
‐dithiolene group of the molybdopterin, plus two oxo and one hydroxyl/water ligand. It hydroxylates a wide range of aldehydes with little specificity but its physiological role is not totally clear.
Sulfite Oxidase
Authors: Kisker Caroline
Published: April 2006

Sulfite oxidase catalyzes the physiologically vital oxidation of sulfite to sulfate, the terminal reaction in the oxidative degradation of the sulfur‐containing amino acids, cysteine and methionine. It belongs to the molybdenum cofactor (Moco)‐containing family of enzymes that are characterized by the presence of a mononuclear Mo atom coordinated to the sulfur atoms of a pterin derivative, named molybdopterin. The homodimeric sulfite oxidase is located in the mitochondrial intermembrane space and each subunit contains a larger Moco‐containing domain and a smaller heme‐containing domain. Oxidation of sulfite to sulfate occurs at the molybdenum center with concomitant reduction of Mo(VI) to Mo(IV). Two electrons are singly transferred to theb5heme of the enzyme and from there to cytochromec. Sulfite oxidase deficiency results from defects either in the genes encoding proteins involved in molybdenum cofactor biosynthesis or in the sulfite oxidase gene itself. Several point mutations in the sulfite oxidase gene have been identified in patients with this disease worldwide. The crystal structure of wild‐type chicken sulfite oxidase provides the first atomic model for this enzyme and suggests possible reasons for how these substitutions interfere with catalysis or substrate binding.
Eukaryotic Copper Amine Oxidases
Authors: Wertz Diana L , Klinman Judith P
Published: April 2006

Copper amine oxidases contain the covalently bound quinone cofactor, topaquinone, in addition to an active site copper. These proteins are widely distributed among both prokaryotes and eukaryotes and have been characterized with regard to kinetic and structural properties. The function of the eukaryotic proteins is only now beginning to be understood with the hypothesis ranging from a role in cell–cell adhesion to a role in insulin signaling.
Ascorbate Oxidase
Authors: Messerschmidt Albrecht
Published: April 2006

Ascorbate oxidase (AO) is a multicopper oxidase related to laccase and ceruloplasmin. It catalyzes the four‐electron reduction of dioxygen to water with concomitant one‐electron oxidation of the substrate. The most efficient reducing substrate is l‐ascorbate, but several one‐electron reductants may interact with AO. It occurs in higher plants in both vegetative and reproductive organs in the cytoplasm of the cells. The biological function of AO is still unclear. A very attractive function is its involvement in anti‐oxidative defense. AO has been intensively characterized by spectroscopic, kinetic, electrochemical, and X‐ray crystallographic methods. The amino acid sequences have been determined from several plant sources and fungi. The X‐ray structure of AO from zucchini shows that the monomer of 552 residues is built up by three domains arranged sequentially on the polypeptide chain. The folding of all three domains is of a ß‐barrel type. Each monomer has three disulfide bridges. It contains a mononuclear type 1 copper site in domain 3 and a trinuclear type 2/type 3 copper site between domains 1 and 3. The mononuclear copper site has the four canonical type 1 copper ligands (His, Cys, His, Met) also found in plastocyanin and azurin. The trinuclear copper site has eight histidine ligands (symmetrically supplied by domains 1 and 3) and two oxygen ligands. The type 3 copper pair is bridged by an OH
−
or O
2−
. The remaining copper has two histidine ligands and an OH
−
or H
2
O ligand. The average copper–copper distance in oxidized AO is 3.74 Å. The shortest distance between the type 1 copper center and the trinuclear copper center is 12.2 Å. X‐ray structures of the fully reduced, peroxide and azide forms of AO have been determined. In the fully reduced form, the trinuclear site undergoes strong changes. The bridging oxygen ligand is released and the copper–copper distances increase from an average of 3.7 Å to 5.1 Å for the copper pair and to about 4.2 Å from the paired atoms to the third copper atom. In the peroxide form, the peroxide is bound end‐on to one copper atom of the copper pair while two azide molecules are bound in the same fashion to the same copper atom. Spectroscopic and kinetic studies reveal that the entry site for electrons from the reducing substrate is the mononuclear copper and the dioxygen binding site is the trinuclear copper species. The enzyme acts in a ‘two‐site ping‐pong bi‐bi’ mechanism. A proposal for the catalytic mechanism of AO based on the available data is given. Aspects of intramolecular electron transfer are discussed.
Ceruloplasmin
Authors: Lindley Peter F.
Published: April 2006

Ceruloplasmin is a multi‐copper oxidase that contains most of the copper present in the plasma. It is an acute‐phase reactant that exhibits a two‐ to three‐fold increase over the normal concentration of 300 mg ml
−1
in adult plasma. However, the precise physiological role(s) of ceruloplasmin has been the subject of intensive debate and it is likely that the enzyme has a multi‐functional role, including iron oxidase activity and oxidation of biogenic amines. The three‐dimensional X‐ray structure of the human enzyme shows that the molecule is composed of six cupredoxin‐type domains arranged in a triangular array. There are six integral copper atoms per molecule (mononuclear sites in domains 2, 4, and 6 and a trinuclear site between domains 1 and 6) and two labile sites with roughly 50% occupancy. Further structural studies on the binding of metal cations by the enzyme have indicated a putative mechanism for ferroxidase activity. Other studies have located the binding sites for an inhibitor (azide) and various substrates [aromatic diamines, biogenic amines, and
D
‐lysergic acid diethylamide (LSD)]. The binding site of the azide moiety is topologically equivalent to one of the sites reported for ascorbate oxidase. However, there are two distinct binding sites for amine substrates; aromatic diamines bind at the base of domain 4 remote from the mononuclear copper site, whereas the biogenic amine series typified by serotonin, epinephrine, and dopa bind in close vicinity to that site utilized by cations in domain 6 and close to the mononuclear copper.
Yeast Copper Metallothionein
Authors: Peterson Cynthia W
Published: April 2006

The first structure of yeast copper metallothionein (1) was determined from solution NMR data using experimental NOEs and dihedral angle constraints along with specific metal to Cys connectivities derived for the isomorphic Ag(I) substituted Cu(I) yeast MT. In solution, both MTs bind seven moles of Cu(I) or Ag(I) ions, respectively, in a single cluster embedded in a cleft between two large parallel protein loops with only the metals on the open side of the cleft exposed to the solvent.

It is reassuring to see the precision of the earlier solution structure compared to the recently published crystal structure (2) of a yeast copper thionein construct lacking the first 4 and last 13 residues of the intact protein. All of the crystal metal–Cys connectivities are identical to the previous solution structure, with the additional verification of the earlier postulated third Cys ligand to metal VI. The only difference is that the truncated, crystallized CuMT protein binds an eighth Cu(I) ion, labeled Cu39. (Note error in (2) where the “copper ion missing in solution structure” is misidentified as Cu44). Considering the fact that two of the three coordinating cysteines for Cu39 in (2) come from the N terminus, it is conceivable that cutting off four residues from this end enables an eighth metal to bind. Unfortunately, no solution study of the Cu(I) binding stoichiometry to this truncated form of the protein was reported. Naturally, the important structure is the structure of the native, full‐length yeast MT. We, therefore, recommend that caution be exercised before drawing any conclusions about the native protein structure on the basis of the crystal structure on the truncated yeast MT construct.
Flood Early Warning Systems for Hydrological (Sub) Catchments
Authors: Werner Micha Guido Franciscus , Schellekens Jaap , Kwadijk Jacob Cornelis Jan
Published: April 2006

Provision of early warning is an effective strategy in reducing flood damage and loss of life due to flooding. Flood forecasting and warning systems are important instruments in supporting relevant authorities issuing appropriate warnings. With the advent of computer‐based simulation techniques, computer‐based data processing capabilities, and computer‐based communication facilities, the impact of hydroinformatics on flood forecasting in support of flood warning is manifest. In this article, an overview is given of flood forecasting systems for providing warnings in hydrological catchments. This overview is given from the perspective of the position of flood forecasting within the process of detection, forecasting, warning, and response. A categorization of flood forecasting systems is introduced, and the elements of a flood forecasting system are discussed.
Digital Elevation Model Analysis and Geographic Information Systems
Authors: Moglen Glenn E , Maidment David R
Published: April 2006

This article presents the technology of Geographic Information Systems (GIS) applied to a particular form of representation of topography, the digital elevation model (DEM). It first defines what a DEM is and introduces the basic properties of all DEMs, as well as several common sources of DEM data. Then the basic concepts of GIS technology are presented, defining what a GIS is, what fundamental data types it can store, and what kind of manipulations it can perform. Some of the most common GIS software packages are discussed. The remainder of the article focuses on the use of GIS technology for the interpretation of DEM in a hydrologic context. The principles of flow direction, flow accumulation, watershed delineation, flow lengths, slopes, and travel times as derived from DEM data within a GIS are presented. A brief case study is presented illustrating a number of the concepts presented in this article.
Weather Patterns and Weather Types
Authors: McKendry Ian G
Published: April 2006

In popular usage, the terms “weather pattern” and “weather type” are used variously and often imprecisely to describe states of the atmosphere. An understanding of weather processes and patterns has important applications in such diverse areas as air‐quality management, hydrology, water management, human health, forestry, agriculture, energy demand, transportation safety, the insurance industry, economics, and tourism. These terms are formally defined and the various classification techniques that form the basis of synoptic climatology are described. In summarizing the various methods used to identify weather patterns and types, it is abundantly clear that underlying such approaches are significant assumptions about the state of the atmosphere together with varying degrees of subjectivity inherent in the techniques themselves. It is important that these constraints are adequately acknowledged in all applications of the techniques outlined. Finally, the impacts of computing advances, new techniques, and enhanced datasets on synoptic climatology are described.
Models of Clouds, Precipitation and Storms
Authors: Flossmann Andrea I
Published: April 2006

Clouds play an important role for life on earth. Apart from influencing, for example, the radiative balance of the atmosphere and the lifetime of atmospheric trace constituents, they are the essential element in the hydrological cycle. Clouds transport the evaporated water of the oceans to the continents where the precipitation releases the water load. This release of water can be more or less vigorous depending on the energy stored in the cloud in the form of condensed hydrometeors (liquid or solid). This energy depends on the amount of available moisture and the way the vertical lifting necessary for cloud formation proceeds. We distinguish here mainly two different forms with varying extensions on the horizontal scale: the gentle uplift associated to the large‐scale lifting, for example at a frontal zone, and the vigorous small‐scale ascent associated with convection, knowing that also mixed forms of the lifting occur.

This article provides an introduction to the complex subject of modeling clouds, the production of precipitation, and the development of cloud and storm systems. The elements intervening in cloud modeling are exposed, starting from a description of the physical phenomena. On the basis of the occurring scale problem, a number of approaches for simplification are presented. These simplifications concern the dynamics as well as the microphysics. Bulk and bin modeling approaches are explained, as well as cumulus parameterizations. Some numerical problems are discussed. This approach gives an insight into current state‐of‐the‐art cloud modeling and the necessary balance between the degree of parameterization, the number of physical and chemical processes relevant to a particular problem, and the available computing resources.
Rainfall Trend Analysis: Return Period
Authors: Clarke Robin T
Published: April 2006

This article describes the concept of return period, with particular reference to the analysis of rainfall records. Methods are described for calculating return levels, corresponding to different return probabilities, when rainfall is accumulated over different time intervals. In the case of intense, short‐duration rainfalls, threshold models are illustrated. The article points out that the concept of return period is most easily interpreted where stationarity in the rainfall regime can be assumed, so that it is important to establish whether rainfall records show evidence of trends over time. Procedures are discussed for testing whether time trends exist in annual and monthly rainfall, in the occurrence and magnitude of daily rainfalls, and in annual maximum rainfall intensities over different durations. Where a trend in rainfall regime is apparent, an alternative to the concept of return period is suggested, on the basis of the probability of occurrence of an extreme event of specified magnitude, during a period extending into the future during which the observed trend can be assumed to continue.
Fog as a Hydrologic Input
Authors: Sampurno Bruijnzeel LA , Eugster Werner , Burkard Reto
Published: April 2006

This article reviews the hydrologic importance of fog in its various forms. Meteorologically, fog is defined as a ground‐touching cloud with a visibility in the horizontal of less than 1000 m. The most widely occurring fog types include radiation fog, sea fog and steam fog, and advection fog, but often fog is also referred to by its location of occurrence (coastal, valley, or mountain fog). The physical processes underlying the various types of fog are described briefly. The use, advantages, and limitations of the most common types of fog collectors, fog detectors, and fog droplet spectrometers are dealt with before embarking on a discussion of techniques for the measurement and modeling of fog deposition on forest vegetation. Results of fog deposition measurements made at selected locations (representing coastal vs. inland, lowland vs. montane, and temperate vs. tropical conditions) are compared. The data confirm the importance of fog interception at many coastal and montane sites across the tropical to mediterranean and warm‐temperate climatic spectrum. Under more continental conditions, contributions by fog are usually more modest except on windy mountain ridges and summits. Finally, the paper indicates the chief gaps in knowledge regarding the measurement and importance of fog as a hydrologic input.
Evaporation Modeling: Potential
Authors: Allen Richard G
Published: April 2006

Potential evaporation (
E
p
) has had a relatively broad range of definition over the past century. It is defined here as the quantity of water evaporated per unit area per unit time from an idealized extensive free‐water surface under existing atmospheric conditions. Three primary, common means to estimate
E
p
have been used during the past century. These are (i) pan evaporation measurement, (ii) an estimate of potential evapotranspiration based on weather data, and (iii) a reference evapotranspiration. Of these three, reference evapotranspiration (
ET
ref
) has the more practical application. “Potential evapotranspiration” (
ET
p
) had widespread usage from the 1940s through the 1970s, when the term was used to represent a maximum evaporative index from which to derive estimates of actual
ET
from vegetation. However, there are several major, contrasting definitions for
ET
p
and several challenges associated with its usage. One of the primary definitions used for
ET
p
is the rate of evaporation and transpiration from a saturated (free‐water) vegetated surface so that the evaporation process occurs at the potential level. Challenges in sustaining a saturated surface and in measuring weather data that are coincident with such a surface make this definition for
ET
p
theoretically attractive, but practically difficult. Standardized parameterizations of the Penman–Monteith equation are described for calculating
ET
for grass and alfalfa references. The reference evapotranspiration, despite some shortcomings, can be a consistent and reproducible index for a weather‐based potential evaporation.
Evaporation of Intercepted Rainfall
Authors: David Jorge Soares , Valente Fernanda , Gash John HC
Published: April 2006

When rain falls on to a vegetated surface (gross rainfall), a part is intercepted by the canopy and evaporated directly back into the atmosphere (interception loss). The remainder of the rainfall reaches the ground (net rainfall) either through gaps and by dripping from the canopy (throughfall), or by running down the main stem (stemflow). The canopy storage capacity is the minimum amount of water necessary to completely saturate the canopy surface. Interception loss is conventionally measured as the difference between the incident gross rainfall, and the sum of throughfall and stemflow. It is usually a significant component of the overall evaporation and may play an important role in watershed water balance. The total amount of interception loss depends on the rate of evaporation from the wet canopy, the canopy storage capacity, and the distribution and intensity of rainfall. Interception loss is particularly high in forests due to their high aerodynamic roughnesses. Available models range from empirical relationships to physically based conceptual models. Within the latter, the Rutter‐type models are those that have been taken up as the more generally applicable technique. Most of the models rely on the use of the Penman–Monteith equation to estimate the evaporation rate. Current research is largely directed at modeling in horizontally heterogeneous vegetation, where the Penman–Monteith equation may not be valid.
Characterizing Forest Canopy Structure and Ground Topography Using Lidar
Authors: Dubayah Ralph , Peterson Birgit , Rhoads Joshua , Dietrich William E
Published: April 2006

Remote sensing observations increasingly are used to obtain the detailed information needed about land surface state required for hydrological analyses. However, many of the surface state parameters required for such analyses are related to the vertical structures of surface vegetation and topography, that are often difficult to measure using passive optical and radar remote sensing technologies. A new technology, lidar (light detection and ranging) remote sensing, has proven highly effective for characterizing land surface structure in great detail, including subcanopy topography, canopy height, foliar profile and biomass, among others. In this article, we review the theory and application of lidar remote sensing for characterizing land surface states for hydrological analysis. First we present a brief overview of lidar, and discuss similarities and distinctions between the small‐footprint systems commonly used in commercial applications and large‐footprint approaches used in research and space‐based systems. We next describe common land surface variables that are often used in hydrological analysis and how these are related to vertical structures observable from lidar. Lastly, we present how lidar may be used to recover or parameterize these surface variables; in particular we focus on the observation of forest and topographic structures.
Estimation of Snow Extent and Snow Properties
Authors: Hall Dorothy K , Kelly Richard EJ , Foster James L , Chang Alfred TC
Published: April 2006

Important advances have been made in the measurement of seasonal snow cover since the advent of satellite remote sensing in the mid 1960s. Data from the visible, near‐infrared, infrared, and microwave portions of the electromagnetic spectrum have proven useful for measuring different properties of snow. In terms of snow mapping, sensors employing visible and near‐infrared wavelengths are now capable of accurately and reliably measuring snow‐cover extent with a spatial resolution of up to 250 m on a daily basis, and even higher resolution for less‐frequent coverage. Passive‐microwave data, available since the 1970s, have been utilized for measuring snow extent, depth and snow‐water equivalent (SWE), though at a coarse spatial resolution compared to visible data, while active‐microwave sensors such as scatterometers, provide valuable information on snowpack ripening. Capabilities of synthetic‐aperture radar (SAR) data for snow‐cover studies are still being explored, however, bands on current satellite SAR sensors are not ideal for measuring snow cover. Remote sensing data of snow cover are now well suited for use in hydrologic and general‐circulation models. Inclusion of remotely‐sensed data significantly enhances our understanding of the Earth's weather and climate, and decadal‐scale climate change. Future improvements include refinement of snow‐cover extent measurements, minimizing SWE errors, and improving our ability to ingest remote sensing data of snow into models.
Soil Hydraulic Properties
Authors: Durner Wolfgang , Flühler Hannes
Published: April 2006

The accurate knowledge of hydraulic properties for unsaturated soils is critical in addressing problems in a variety of disciplines such as hydrology, ecology, environmental sciences, soil science, and agriculture. The purpose of this paper is to review the characterization of unsaturated soil hydraulic properties for their applicability in models simulating unsaturated water transport. In a theoretical section, we present the fundamentals for the definitions of the hydraulic properties in the framework of the continuum theory as well as provide the common parameterizations of the hydraulic functions. The characterization and parameterization of hysteresis and the phenomenon of dynamic effects in hydraulic properties are addressed in subsequent sections. Finally we discuss issues related to the handling of spatial and temporal variability, including geostatistical characterization, upscaling, and scale dependency of effective properties. The review closes with a summary on limits and opportunities for modeling water transport with Richards' equation.
Models of Water Flow and Solute Transport in the Unsaturated Zone
Authors: Šimůnek Jirka
Published: April 2006

A large number of models for simulating water flow and solute transport in the unsaturated zone are now increasingly being used for a wide range of applications in both research and management. Modeling approaches range from relatively simple analytical and semianalytical solutions, to complex numerical codes. While analytical and semianalytical solutions are still popular for some applications, the ever‐increasing power of personal computers and the development of more accurate and numerically stable solution techniques have motivated much wider use of numerical codes in recent decades. The wide use of numerical models is also significantly enhanced by their availability in both the public and commercial domains, and by the development of sophisticated graphics‐based interfaces that can tremendously simplify their use.

In this paper I focus mainly on numerical models, give a brief history of their development, and discuss some of the more often used numerical techniques including relatively efficient matrix solvers that now are available for multidimensional models. Names and web addresses of some of the more popularly used numerical codes simulating vadose zone processes are also provided. Finally, some typical problems in which the numerical codes have been applied are identified.
Sediment Yield Prediction and Modeling
Authors: White Sue
Published: April 2006

The estimation of sediment yield – the amount of sediment reaching or passing a point of interest in a given period of time – is an inherently complex and uncertain science as it is the integrated outcome of erosion, sediment transport, and deposition processes through an often complex landscape. Thus, sediment yield can vary greatly from year to year with variation in climate, land use, and land management. A range of estimation techniques have been developed ranging from simple empirical relationships between sediment yield and river flow or basin characteristics, through methods to scale soil erosion estimates or measurements using delivery ratios, to physically based distributed models. Descriptions of the various approaches, together with advantages and shortcomings of these methods, are given. For prediction of future sediment yields, the uncertainties are even greater as climate and land‐use pressures are not easily defined for hypothetical situations. Here, recommendations are made to incorporate uncertainty into the prediction and decision‐making process.
Suspended Sediment Transport – Flocculation and Particle Characteristics
Authors: Droppo Ian G
Published: April 2006

In the history of sediment transport research within hydrological sciences, there has possibly been no greater paradigm shift than that which has been provided by the identification of flocculation as a dominant mechanism operating within, and mediating, cohesive suspended sediment transport. Flocculation (the process of aggregating smaller particles together to form larger particles) significantly modifies the hydrodynamic properties of the sediment by altering their effective size, shape, density, porosity, and composition. Such changes have a dramatic impact on the downward flux of sediments and as such influence the transportation and fate of suspended sediments. The traditional assumption of suspended sediment being inorganic individual grains for the quantification and modeling of sediment transport is likely to result in erroneous results and management decisions. Flocs settle faster than their individual constituent particles (but orders of magnitude slower than that predicted by Stokes' equation for a similar size), and, for large flocs, can have porosity close to 100% and a corresponding density close to that of water. Flocs are composed of significant living organic components (primarily bacteria) which produce an extracellular polymeric substance (fibrils) which glues particles together giving them greater strength than an electrochemically bound floc, and a pseudo plastic nature. Because of this active living component, flocs should be thought of as micro ecosystems (composed of a matrix of water, inorganic, and organic particles) with autonomous and interactive physical, chemical, and biological functions or behaviors operating within the floc matrix. A better understanding of how floc structure influences floc behavior will help to refine our knowledge and management of suspended sediment transport in a variety of aquatic ecosystems.
Lake Sediments as Records of Past Catchment Response
Authors: Dearing John
Published: April 2006

The sediments that accumulate at the beds of lakes are natural archives of information about catchment processes that extend back far further than instrument records. This article reviews the kinds of questions that long records can address, and summarises the technical and analytical approaches taken. Records of river discharge, sediment delivery, and soil erosion obtained in this way over decades and centuries are increasingly used to understand the behaviour of fluvial systems, especially the combined effects of human activity and climate. Case‐studies now available for different parts of the world can be used to provide the temporal perspective to the current levels of fluvial and erosional processes in human‐dominated landscapes, and together show the strong dependence of sediment delivery on catchment size.
Water Quality Monitoring
Authors: Chapman Deborah V , Meybeck Michel , Peters Norman E
Published: April 2006

Water quality monitoring is the process of gathering data that describes the physical, chemical, and biological condition of a water body. This chapter presents an overview of the processes involved in water quality monitoring and illustrates some of the approaches used with examples of existing monitoring programs. Over the last century, improved understanding of water quality, combined with advances in measurement and monitoring technology have increased the possibility of measuring hundreds of different variables in surface and groundwaters. However, efficient use of resources for monitoring depends on careful selection of objectives for the water quality monitoring program and on targeting variables and monitoring methods that address those objectives. Recent appreciation of the close link between the physical and chemical condition of a water body and its biological component has led to the incorporation of biological approaches in many large‐scale programs to assess surface water quality. Today, monitoring programs take many forms, from measurement of a few specific variables to establish trends or effectiveness of remediation measures, to sophisticated evaluation of toxic impacts of wastewaters, to relatively simple determination of the state of the aquatic environment using citizen participation. Confidence in all data gathered and its resultant usefulness for management and policy development is essential; this can only be achieved by a careful program of quality assurance that extends from sample collection in the field, to analysis in the laboratory, to data handling and manipulation.
Effects of Human Activities on Water Quality
Authors: Peters Norman E , Meybeck Michel , Chapman Deborah V
Published: April 2006

Water quality comprises the physical, chemical, and biological characteristics of a water body. The water body acquires these characteristics from a suite of complex interactions among the water, atmosphere, soils, and lithology. Human activities affect both water quality and quantity. Human activities change land use and land cover, which changes the water balance and usually changes the relative importance of processes that control water quality. Furthermore, most human activities generate waste ranging from gases to concentrated radioactive wastes. Although each issue can be subdivided into a myriad of individual processes or activities, the primary water‐quality issues affected by human activities include organic material, trace elements (heavy metals), acidic atmospheric deposition and runoff, salinization, nutrients (primarily nitrogen and phosphorus), pathogenic agents including bacterial pathogens, enteric viruses, and protozoans, suspended sediment, oil and grease, synthetic organic compounds, thermal pollution, exotic and invasive species, pesticides and herbicides, and radioactivity. In addition to the various issues, each human activity has a potential cyclical and cascading effect on water quality and quantity along hydrologic pathways. The degradation of water quality in one part of a watershed can have negative effects on users downstream; the timescale of effects is determined by the residence time of that substance along various hydrological pathways. An extremely important factor is that substances added to the atmosphere, land, and water generally have relatively long timescales for removal or cleanup. The nature of the substance, including its affinity for adhering to soil and its ability to be transformed, affect the mobility and the timescale for the removal of the substance and its effects on water quality, for example, biota.