bluuebunny/crossref_metadata_2025 huggingface dataset:
Late-summer carbon fluxes from Canadian forests and peatlands along an eastwest continental transect
Authors: Coursolle Carole , Margolis Hank A , Barr Alan G , Black T Andrew , Amiro Brian D , McCaughey J Harry , Flanagan Lawrence B , Lafleur Peter M , Roulet Nigel T , Bourque Charles P.-A , Arain M Altaf , Wofsy Steven C , Dunn Allison , Morgenstern Kai , Orchansky Alberto L , Bernier Pierre Y , Chen Jing M , Kidston Joe , Saigusa Nobuko , Hedstrom Newell
Published: April 2006

Net ecosystem productivity (NEP) during August 2003 was measured by using eddy covariance above 17 forest and 3 peatland sites along an eastwest continental-scale transect in Canada. Measured sites included recently disturbed stands, young forest stands, intermediate-aged conifer stands, mature deciduous stands, mature conifer stands, fens, and an open shrub bog. Diurnal courses of NEP showed strong coherence within the different ecosystem categories. Recently disturbed sites showed the weakest diurnal cycle; and intermediate-aged conifers, the strongest. The western treed fen had a more pronounced diurnal pattern than the eastern shrub bog or the Saskatchewan patterned fen. All but three sites were clearly afternoon C sinks. Ecosystem respiration was highest for the young fire sites. The intermediate-aged conifer sites had the highest maximum NEP (NEPmax) and gross ecosystem productivity (GEPmax), attaining rates that would be consistent with the presence of a strong terrestrial C sink in regions where these types of forest are common. These results support the idea that large-scale C cycle modeling activities would benefit from information on the age-class distribution and disturbance types within larger grid cells. Light use efficiency followed a pattern similar to that of NEPmax and GEPmax. Four of the five recently disturbed sites and all three of the peatland sites had low water use efficiencies.
Effects of organic matter removal, soil compaction, and vegetation control on 5-year seedling performance: a regional comparison of Long-Term Soil Productivity sites
Authors: Fleming Robert L , Powers Robert F , Foster Neil W , Kranabetter J Marty , Scott D Andrew , Ponder Jr. Felix , Berch Shannon , Chapman William K , Kabzems Richard D , Ludovici Kim H , Morris David M , Page-Dumroese Deborah S , Sanborn Paul T , Sanchez Felipe G , Stone Douglas M , Tiarks Allan E
Published: April 2006

We examined fifth-year seedling response to soil disturbance and vegetation control at 42 experimental locations representing 25 replicated studies within the North American Long-Term Soil Productivity (LTSP) program. These studies share a common experimental design while encompassing a wide range of climate, site conditions, and forest types. Whole-tree harvest had limited effects on planted seedling performance compared with the effects of stem-only harvest (the control); slight increases in survival were usually offset by decreases in growth. Forest-floor removal improved seedling survival and increased growth in Mediterranean climates, but reduced growth on productive, nutrient-limited, warmhumid sites. Soil compaction with intact forest floors usually benefited conifer survival and growth, regardless of climate or species. Compaction combined with forest-floor removal generally increased survival, had limited effects on individual tree growth, and increased stand growth in Mediterranean climates. Vegetation control benefited seedling growth in all treatments, particularly on more productive sites, but did not affect survival or alter the relative impact of organic matter removal and compaction on growth. Organic matter removal increased aspen coppice densities and, as with compaction, reduced aspen growth.
Factors affecting distribution of wood, detritus, and sediment in headwater streams draining managed young-growth red alder  conifer forests in southeast Alaska
Authors: Gomi Takashi , Johnson Adelaide C , Deal Robert L , Hennon Paul E , Orlikowska Ewa H , Wipfli Mark S
Published: April 2006

Factors (riparian stand condition, management regimes, and channel properties) affecting distributions of wood, detritus (leaves and branches), and sediment were examined in headwater streams draining young-growth red alder (Alnus rubra Bong.)  conifer riparian forests (< 40 years old) in southeast Alaska. More riparian red alder were found along streams affected by both timber harvesting and mass movement than in streams affected by timber harvesting alone. Young-growth stands produced little large wood material (diameter ≥10 cm) and had little effect on altering the size distribution of functional large wood in channels, although more alder wood pieces were found in streams with greater numbers of riparian alder trees. Legacy wood pieces (>40 years old) remained in channels and provided sites for sediment and organic matter storage. Despite various alderconifer mixtures and past harvesting effects, the abundance of large wood, fine wood, and detritus accumulations significantly decreased with increasing channel bank-full width ( 0.53.5 m) along relatively short channel distances (up to 700 m). Changes in wood, detritus, and sediment accumulations together with changes in riparian stand characteristics create spatial and temporal variability of in-channel conditions in headwater systems. A component of alder within young-growth riparian forests may benefit both wood production and biological recovery in disturbed headwater stream channels.
A lack of native congeners may limit colonization of introduced conifers by indigenous insects in Europe
Authors: Roques Alain , Auger-Rozenberg Marie-Anne , Boivin Solen
Published: April 2006

We compared the recruitment of phytophagous arthropod pests onto exotic conifers introduced in Europe without any congeners with that of exotic conifers that have native congeners. In 130 years of extensive plantation forestry in Europe, Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) recruited only 87 arthropod species, i.e., only 33.9% of the number of associated arthropod species in its native range (257 spp.). Exotic species of Cupressaceae without indigenous congeners also recruited only a portion (3.4% to 57.9%) of the arthropod fauna observed in their native range. In both cases, the majority of the recruited species were polyphagous, i.e., that they can feed on plants of different families of conifers and (or) angiosperms. In contrast, exotic conifers with native congeners recruited most of the insects colonizing the native congeneric conifers. Differences in arthropod recruitment were observed according to both guild and feeding habit, with the externally feeding herbivores being dominant. Typically, the damage caused by native insects that had been recruited by exotic conifers without congeners was limited, whereas the damage caused by native insects that had been recruited by exotic conifers with congeners often led to severe outbreaks at the time the shift between hosts occurred. However, when a highly specialized exotic insect was introduced along with the host, the invasive insect tended to occupy the entire niche, causing more damage than in the original range, in the absence of natural enemies and indigenous competitors.
Application of slow-release tablets to enhance white pine regeneration: growth response and efficacy against white pine blister rust
Authors: Pitt Douglas G , Meyer Timothy , Park Mya , MacDonald Linda , Buscarini Teresa , Thompson Dean G
Published: April 2006

Three field studies were established in northeastern Ontario to test the ability of slow-release tablets to provide prophylactic protection against white pine blister rust (caused by Cronartium ribicola J.C. Fisch.) and thereby improve the long-term survival, health, and growth of eastern white pine (Pinus strobus L.) seedlings. Experimental treatments included factorial rate combinations the fungicide triadimefon (Bayleton®), the insecticide imidacloprid (Merit®), and fertilizer (NPK, 15:8.5:3.75). Mean foliar fungicide residues increased to maximal levels (0.21 to 3.1 µg/g fresh mass (fm)) within 1 to 2 years posttreatment and declined markedly to <0.3 µg/g fm 3 to 4 years posttreatment. Dose-dependent and temporal trends observed in foliar residue levels were reflected by parallel trends in efficacy. At ≥2000 ppm triadimefon, infection rates were reduced to between 35% and 70% and mortality rates were reduced to between 6% and 52% over seven growing seasons across the three sites. In contrast, untreated seedlings had infection rates between 60% and 98% and mortality rates between 30% and 90%. Neither fungicide nor insecticide treatments had significant effects on surviving seedling growth. Differences in fungicide uptake, disease incidence, and seedling growth in response to fertilization were observed among the three sites. Direct weed control, provided at one site, appeared to offer relatively greater health and growth benefits than fertilization.
Long-Term Soil Productivity: genesis of the concept and principles behind the program
Authors: Powers Robert F
Published: April 2006

The capacity of a forest site to capture carbon and convert it into biomass defines fundamental site productivity. In the United States, the National Forest Management Act (NFMA) of 1976 mandates that this capacity must be protected on federally managed lands. Responding to NFMA, the USDA Forest Service began a soil-based monitoring program for its managed forests. Lacking an extensive research base, soil-based standards were predicated largely on professional judgment. To provide a stronger foundation, a national program of Long-Term Soil Productivity (LTSP) research was established. The LTSP program addresses both short- and long-term consequences of site and soil disturbance on fundamental forest productivity. Research centers on two key properties affecting a site's long-term productive capacity, site organic matter and soil porosity, each of which is readily influenced by management. A coordinated research network of more than 100 field installations in the United States and Canada is examining how pulse changes in these properties affect soil processes supporting vegetative growth and potential productivity. Results from installations with ≥5 years of response were presented on the 10th anniversary of LTSP, and the latest findings are assembled here. This paper describes the evolution of the study and the characteristics of the oldest field installations.
Cambial activity of Populus tremula × Populus alba clone 717-1B4 in hydroponic culture
Authors: Morabito Domenico , Caruso Aurore , Carpin Sabine , Carli Cédric , Laurans Françoise , Depierreux Christiane , Kahlem Guy , Label Philippe
Published: April 2006

Populus tremula Michx. × Populus alba L. clone 717-1B4 plants were grown in a hydroponic system in an effort to detect cambial activity in a changing nutrient environment. The secondary growth of the stem was determined by automated measurement of radial growth, as well as by histological study. This is the first time poplar cambial activity has been recorded in a hydroponic system. Further, we demonstrate that nutrient limitations can be tested with progressive deprivation of liquid medium. The system lends itself to measurements of stomatal conductance, primary stem growth, leaf growth, and radial stem growth. In this study we found that primary and secondary growth were affected by nutrient solution limitations. This hydroponic system will be valuable in elucidating the impact of environmental, physiological, and molecular factors on cambial activity and wood formation.
Effects of low-calcium reperfusion and adenosine on diastolic behavior during the transitory systolic overshoot of the stunned myocardium in the rabbit
Authors: González Germán E. , Rodríguez Manuel , Donato Martín , Palleiro Jimena , D'Annunzio Verónica , Morales Celina , Gelpi Ricardo J.
Published: April 2006

The aims of the present study were to determine whether the transitory systolic overshoot (TSO) that occurs in the early reperfusion (R) of the stunned myocardium is accompanied by diastolic alterations, and to determine whether the R with low Ca2+ Krebs–Henseleit’s solution or with adenosine modifies these alterations. Isolated–isovolumic rabbit hearts were divided in 3 groups (G). G1 (n = 11) was perfused with Krebs–Henseleit's solution, subjected to 15 min of global ischemia and 30 min R; G2 (n = 10) was reperfused during the first 10 min with Krebs–Henseleit's solution [Ca2+] = 1 mmol/L, which was increased in the perfusate to 1.5 mmol/L up to 20 min R and at 2.5 mmol/L from 20 to 30 min R. G3 (n = 12) was perfused with Krebs–Henseleit's solution with adenosine (0.03 μg·kg–1·min –1) from 10 min before ischemia and during all R. Left ventricular (LV) +dP/dtmax (mmHg/s), LV end diastolic pressure (LVEDP, mmHg), and 1 relaxation index (t1/2) were measured in preischemic state, at 30, 50, 60, 70, 90, and 120 s R, and then at 5 and 30 min R. The +dP/dtmax recovered to 621 ± 77 mmHg/s (p > 0.05), 346 ± 31 mmHg/s (p < 0.05 vs. G1), and 533 ± 76 mmHg/s (p > 0.05) from preischemic value of 730 ± 39, 690 ± 32, and 758 ± 57 in G1, G2, and G3, respectively. The LVEDP in G1 and G3 increased early in the R, and it was negatively correlated with the +dP/dtmax (r = –0.63, p = 0.0369; and r = –0.71, p = 0.0090, respectively). The R with low Ca2+ abolished this correlation and attenuated the TSO phase. The correlation between LVEDP and +dP/dtmax in G1 and G3 and the lack of correlation in G2 suggests there are common mechanisms for the systolic and diastolic alterations during the TSO phase that are possibly related to Ca2+ overload but not with the vascular tone.
Dual X-ray absorptiometry model for characterizing water in the human forearm using multiple frequency bioimpedance analysis
Authors: Bartolini Miria E. , Wilson Kyle , Raja Mohan , Raymer Graydon H. , Thompson R. Terry , Webber Colin E. , Moran Gerald R.
Published: April 2006

The purpose of this study was to develop a method for measuring intracellular (ICW) and extracellular water (ECW) in the human forearm using multiple frequency bioimpedance analysis (MFBIA). The approach was (i) to measure whole-body and forearm fat-free mass using dual X-ray absorptiometry (DXA); (ii) to use these measurements to estimate the fat-free mass (FFM) resistivity in both the forearm and in the whole body; and (iii) to use the ratio of these FFM resistivities to estimate the resistivity in the ICW and ECW compartments of the forearm. To first demonstrate the accuracy of the DXA software in differentiating lean body mass from fat and bone within a volume of tissue, ex-vivo bovine muscle tissue samples (n = 3) were used to approximate the physical properties of the human forearm. It was found that although the human whole-body software overestimates FFM, it was slightly underestimated by the small animal software. Using this technique, DXA measures of FFM were obtained from human volunteers (n = 11; age = 20 ± 5 years; height = 170 ± 12 cm; mass = 64 ± 16 kg). These measures were used in conjunction with MFBIA measures of impedance of the whole body and of the forearm to determine the resistivities of the ICW and ECW compartments of the forearm, namely 375.8 ± 25.2 Ωcm and 55.6 ± 3.7 Ωcm, respectively. These were used in MFBIA equations to calculate the ICW, ECW, and total arm water (TAW) volumes of the human forearm. The calculated TAW and the ECW (± SD) volume fraction (667.29 ± 200.15 mL and 0.169 ± 0.039 mL, respectively) were in agreement with literature values. MFBIA results were compared with those obtained using nuclear magnetic resonance relaxometry (NMRR). MFBIA was performed on 15 subjects before and after an intense maximal handgrip exercise to estimate changes in water volume in muscle. Following exercise, the total and intracellular water of the forearm increased on average by 8% ± 3% and 10% ± 4% (mean ± SD), respectively. In 5 healthy volunteers, MFBIA and NMRR were performed before and after a similar exercise of the forearm muscle. The changes with exercise of intracellular and total arm water volumes as measured by MFBIA were estimated. The percent increases in total water were found to be 9.4% ± 4.2% and 9.4% ± 2.6% and in intracellular water were found to be 10.6% ± 4.6% and 12.0% ± 2.8% (mean ± SD) for NMRR and MFBIA, respectively. The results show that the exercise-induced changes in ICW and TAW determined with the MFBIA model are consistent with those observed with NMRR and radiotracer literature.
Microglia in cerebral ischemia: molecular actions and interactionsThis paper is one of a selection of papers published in this Special Issue, entitled Young Investigator's Forum.
Authors: Lai Aaron Y. , Todd Kathryn G.
Published: April 2006

The precise role of microglia in stroke and cerebral ischemia has been the subject of debate for a number of years. Microglia are capable of synthesizing numerous soluble and membrane-bound biomolecules, some known to be neuroprotective, some neurotoxic, whereas others have less definitive bioactivities. The molecular mechanisms through which microglia activate these molecules have thus become an important area of ischemia research. Here we provide a survey review that summarizes the key actions of microglial factors in cerebral ischemia including complement proteins, chemokines, pro-inflammatory cytokines, neurotrophic factors, hormones, and proteinases, as well several important messenger molecules that play a part in how these factors respond to extracellular signals during ischemic injuries. We also provide some new perspectives on how microglial intracellular signaling may contribute to the seemingly contradictory roles of several microglial effector molecules.
Versican: signaling to transcriptional control pathwaysThis paper is one of a selection of papers published in this Special Issue, entitled Young Investigator's Forum.
Authors: Rahmani Maziar , Wong Brian W. , Ang Lisa , Cheung Caroline C. , Carthy Jon M. , Walinski Hubert , McManus Bruce M.
Published: April 2006

Versican, a chondroitin sulfate proteoglycan, is one of the main components of the extracellular matrix, which provides a loose and hydrated matrix during key events in development and disease. Versican participates in cell adhesion, proliferation, migration, and angiogenesis, and hence plays a central role in tissue morphogenesis and maintenance. In addition, versican contributes to the development of a number of pathologic processes including atherosclerotic vascular diseases, cancer, tendon remodeling, hair follicle cycling, central nervous system injury, and neurite outgrowth. Versican is a complex molecule consisting of modular core protein domains and glycosaminoglycan side chains, and there are various steps of synthesis and processes regulating them. Also, there is differential temporal and spatial expression of versican by multiple cell types and in different developmental and pathological time frames. To fully appreciate the functional roles of versican as it relates to changing patterns of expression in development and disease, an in depth knowledge of versican’s biosynthetic processing is necessary. The goal of this review is to evaluate the current status of our knowledge regarding the transcriptional control of versican gene regulation. We will be focusing on the signal transduction pathways, promoter regions, cis-acting elements, and trans-factors that have been characterized.
Participatory role of natural killer and natural killer T cells in atherosclerosis: lessons learned from in vivo mouse studiesThis paper is one of a selection of papers published in this Special Issue, entitled Young Investigator's Forum.
Authors: Whitman Stewart C. , Ramsamy Tanya A.
Published: April 2006

Atherosclerosis is a multifactor, highly complex disease with numerous aetiologies that work synergistically to promote lesion development. One of the emerging components that drive the development of both early- and late-stage atherosclerotic lesions is the participation of both the innate and acquired immune systems. In both humans and animal models of atherosclerosis, the most prominent cells that infiltrate evolving lesions are macrophages and T lymphocytes. The functional loss of either of these cell types reduces the extent of atherosclerosis in mice that were rendered susceptible to the disease by deficiency of either apolipoprotein E or the LDL (low density lipoprotein) receptor. In addition to these major immune cell participants, a number of less prominent leukocyte populations that can modulate the atherogenic process are also involved. This review will focus on the participatory role of two “less prominent” immune components, namely natural killer (NK) cells and natural killer T (NKT) cells. Although this review will highlight the fact that both NK and NKT cells are not sufficient for causing the disease, the roles played by both these cells types are becoming increasingly important in understanding the complexity of this disease process.
Embryogenesis and larval differentiation in sponges
Authors: Leys S P , Ereskovsky A V
Published: April 2006

Having descended from the first multicellular animals on earth, sponges are a key group in which to seek innovations that form the basis of the metazoan body plan, but sponges themselves have a body plan that is extremely difficult to reconcile with that of other animals. Adult sponges lack overt anterior–posterior polarity and sensory organs, and whether they possess true tissues is even debated. Nevertheless, sexual reproduction occurs as in other metazoans, with the development of embryos through a structured series of cellular divisions and organized rearrangements of cellular material, using both mesenchymal and epithelial movements to form a multicellular embryo. In most cases, the embryo undergoes morphogenesis into a spatially organized larva that has several cell layers, anterior–posterior polarity, and sensory capabilities. Here we review original data on the mode of cleavage, timing of cellular differentiation, and the mechanisms involved in the organization of differentiated cells to form the highly structured sponge larva. Our ultimate goal is to develop interpretations of the phylogenetic importance of these data within the Porifera and among basal Metazoa.
Phylogeny and evolution of calcareous sponges
Authors: Manuel M
Published: April 2006

The most recent advances concerning the phylogeny and evolution of calcareous sponges (Calcarea or Calcispongia) are reviewed here, in the light of the history of taxonomy of the group and conceptions about its evolution, starting from Haeckel's works at the end of the 19th century. Calcisponge phylogeny has recently started to be addressed using modern tools of phylogenetic reconstruction: cladistic analysis of morphological characters and molecular phylogeny (so far using 18S and 28S rDNA sequences). The monophyly of calcareous sponges is strongly supported in these works, as is their subdivision into two clades, Calcinea (whose proposed synapomorphy is the basal position of nuclei in choanocytes, with no relation to the flagella) and Calcaronea (whose possible synapomorphy is the formation of the amphiblastula larva through the original process of eversion of the stomoblastula). While the molecular phylogeny of Calcinea is still in its infancy because of insufficient taxonomic sampling, several lines are emerging for the phylogeny of Calcaronea, and these are in strong disagreement with the classification issued from the "traditional" morphological approach. Phylogenetic hypotheses also permit the reconstruction of morphological character evolution, which appears complex and subject to a high level of homoplasy.
Adjustment of submerged swimming to changes in buoyancy in cormorants
Authors: Ribak G , Klein N , Weihs D , Arad Z
Published: April 2006

Waterbirds are buoyant because of volumes of air in their plumage and respiratory tract. When they are submerged, their buoyancy is reduced, owing to compression of these volumes of air with depth. We tested how the horizontal submerged swimming of cormorants (Phalacrocorax carbo sinensis (Blumelbach, 1798)) changed when their buoyancy was artificially reduced. Birds were filmed swimming under water once with lead weights (density 11 000 kg·m–3) and again with "dummy" weights (density 1100 kg·m–3) attached to their body. The dummy weights had negligible weight under water and served as control for the increased drag in the experiment. Cormorants swimming with weights tilted their bodies at an angle of 3°–7° below the swimming direction, whereas the body of birds in the control groups was tilted at 14°–16°. The tilt of the body affected the orientation and trajectory of the tail and feet during swimming. A hydrodynamic analysis showed that the lesser tilt of the body (while swimming with weights equivalent to 26% of body weight) resulted in a 55%–57% reduction of the vertical hydrodynamic forces (lift, drag, and thrust) generated by the birds to overcome buoyancy. When more weights were added and the birds became negatively buoyant, these vertical forces changed direction to prevent sinking. Thus, by adjusting the tilt of the body, the birds may dynamically control their buoyancy to maintain straight horizontal swimming despite changes in buoyancy.
Red blood cell size and the Fåhraeus–Lindqvist effect
Authors: Snyder G K , Sears R D
Published: April 2006

The reason for the large interspecies variation in vertebrate red blood cell (RBC) size is poorly understood. To test the effect of RBC size on blood viscosity, blood samples from two vertebrates, the dog (Canis familiaris L., 1758) and the greater siren (Siren lacertina L., 1766), with extremely different RBC sizes were examined. In this study, we examined whether RBC size altered the relationship of viscosity and viscometer tube diameter, the well-known Fåhraeus–Lindqvist effect (FLE). We used a glass capillary viscometer that incorporates tubes with a diameter narrow enough to evoke the FLE. At similar RBC concentrations, viscosity of suspensions with the larger siren RBCs were greater than the viscosity of suspensions with the smaller dog RBCs. However, the relationship between viscosity and tube diameter is independent of RBC size. The results of this study allow us to conclude that the FLE is not related to RBC size. While packaging hemoglobin in RBCs appears adaptive by reducing blood viscosity through the FLE, RBC size does not contribute to the reductions in tube-relative viscosity.
Bentho-pelagic distribution of early stages of softshell clams (Mya arenaria) in tidally contrasted regimes
Authors: LeBlanc Sophie , Miron Gilles
Published: April 2006

We examined the settlement and recruitment of the softshell clam (Mya arenaria L., 1758) in two tidally contrasted regimes in eastern Canada. The Bay of Fundy (strong tides) and the Northumberland Strait (weak tides) were used to describe the distribution of planktonic larvae and early settlers. These distributions were compared with those of juvenile and adult forms observed in the same intertidal habitats. Results showed that the abundances of planktonic stages were the same at all tidal levels except in one site of the Bay of Fundy. Early settlers varied according to a site × intertidal level interaction. Juveniles and adults also varied according to a similar interaction, most being in the upper intertidal level. Simple linear regressions demonstrated that no relationship exists between the number of planktonic larvae and the number of early settlers. The only significant relationship observed was the one between the number of juveniles (1–5 mm size class) and the number of adults in one of the Northumberland Strait sites. Our results show, through the high spatial resolution and wide range of spatial scales covered by the study, that the dominant regional tidal regime does not have an effect on the distribution of the softshell clam. Local hydrodynamic effects appear to drive the intertidal distribution of the softshell clam life-cycle stages.
Progress in sponge biology
Authors: Mackie G O
Published: April 2006

This is an introduction to a set of reviews covering aspects of the systematics, phylogeny and evolution of extant and fossil sponges, sponge embryogenesis and reproductive biology, cell culture and cell death, coordination, ecology, and mineral skeletogenesis.
Mineral skeletogenesis in sponges
Authors: Uriz María-J.
Published: April 2006

Sponges secrete a variety of mineral skeletons consisting of calcite, aragonite, and (or) amorphous silica that confer strength and protect them from physical perturbations. Calcification takes place in a solution of bicarbonate and calcium ions, which is supersaturated with respect to both calcite and aragonite. In contrast, siliceous spicules are formed from an environment that is undersaturated with respect to silicon. Silification is the predominant process of biomineralization in extant sponges (92% of the species). The number of axes of symmetry in the large skeletal elements (megasclere spicules) is the main skeletal difference between the classes Hexactinellida (monaxons and triaxons) and Demospongiae (monaxons and tetraxons). Hypersilification occurs in both lithistid demosponges and hexactinellids, which are mostly confined to silicon-rich environments. Both siliceous and calcareous sponge skeletons are deposited within a well-defined restricted space by the so-called matrix-mediated mineralization. Both processes require organic molecules, which are secreted by a particular cell type (sclerocytes) and guide spicule formation. In most siliceous sponges, these molecules form a discrete filament, which is mainly triangular or quadrangular in cross section in demosponges and hexactinellids, respectively. No discrete axial filament has been reported for calcareous sponges. Silica polycondensation produces nanospheres to microspheres, which are arranged in concentric layers to form the spicules. The potential number of siliceous spicule types in a sponge species appears to be fixed genetically, but the environmental conditions (specifically the availability of silicon) may determine whether a genetically determined spicule type is finally expressed. In this study I review the current knowledge on sponge skeletogenesis, from molecular, cellular, and structural points of view. The contribution of environment variables, as well as the proliferation and decay of the main skeleton types in the past, are also considered.
CAN WORMHOLES HAVE NEGATIVE TEMPERATURES?
Authors: HONG SOON-TAE , KIM SUNG-WON
Published: April 2006

We study (3+1) Morris–Thorne wormhole to investigate its thermodynamic properties. It is shown that the wormhole temperature can be evaluated by exploiting Unruh effects. We also propose a possibility of negative temperature originated from exotic matter distribution of the wormhole.
INFLUENCE OF THE NONLINEAR POLARIZATION ROTATION ON A NONLINEAR FIBER LOOP
Authors: HABOUCHA A. , SALHI M. , KOMAROV A. , LEBLOND H. , SANCHEZ F.
Published: April 2006

A nonlinear fiber loop is considered including four-wave mixing terms. It is shown that these terms lead to considerable modification of the transmission coefficient of the nonlinear fiber loop. The transmission through an output polarizer is also investigated. Very irregular output intensity is obtained when the input intensity is increased.
TRUNCATED SUM RULES AND THEIR USE IN CALCULATING FUNDAMENTAL LIMITS OF NONLINEAR SUSCEPTIBILITIES
Authors: KUZYK MARK G.
Published: April 2006

Truncated sum rules have been used to calculate the fundamental limits of the nonlinear susceptibilities and the results have been consistent with all measured molecules. However, given that finite-state models appear to result in inconsistencies in the sum rules, it may seem unclear why the method works. In this paper, the assumptions inherent in the truncation process are discussed and arguments based on physical grounds are presented in support of using truncated sum rules in calculating fundamental limits. The clipped harmonic oscillator is used as an illustration of how the validity of truncation can be tested and several limiting cases are discussed as examples of the nuances inherent in the method.
LINEAR AND NONLINEAR OPTICAL PROPERTIES OF GOLD NANOPARTICLES WITH BROKEN SYMMETRY
Authors: CANFIELD BRIAN K. , KUJALA SAMI , LAIHO KAISA , JEFIMOVS KONSTANTINS , VALLIUS TUOMAS , TURUNEN JARI , KAURANEN MARTTI
Published: April 2006

We describe our research involving arrays of gold nanoparticles fabricated with electron beam lithography. Small defects in the particles introduced during the fabrication process result in broken design symmetry. The broken symmetry renders the arrays chiral, and signatures of chirality can be observed in both the linear and nonlinear optical responses through precise polarization measurements. The defects enhance the local electric field, enabling more efficient nonlinear optical generation and therefore making nonlinear optical measurements more sensitive to their presence. We also discuss future objectives for clarifying the microscopic processes underlying the optical responses in gold nanoparticle arrays.
MICRORAMAN AND PHOTOREFRACTIVITY STUDY OF HAFNIUM-DOPED LITHIUM NIOBATE CRYSTALS
Authors: GALINETTO PIETRO , ROSSELLA FRANCESCO , MINZIONI PAOLO , RAZZARI LUCA , CRISTIANI ILARIA , DEGIORGIO VITTORIO , KOKANYAN EDVARD P.
Published: April 2006

We present an investigation of the properties of HfO 2-doped lithium niobate crystals, in view of their possible utilization as low-photorefractivity crystals for wavelength converters operating at room temperature. MicroRaman measurements indicate that the linewidth of a specific mode can be used as a local indicator of crystal composition, and show that the grown crystals present very good uniformity. The mechanism by which the photorefractivity is strongly reduced when the HfO 2 concentration is above 4 mol% is studied by combining measurements of birefringence variation, under green-light illumination, with electrical phototransport data.
SIGNAL PROCESSING IN PHOTONIC CRYSTALS AND NANOSTRUCTURES
Authors: WABNITZ S.
Published: April 2006

Optical devices employing photonic crystals and novel nanostructure materials may exhibit useful properties for applications to all-optical signal processing. In this work we analyze as a first example four-wave mixing of polarized beams in photonic crystal fibers. We show that by properly tuning the pump wavelength and the linear dispersion properties of the fiber one may obtain broadband parametric amplification and frequency conversion. Next we consider the in-line periodic amplification of short optical pulses by means of quantum-dot semiconductor optical amplifiers. We show by numerical simulations that pattern-free amplification of a 40 Gbit/s soliton signal at 1300 nm is possible without any inter-symbol interference or nonlinear pulse distortion caused by the fast gain dynamics.
FROM QUALITY MANAGEMENT TO KNOWLEDGE MANAGEMENT IN RESEARCH ORGANISATIONS
Authors: JAIME ASTRID , GARDONI MICKAËL , MOSCA JOËL , VINCK DOMINIQUE
Published: April 2006

Some scholars have recognized the important role of publicly funded basic research (Salter, AJ and BR Martin (2001). Research Policy, 30(3), 509–532; Szulanski, G (2000). Organizational Behavior and Human Decision Processes, 82(1), 9–27) for the production of knowledge. Among the identified benefits is an increase in "the stock of useful knowledge" available to society, which could be used for innovation and in this way contribute to economic growth (Szulanski, G (2000). Organizational Behavior and Human Decision Processes, 82(1), 9–27). Thus, it is important to support scientific activities. We claim that a way to support them is to use quality management complemented by knowledge management as a way of improving the process followed when carrying out research activities. Consequently, we studied the methods used while implementing a quality management system within various research organisations. This lead us to propose an approach which integrates quality management and knowledge management as a way to support the scientific activity.
BIOINFORMATICS AND ITS APPLICATIONS IN PLANT BIOLOGY
Authors: Rhee Seung Yon , Dickerson Julie , Xu Dong
Published: April 2006

Bioinformatics plays an essential role in today's plant science. As the amount of data grows exponentially, there is a parallel growth in the demand for tools and methods in data management, visualization, integration, analysis, modeling, and prediction. At the same time, many researchers in biology are unfamiliar with available bioinformatics methods, tools, and databases, which could lead to missed opportunities or misinterpretation of the information. In this review, we describe some of the key concepts, methods, software packages, and databases used in bioinformatics, with an emphasis on those relevant to plant science. We also cover some fundamental issues related to biological sequence analyses, transcriptome analyses, computational proteomics, computational metabolomics, bio-ontologies, and biological databases. Finally, we explore a few emerging research topics in bioinformatics.
Responding to Color: The Regulation of Complementary Chromatic Adaptation
Authors: Kehoe David M. , Gutu Andrian
Published: April 2006

The acclimation of photosynthetic organisms to changes in light color is ubiquitous and may be best illustrated by the colorful process of complementary chromatic adaptation (CCA). During CCA, cyanobacterial cells change from brick red to bright blue green, depending on their light color environment. The apparent simplicity of this spectacular, photoreversible event belies the complexity of the cellular response to changes in light color. Recent results have shown that the regulation of CCA is also complex and involves at least three pathways. One is controlled by a phytochrome-class photoreceptor that is responsive to green and red light and a complex two-component signal transduction pathway, whereas another is based on sensing redox state. Studies of CCA are uncovering the strategies used by photosynthetic organisms during light acclimation and the means by which they regulate these responses.
MICROTUBULE DYNAMICS AND ORGANIZATION IN THE PLANT CORTICAL ARRAY
Authors: Ehrhardt David W. , Shaw Sidney L.
Published: April 2006

Live-cell studies have brought fresh insight into the organizational activities of the plant cortical array. Plant interphase arrays organize in the absence of a discrete microtubule organizing center, having plus and minus ends distributed throughout the cell cortex. Microtubule nucleation occurs at the cell cortex, frequently followed by minus-end detachment from origin sites. Microtubules associate tightly with the cell cortex, resisting lateral and axial translocation. Slow, intermitant loss of dimers from minus ends, coupled with growth-biased dynamic instability at the plus ends, results in the migration of cortically attached microtubules across the cell via polymer treadmilling. Microtubule-microtubule interactions, a direct consequence of treadmilling, result in polymer reorientation and creation of polymer bundles. The combined properties of microtubule dynamics and interactions among polymers constitute a system with predicted properties of self-organization.
Obesity-Related Derangements in Metabolic Regulation
Authors: Muoio Deborah M. , Newgard Christopher B.
Published: April 2006

An epidemic surge in the incidence of obesity has occurred worldwide over the past two decades. This alarming trend has been triggered by lifestyle habits that encourage overconsumption of energy-rich foods while also discouraging regular physical activity. These environmental influences create a chronic energy imbalance that leads to persistent weight gain in the form of body fat and a host of other abnormalities in metabolic homeostasis. As adiposity increases, so does the risk of developing comorbidities such as diabetes, hypertension, and cardiovascular disease. The intimate association between obesity and systemic metabolic dysregulation has inspired a new area of biochemistry research in which scientists are seeking to understand the molecular mechanisms that link chronic lipid oversupply to tissue dysfunction and disease development. The purpose of this chapter is to review recent findings in this area, placing emphasis on lipid-induced functional impairments in the major peripheral organs that control energy flux: adipose tissue, the liver, skeletal muscle, and the pancreas.
Energy Converting NADH: Quinone Oxidoreductase (Complex I)
Authors: Brandt Ulrich
Published: April 2006

NADH:quinone oxidoreductase (complex I) pumps protons across the inner membrane of mitochondria or the plasma membrane of many bacteria. Human complex I is involved in numerous pathological conditions and degenerative processes. With 14 central and up to 32 accessory subunits, complex I is among the largest membrane-bound protein assemblies. The peripheral arm of the L-shaped molecule contains flavine mononucleotide and eight or nine iron-sulfur clusters as redox prosthetic groups. Seven of the iron-sulfur clusters form a linear electron transfer chain between flavine and quinone. In most organisms, the seven most hydrophobic subunits forming the core of the membrane arm are encoded by the mitochondrial genome. Most central subunits have evolved from subunits of different hydrogenases and bacterial Na+/H+ antiporters. This evolutionary origin is reflected in three functional modules of complex I. The coupling mechanism of complex I most likely involves semiquinone intermediates that drive proton pumping through redox-linked conformational changes.
Biosynthesis and Assembly of Capsular Polysaccharides in Escherichia coli
Authors: Whitfield Chris
Published: April 2006

Capsules are protective structures on the surfaces of many bacteria. The remarkable structural diversity in capsular polysaccharides is illustrated by almost 80 capsular serotypes in Escherichia coli. Despite this variation, the range of strategies used for capsule biosynthesis and assembly is limited, and E. coli isolates provide critical prototypes for other bacterial species. Related pathways are also used for synthesis and export of other bacterial glycoconjugates and some enzymes/processes have counterparts in eukaryotes. In gram-negative bacteria, it is proposed that biosynthesis and translocation of capsular polysaccharides to the cell surface are temporally and spatially coupled by multiprotein complexes that span the cell envelope. These systems have an impact on both a general understanding of membrane trafficking in bacteria and on bacterial pathogenesis.
Tyrphostins and Other Tyrosine Kinase Inhibitors
Authors: Levitzki Alexander , Mishani Eyal
Published: April 2006

The development of tyrosine phosphorylation inhibitors has transformed the approach to cancer therapy and is likely to affect other fields of medicine. In spite of the conservation among protein tyrosine kinases (PTKs), one can develop small molecules that block the activity of a narrow spectrum of PTKs and that exhibit much less toxicity than the currently used chemotherapeutic agents. In this review, we discuss principles for inhibiting specific PTKs. We discuss (a) the birth of the concept of generating targeted, nontoxic signal transduction inhibitors, (b) the potential of substrate-competitive versus the more common ATP-competitive PTK inhibitors, (c) the combination of PTK inhibitors with other signal transduction inhibitors to induce apoptosis—the best way to induce the demise of the cancer cell, and (d) the potential to utilize PTK inhibitors/tyrphostins to attenuate nonmalignant pathological conditions, such as immune disorders, tissue rejection, and restenosis.
G Protein–Coupled Receptor Rhodopsin
Authors: Palczewski Krzysztof
Published: April 2006

The rhodopsin crystal structure provides a structural basis for understanding the function of this and other G protein–coupled receptors (GPCRs). The major structural motifs observed for rhodopsin are expected to carry over to other GPCRs, and the mechanism of transformation of the receptor from inactive to active forms is thus likely conserved. Moreover, the high expression level of rhodopsin in the retina, its specific localization in the internal disks of the photoreceptor structures [termed rod outer segments (ROS)], and the lack of other highly abundant membrane proteins allow rhodopsin to be examined in the native disk membranes by a number of methods. The results of these investigations provide evidence of the propensity of rhodopsin and, most likely, other GPCRs to dimerize, a property that may be pertinent to their function.
Transmembrane Traffic in the Cytochrome b 6 f Complex
Authors: Cramer William A. , Zhang Huamin , Yan Jiusheng , Kurisu Genji , Smith Janet L.
Published: April 2006

Crystal structures and their implications for function are described for the energy transducing hetero-oligomeric dimeric cytochrome b 6 f complex of oxygenic photosynthesis from the thermophilic cyanobacterium, Mastigocladus laminosus, and the green alga, Chlamydomonas reinhardtii. The complex has a cytochrome b core and a central quinone exchange cavity, defined by the two monomers that are very similar to those in the respiratory cytochrome bc 1 complex. The pathway of quinol/quinone (Q/QH2) transfer emphasizes the labyrinthine internal structure of the complex, including an 11×12 Å portal through which Q/QH2, containing a 45-carbon isoprenoid chain, must pass. Three prosthetic groups are present in the b 6 f complex that are not found in the related bc 1 complex: a chlorophyll (Chl) a, a β-carotene, and a structurally unique covalently bound heme that does not possess amino acid side chains as axial ligands. It is hypothesized that this heme, exposed to the cavity and a neighboring plastoquinone and close to the positive surface potential of the complex, can function in cyclic electron transport via anionic ferredoxin.
Relating Protein Motion to Catalysis
Authors: Hammes-Schiffer Sharon , Benkovic Stephen J.
Published: April 2006

This review examines the linkage between protein conformational motions and enzyme catalysis. The fundamental issues related to this linkage are probed in the context of two enzymes that catalyze hydride transfer, namely dihydrofolate reductase and liver alcohol dehydrogenase. The extensive experimental and theoretical studies addressing the role of protein conformational changes in these enzyme reactions are summarized. Evidence is presented for a network of coupled motions throughout the protein fold that facilitate the chemical reaction. This network is comprised of fast thermal motions that are in equilibrium as the reaction progresses along the reaction coordinate and that lead to slower equilibrium conformational changes conducive to the chemical reaction.
Introduction to the Membrane Protein Reviews: The Interplay of Structure, Dynamics, and Environment in Membrane Protein Function
Authors: Sachs Jonathan N. , Engelman Donald M.
Published: April 2006

In our review, we introduce an organizational scheme for membrane protein function. It is the relationship between structure, dynamics, and environment that endows the membrane and its constituents with remarkable sensitivity and robustness. Our understanding begins with landmark advances like those presented in the following chapters. Membrane proteins are notoriously difficult to study, and so the work presented here on the ADP/ATP carrier [Nury et al. ( 2 )], rhodopsin [Palczewski ( 24 )], and the cytochrome b 6 f complex [Cramer et al. ( 35 )] represents incredible progress in this now blossoming field.