bluuebunny/crossref_metadata_2025 huggingface dataset:
Wavelength and polarization selective multi-band tunnelling quantum dot detectors
Authors: Perera A. , Ariyawansa G. , Apalkov V. , Matsik S. , Su X. , Chakrabarti S. , Bhattacharya P.
Published: October 2007

The reduction of the dark current without reducing the photocurrent is a considerable challenge in developing far-infrared (FIR)/terahertz detectors. Since quantum dot (QD) based detectors inherently show low dark current, a QD-based structure is an appropriate choice for terahertz detectors. The work reported here discusses multi-band tunnelling quantum dot infrared photo detector (T-QDIP) structures designed for high temperature operation covering the range from mid-to far-infrared. These structures grown by molecular beam epitaxy consist of a QD (InGaAs or InAlAs) placed in a well (GaAs/AlGaAs) with a double-barrier system (AlGaAs/InGaAs/AlGaAs) adjacent to it. The photocurrent, which can be selectively collected by resonant tunnelling, is generated by a transition of carriers from the ground state in the QD to a state in the well coupled with a state in the double-barrier system. The double-barrier system blocks the majority of carriers contributing to the dark current. Several important properties of T-QDIP detectors such as the multi-colour (multi-band) nature of the photoresponse, the selectivity of the operating wavelength by the applied bias, and the polarization sensitivity of the response peaks, are also discussed.
Homography of central points for optical distortion compensation
Authors: Nowakowski A. , Skarbek W.
Published: October 2007

The paper presents a novel radial lens distortion modelling method for vision systems. It is based on single images of chessboard planar pattern, in which calibration points (corners of chessboard squares) are localised. The points, which are situated near the image centre, where the distortion is negligible, are used to determine undistorted grid of calibration points by the estimation of homographic matrix. The differences in the localisation of undistorted and distorted points are used to find parameters of radial model by the linear least square method. Having the distortion model, the dense compensation is performed with support of bilinear interpolation and a sparse compensation by Newton iterative scheme providing subpixel accuracy.
The Basis of the Study of the Age of the Holocene Diluvium on Loess Areas of Polish Highlands
Authors: Bluszcz Andrzej , Poręba Grzegorz , Śnieszko Zbigniew
Published: October 2007

Large part of slope sediments (pediment) which are the effect of water induced soil erosion in the loess areas of Polish Uplands, has a close relationship with pre-historical, historical and "present" agricultural activity. The sediments accumulated in different periods are often separated by fossil soils. These soils are correlated with the periods of relinquishment of agricultural land use in a given area. A precise dating of the cycles of fossil soil formation is practically impossible. Therefore it is important to gain a possibility to establish the age of sediments between old fossil soils corresponding with the phases of soil erosion. The organic material in the floor or roof of deposits permitting a 14C dating is very seldom. This is why attempts were made to use the OSL method to date mineral parts of slope sediments. In connection with pedological and sedimentological methods, the OSL method makes it possible to give some information about the age of pre-historical and historical phases of intensive soil erosion. In order to date sediments accumulated during the last 50 years, the method based on measurement of 137Cs isotope in products of soil erosion is used. This paper shows some examples of the application of 14C, OSL and 137Cs methods in some selected research sites. In each case there is a discussion of limitations of the methods used.
Evolution of the River Rega Valley Near Łobez in Late Pleistocene and Early Holocene
Authors: Cedro Bernard
Published: October 2007

The River Rega valley near Łobez was formed by a rapid icesheet degradation. Evolution of valleys of rivers (including the Rega) discharging into the Baltic Sea began in late Plenivistulian; it was then that glacifluvial outwash levels and kame terraces were formed. At that time, the water was flowing southward and further on towards the south-west, in a broad channel. That period was terminated at the turn of Plenivistulian and late Vistulian, when the discharge became directed northwards. The net result was the onset of the formation of the modern Rega valley system, buried chunks of dead ice still in the process of melting. Dead ice melt-down proceeded at the fastest rate during Allerød. It was then that deposits of organic matter were formed, the deposits being most probably remnants of fossil soil. Plant macro-fossils and remains of freshwater malacofauna point to a sporadic occurrence of sediments of a shallow water body which existed on the melt-down site of a huge chunk of dead ice. The thickness of the overlaying mineral cover (up to 6 m) is indicative of a fast sediment accretion rate. Sandy and silty sediments were deposited in synchrony with the dead ice melting. As a result, today's Rega valley features traces of small melt-water lakes as well as fossil sedimentation basins (underlain by the Allerød organic level), rapidly filled with fluvial and fluviolimnic sediments. Since the Preboreal, the Rega has been flowing along a meandering channel.
Residual Doses in Recent Alluvial Sediments From the Ardenne (S Belgium)
Authors: Vandenberghe Dimitri , Derese Cilia , Houbrechts Geoffrey
Published: October 2007

We report on our first investigations into the potential of optical dating for determining the rate of river flood sedimentation in the Ardenne region (S Belgium). Two samples collected from a recent alluvial deposit were used to investigate the extent of resetting in different particle size fractions of quartz (4-11 μm, 63-90 μm, 90-125 μm, 125-180 μm, 180-212 μm and 212-250 μm) as well as in polymineral fine (4-11 μm) grains. Both samples show satisfactory OSL and IRSL characteristics. The IRSL signals from the polymineral fine grains yield an equivalent dose (De) of 3-4 Gy, while a De of 0.3-0.6 Gy was measured using large aliquots of quartz. Small aliquot analyses of 63-90 μm and 212-250 μm quartz grains confirm that the coarser fraction contains more grains with lower De's. Furthermore, for a modern sample (< 3 years old), ~60% of the aliquots yields a De consistent with zero, indicating that these contain only well-bleached grains. These findings suggest that it might be possible to extract the true burial dose from dose distributions measured using small aliquots of coarse-grained (e.g. 212-250 μm) quartz.
Intracellular Cytoskeletal Elements and Cytoskeletons in Bacteria
Authors: Madkour Mohamed H.F. , Mayer Frank
Published: October 2007

Within a short period of time after the discovery of bacterial cytoskletons, major progress had been made in areas such as general spatial layout of cytoskeletons, their involvement in a variety of cell functions (shape control, cell division, chromosome segregation, cell motility). This progress was achieved by application of advanced investigation techniques. Homologs of eukaryotic actin, tubulin, and intermediate filaments were found in bacteria; cytoskeletal proteins not closely or not at all related to any of these major cytoskeletal proteins were discovered in a number of bacteria such as Mycoplasmas, Spiroplasmas, Spirochetes, Treponema, Caulobacter. A structural role for bacterial elongation factor Tu was indicated. On the basis of this new thinking, new approaches in biotechnology and new drugs are on the way.
Illuminating Cellular Physiology: Recent Developments
Authors: Brovko Lubov Y. , Griffiths Mansel W.
Published: October 2007

Bioluminescent methods are gaining more and more attention among scientists due to their sensitivity, selectivity and simplicity; coupled with the fact that the bioluminescence can be monitored both in vitro and in vivo. Since the discovery of bioluminescence in the 19th century, enzymes involved in the bioluminescent process have been isolated and cloned. The bioluminescent reactions in several different organisms have also been fully characterized and used as reporters in a wide variety of biochemical assays. From the 1990s it became clear that bioluminescence can be detected and quantified directly from inside a living cell. This gave rise to numerous possibilities for the in vivo monitoring of intracellular processes non-invasively using bioluminescent molecules as reporters. This review describes recent developments in the area of bioluminescent imaging for cell biology. Newly developed imaging methods allow transcriptional/translational regulation, signal transduction, protein–protein interaction, oncogenic transformation, cell and protein trafficking, and target drug action to be monitored in vivo in real-time with high temporal and spatial resolution; thus providing researchers with priceless information on cellular functions. Advantages and limitations of these novel bioluminescent methods are discussed and possible future developments identified.
Studies of Radio-Labelled Free Radicals Derived from a VOC (Volatile Organic Compound), Benzaldehyde, Adsorbed in Cation-Exchanged Zeolite X
Authors: Rhodes Christopher J.
Published: October 2007

Radio-labelled free radicals were formed by the addition of muonium-a radioactive hydrogen atom with a positive muon as its nucleus-to benzaldehyde, as adsorbed in cation-exchanged zeolite X. PhCHOMu• radicals were the major species formed and the activation parameters associated with their reorientational motion were measured using longitudinal-field muon spin relaxation (LF-MuSRx). Two distinct adsorbed fractions were detected in each of the samples containing Li+, Na+, K+, Ca2+, Sr2+ and Ba2+ cations, believed to be from (1) an effectively bulk benzaldehyde component with an almost common activation energy for molecular reorientation of ca 3kJ/mol, and (2) benzaldehyde adsorbed inside the zeolite supercages. MgX showed only the supercage fraction clearly.
Radiolabelling Measurements of Radicals Derived from Terpenoid Volatile Organic Conpounds (VOCs) Adsorbed in Porous Carbon
Authors: Rhodes Christopher J.
Published: October 2007

Radiolabelled free radicals were formed by the addition of muonium-a radioactive hydrogen atom with a positive muon as its nucleus-to α-pinene, β-pinene, dihydrocarvone, dihydrocarveol and dipentene, each as adsorbed in porous carbon. The radicals were identified using transverse-field muon spin rotation (TF-MuSR) and the activation parameters associated with their reorientational motion were measured using longitudinal-field muon spin relaxation (LF-MuSRx). Two distinct adsorbed fractions were detected in each sample, characterised by activation energies in the range 2-6 kJ/mol and 12-16 J/mol respectively.
Nitroso Group Transfer Reactions between N-Methyl-N-Nitroso-P-Toluene Sulfonamide and N-Alkylamines in CTACL Micellar Aggregates
Authors: García-Río L. , Mejuto J.C. , Pérez-Lorenzo M. , Rodríguez-Dafonte P.
Published: October 2007

The influence of micellar media upon the transnitrosation reaction between N-methyl-N-nitroso-p-toluensulfonamide (MNTS) and three linear alkylamines (n-octylamine (OA), N-methyl-n-octylamine (MOA) and N,N-dimethyl-n-octylamine (DMOA)) in micelles of Cetyltrimethylammonium Chloride (CTACl) has been studied. The rate constants were obtained and the pseudophase model allowed us to obtain the intrinsic reactivity constants in the aqueous pseudophase and in the micellar pseudophase (ki2 and kw2) and the binding constant of the amines to the micellar phase (Ka).
Effects of Non-Ionic Micelles on the Rates of Intramolecular General Base-Assisted Nucleophilic Reactions of Piperidine with Ionized Phenyl Salicylate
Authors: Khan M. Niyaz , Ismail Emran
Published: October 2007

Pseudo-first-order rate constants (kobs) for piperidinolysis of ionized phenyl salicylate (PS-), obtained at a constant concentration of polyoxyethylene (23) dodecyl ether ([C12E23]T) and 0.02 M NaOH, follow the relationship: kobs=k0+knapp[zPip]T (where [Pip]T is the total concentration of piperidine). The nonlinear decrease in knapp with increase in [C12E23]T (from 0.001 to 0.080) is explained in terms of the pseudophase (PP) model of the micelle. The fraction of PS- (fPS-) decreases from 1.0 to 0.87, 1.0 to 0.69, and 1.0 to 0.03 with the respective increase in [C12E23]T from 0.06 to 0.08 M at 0.07 M Pip, 0.03 to 0.08 M at 0.04 M Pip and 0.02 to 0.08 M at 0.01 M Pip due to irreversible micellar entrapment of non-ionized phenyl salicylate (PSH) molecules. The values of kobs, obtained for piperidinolysis of PS- at 0.1 M Pip and 0.02 M NaOH, show an ∼5-fold monotonic decrease with increase in [C16E20]T from 0.0 to 0.16 M. These data follow the PP model of the micelle.
Kinetic Analysis of Thermal Decomposition of Unirradiated and γ-Irradiated Tris(ACEtylacetonato)-Ruthenium(III) [Ru(acac)3]
Authors: Mahfouz R. M. , Siddiqui M. R. H. , Al-Ahmari Sh. A. , Alkayali W. Z.
Published: October 2007

The thermal decompositions of unirradiated and γ-irradiated Ru(acac)3 were studied in air. The results show that decomposition proceeds in one major step in the temperature range of 150-250°C with the formation of RuO2 as a final solid residue for unirradiated Ru(acac)3. For γ-irradiated Ru(acac)3, with a total γ-ray dose of 102kGy, the decomposition goes eventually to completion with almost 100% decomposition and proceeds in one major step which contains four overlapping decomposition stages in the temperature range of 200 −320°C. The kinetics were followed isothermally and non-isothermally using both model-fitting and model-free approaches. IR spectroscopy and X-ray powder diffraction techniques were employed to follow the chemical composition of the solid residues obtained at different temperatures. In a model-fitting approach, the kinetic triplet, i.e. the apparent activation energy Ea, the pre-exponential factor, ln A, and the reaction model f (α), were analyzed and calculated using straight line plots, and reduced time plots by isothermal measurements. For non-isothermal measurements we have applied the Coats and Redfern, and Kennedy and Clark methods. In the model-free approach, the non-thermal data for both unirradiated and γ-irradiated Ru(acac)3 samples were analyzed using the Flynn-Wall-Ozawa (FWO), Tang (T), and Vyazovkin (Vyz) isoconversional methods.

The results of application of model-free and model-fitting approaches to the thermal decompositions of both unirradiated and γ-irradiated Ru(acac)3 were compared and evaluated to deduce the most probable kinetic triplet that describes correctly the thermal behavior of Ru(acac)3. Discussion of the results is preceded by a short review of the models relevant to this study.
Theoretical Study of Kinetics and Mechanism of Reactions of Hydroxylamine and Amineoxide Anion with Methyl Iodide in Gas and Aqueous Phases
Authors: Haqghu M. , Irani M. , Gholami M. R.
Published: October 2007

The kinetics and mechanism of the reactions of hydroxylamine and aminoxide anion with methyl iodide were studied with ab initio calculations, Monte-Carlo and QM/MM simulations in gas and aqueous phases. Geometrical parameters and charge calculations show that these reactions proceed through the SN2 (bimolecular nucleophilic displacement) mechanism only. The solvent effects on these reactions were studied by inserting water molecules in reaction media, Onsager model, Monte-Carlo and QM/MM simulations. Activation parameters indicate the expected variation in activation energy and rate coefficient in aqueous phase in comparison to the gas phase. The shift of potential energy barrier through the reactants or products for the studied reactions in the gas phase is in the opposite direction in comparison to the aqueous phase.
Nature of Salt Effects and Mechanism of Covalent Bond Heterolysis
Authors: Dvorko Genrih F. , Ponomareva Engelsine A. , Ponomarev Mykola E. , Stambirsky Mikhailo V.
Published: October 2007

Data on the influence of neutral salts on the rates of unimolecular heterolyses of organic substrates, obtained mainly by the verdazyl method, are summarized here. It is assumed that heterolysis takes place with consecutive formation of four ion pairs: contact (CIP), cavity-separated (CSIP), one solvent moleculeseparated (SIP) and solvent-separated (SSIP). [Formula: see text]

In the limiting step, the CIP interacts with a solvent cavity and the CSIP is formed, which converts quickly into the SIP and subsequently to the SSIP, which also quickly gives the reaction products. In the transition state, bonds between the molecules solvating the CIP are broken. In the absence of salt, the return from external ion pairs does not have much importance. The verdazyl indicator quickly and quantitatively reacts with the SSIP.

The normal salt effect takes place due to the action of salt on the covalent substrate, which catalyses CIP formation. The special salt effect is caused by the association of the salt with the CIP, which prolongs the lifetime of the intermediate and increases the probability of its contact with a solvent cavity.

The negative special salt effect is caused by association of the salt with the SIP or SSIP, which prolongs the lifetime of the intermediates and increases the probability of their contact with a solvent cavity to return to the covalent substrate. When the salt reacts with the SIP, the salt effect does not depend on the concentration and nature of verdazyl, but such a dependence takes place when the salt reacts with the SSIP.

The site of the action of the salt is determined by the Hard and Soft Acids and Bases (HSAB) principle.
Chemosensory Systems
Authors: Spielman Andrew I , Yan Wentao , Brand Joseph G
Published: October 2007

Chemosensory systems are highly specialized sensory systems of which taste, smell and the vomeronasal system are prototypical examples. These systems detect a variety of soluble and volatile stimulants with a range of biological effects on feeding, reproduction, social interactions, mood, territoriality, etc.
Colour Vision
Authors: Gouras Peter
Published: October 2007

Our daylight photoreceptors, cones, mediate colour vision but by themselves cannot distinguish wavelength from the energy of the light they absorb. By comparing the responses of two cone types, one absorbing best from one end and the other best from the other end of the visible spectrum, energy and wavelength contrasts can be determined independently, and thereby colour vision. In man and many primates, three cone mechanisms are compared; the long wavelength sensitive (L) cones are compared with the middle wavelength sensitive (M) cones to create ‘red/green’ colour vision and the short wavelength sensitive (S) cones are compared with both M and L cones for ‘yellow/blue’ form of colour vision. The latter is the only form of colour vision in most mammals and in 2% of human males. This process involves hierarchical circuits from retina to visual cortex including antagonistic interactions between these cone pairs in the same areas of visual space, ‘single opponency’ in the retina and lateral geniculate nucleus, to comparisons between adjacent areas of visual space, ‘dual opponency’ in visual cortex. By this means energy is dissociated from wavelength contrast to create colour vision where both variables are processed separately and used to sense hue, saturation and brightness, the qualities of colour vision, creating about a million varieties of colour.
Dendritic Spines
Authors: Bourne Jennifer N , Harris Kristen M
Published: October 2007

Dendritic spines are important sites of excitatory synaptic transmission and changes in the strength of these synapses are likely to underlie important higher brain functions such as learning and memory. Spines form biochemical compartments for isolating reactions that occur at one synapse from those at other synapses thereby providing a possible way to ensure the specificity of connections between neurons in the brain.
Brain Imaging: Localization of Brain Functions
Authors: Odludaş Yalçin , Posner Michael I
Published: October 2007

Neuroimaging provides a method to locate areas of the brain activity when organisms perceive or respond to sensory events or carry out a wide variety of tasks. The methods have made it possible to examine where in the brain cognitive and emotional systems are located, thus providing new approaches to understanding normal and pathological human information processing.
Long‐term Potentiation
Authors: Lisman John
Published: October 2007

Long‐term potentiation is an activity‐dependent strengthening of synapses that is thought to underlie memory.
NMDA
Receptors
Authors: Cull‐Candy Stuart G
Published: October 2007

N
‐methyl‐
D
‐aspartate (NMDA) receptors are activated during excitatory neurotransmission at most synapses in the central nervous system. Their unique properties allow them to play key roles in synaptic transmission and plasticity; the functional importance of some NMDAR subtypes is becoming clearer.
Bacterial Intracellular Membranes
Authors: Stolz John F
Published: October 2007

This article describes the occurrence, structure, arrangement and function of bacterial intracytoplasmic membranes (ICMS) including magnetosomes of magnetotactic bacteria, the thylakoids of cyanobacteria and chloroxybacteria, the ICMS of purple bacteria and chemoautotrophic bacteria and the chlorosomes of green bacteria.
Algal Carbon Dioxide Concentrating Mechanisms
Authors: Moroney James V
Published: October 2007

The carbon dioxide concentrating mechanism is a variation of photosynthesis in which the algae raise the level of carbon dioxide in the cell many times over the environmental concentration of carbon dioxide. The carbon dioxide concentrating mechanism enhances carbon dioxide fixation and growth in algae.
Bacterial Ecology
Authors: Fenchel Tom
Published: October 2007

Bacterial ecology is concerned with the interactions between bacteria and their environments and with the role of bacteria in biogeochemical element cycling.
Thermophiles
Authors: Ferrera Isabel , Reysenbach Anna‐Louise
Published: October 2007

Thermophiles are organisms that grow best at temperatures above 45°C, and are found in all three domains of life: Bacteria, Archaea and Eukarya. These heat‐loving microbes inhabit high‐temperature environments such as deep‐sea vents and terrestrial hot springs, where they flourish with an impressive phylogenetic and metabolic diversity. Thermophiles also exist in artificial environments as coal refuse piles and geothermal power plants. To thrive in such environments, thermophiles have numerous physical and biochemical adaptations that maintain the integrity and the function of the cell.
Virus Host Cell Receptors
Authors: Hyypiä Timo
Published: October 2007

Viruses are intracellular pathogens that use receptor molecules on the cell surface for their entry. Viral receptors are therefore important determinants of tissue tropism and pathogenesis of the disease.
Virus Evolution
Authors: Domingo Esteban
Published: October 2007

Viruses evolve in continuous interaction with their host organisms, following general Darwinian principles.
Bacteriology
Authors: Madigan Michael T , Jung Deborah O
Published: October 2007

Bacteriology is the study of bacteria, small cells that live an independent existence and play key roles in the biosphere. Bacteria include all prokaryotic cells and comprise two major phylogenetic lineages,
Bacteria
and
Archaea
. Bacteriology played a major role in the development of molecular genetics, and bacteria have been excellent tools for basic and applied research. In recent years, bacteria have been harnessed to produce valuable commercial products, and the critical contributions of prokaryotes to the functioning of the biosphere have been revealed.
Chlorinated Hydrocarbon Metabolism
Authors: Reineke Walter , Kaschabek Stefan R , Pieper Dietmar H
Published: October 2007

Aerobic bacteria are able to use chlorinated hydrocarbons as the sole source of carbon and energy, leading to carbon dioxide, chloride and biomass; some anaerobic bacteria can use some chlorinated hydrocarbons as an artificial electron acceptor in reductive dechlorination. The ligninolytic enzyme system of white‐rot fungi exhibits ‘side activities’ for chlorinated aromatic compounds, though without value for the fungi. Liver enzymes are responsible for the formation of hydrophilic intermediates ready for excretion; these detoxifications often lead to highly reactive and potentially toxic intermediates.
Methanogenesis: Ecology
Authors: Barber Robert D
Published: October 2007

Methanogenic Archaea provide an essential metabolic link between aerobic and anaerobic environments in the global carbon cycle as part of microbial consortia that recycle biomass. Understanding methanogenesis and the impact of microbial interactions on this process offers an opportunity to gain significant insight into environmental events such as global warming.
Immunity to Infection
Authors: Pedersen Anders Elm
Published: October 2007

The immune system comprises innate and adaptive immune responses coordinated to prevent infection. Innate immune responses are early responses based on preformed cells and effector molecules with a limited repertoire of antigen receptors. In contrast, adaptive immune responses take several days to mount, but take advantage of a very large repertoire of antigen receptors and comprises memory. The immune system must constantly face pathogen invasion strategies and at the same time avoid destruction of non‐infected host tissue. In the following review the role of the various components of the immune system and their role in immunity to infections is described.
Immunity to Bacteria
Authors: Lowe Devin B , Shearer Michael H , Jumper Cynthia A , Kennedy Ronald
Published: October 2007

Bacterial infections cause a variety of immune responses from the host depending on the specific bacterium involved. Understanding the virulence of bacteria provides insight into the medical approaches that can be used to treat infection and prevent disease.
Phagocytosis
Authors: Russell David G
Published: October 2007

Phagocytosis is the ingestion of particles by cells. The process is usually observed in macrophages and amoebae and almost invariably culminates in the degradation of the ingested particle in the cell's lysosome. The phagosome functions at the fulcrum of the innate and acquired immune systems and promotes the identification of foreign antigens.
Chemoattraction: Basic Concepts and Role in the Immune Response
Authors: Rodríguez‐Fernández José Luis , Riol‐Blanco Lorena
Published: October 2007

Chemoattraction is defined as the unidirectional movement of a cell, in response to a chemical gradient of ligands. During chemoattraction the cells move in the direction from a low to a high concentration of the chemoattractant. Chemoattraction is called ‘chemotaxis’ when the ligand gradient is soluble and ‘haptotaxis’ when this gradient is bound to the substrate. Chemoattraction plays a fundamental role in the regulation of the precise location of leucocytes during the immune response and consequently is fundamental for the adequate functioning of the immune system.
Immune Response: Evolution
Authors: Cooper Edwin L
Published: October 2007

Phagocytosis in unicellular animals represents the most ancient and ubiquitous form of defence against foreign material. Multicellular invertebrates and vertebrates possess phagocytic cells and have evolved more complex functions attributed to immuno‐defence cells that specialized into cellular and humoral immune responses.
The Thymic Niche and Thymopoiesis
Authors: Chidgey Ann , Boyd Richard , Hugo Patrice
Published: October 2007

The thymus, a bilobate gland located in the upper anterior thorax in higher vertebrates, is the major site of T‐lymphocyte production. This primary lymphoid organ composed of various nonlymphoid elements, referred to as the thymic stroma, governs the maturation and tolerance induction of haematopoietic precursors into immune‐competent nonautoreactive T cells. Whilst naturally involuting with age, the thymic stromal compartment remains dynamic in nature throughout life and retains the potential to regenerate.
Proteins: Postsynthetic Modification – Function and Physical Analysis
Authors: Wittmann‐Liebold Brigitte , Choli‐Papadopoulou Theodora
Published: October 2007

Analysis of the entire genome (genomics) provides static information about the genes of an organism. In contrast, total protein analysis (proteomics) reflects the dynamic situation, providing information about the rate of expression and regulation of individual proteins within the cell. Clues as to the function of proteins in diverse cell processes can only be obtained if their structure and modifications or variations are fully understood. Recently, we learned to define important individual posttranslational protein modifications for function.
Protease Complexes
Authors: Schmidt Marion , Finley Daniel
Published: October 2007

Proteolysis is one of the most widespread mechanisms for biological regulation, providing control over such diverse phenomena as cell cycle progression, programmed cell death, blood clotting, complement activation, antigen presentation, inflammation, nutrient utilization, long‐term memory, cell migration and circadian rhythms.
Protein‐derived Cofactors
Authors: Davidson Victor L
Published: October 2007

Protein‐derived cofactors are catalytic or redox‐active centres in proteins, which are formed by posttranslational modification of one or more amino acid residues.
Proteases
Authors: Barrett Alan J , Rawlings Neil D
Published: October 2007

Proteases are catalytically active proteins (enzymes) that break down proteins and their fragments by hydrolysis.
Enzymes: The Active Site
Authors: Ghanem Eman , Raushel Frank M
Published: October 2007

Enzymes are very efficient and specific catalysts. The rate enhancement and specificity of enzymes are derived from a network of general acid/base catalysts, nucleophiles and noncovalent interactions in the active site.
Bacteriophages: Tailed
Authors: Ackermann Hans‐Wolfgang
Published: October 2007

Tailed bacteriophages constitute the order
Caudovirales
with three families. They are the largest and probably the oldest virus group. Although extremely diversified in dimensions and physicochemical properties, they have retained many common properties in morphology and replication, indicating a common monophyletic origin.
Netrins
Authors: Moore Simon W , Tessier‐Lavigne Marc , Kennedy Timothy E
Published: October 2007

Netrins are a family of secreted proteins that function as chemotropic guidance cues, directing cell and axon migration during neural development. By directing cell migration and mediating cell–cell adhesion, netrins also influence the morphogenesis of lung, pancreas, mammary gland and vasculature. Netrin receptors include the transmembrane proteins ‘deleted in colorectal cancer’ (DCC), its relative neogenin, and members of the UNC5 family.
Regulatory Systems: Two‐component
Authors: Raivio Tracy L
Published: October 2007

Two‐component systems constitute a large class of regulatory proteins that function as signal transducers. Each system comprises a sensor or histidine kinase and an effector or response regulator, which communicate through a conserved set of phosphotransfer reactions to effect adaptive changes in response to specific environmental signals.
Enzyme Activity: Allosteric Regulation
Authors: Traut Thomas
Published: October 2007

Cells can respond to changes in their environment by altering the flow through particular metabolic pathways. Such a change in any metabolic step is due to certain key enzymes that have the ability to alter their rate of activity. Such enzymes are defined as allosteric. The extent to which these enzymes adopt either the active conformation or the inactive conformation depends on their response to appropriate positive or negative signals. An easily measured feature of allosteric enzymes is the cooperativity that they show in a kinetic experiment.
Regulation by Covalent Modification
Authors: Martin Bruce L
Published: October 2007

Covalent modifications are enzyme catalysed alterations of synthesized proteins and include the addition or removal of chemical groups. Modifications can target a single type of amino acid or multiple amino acids and will change the chemical properties of the site. Consequences on the structure and functions of the protein modified are manifested providing a sensitive method for cellular regulation.
Caps on Eukaryotic
m
RNAs
Authors: Furuichi Yasuhiro , Shatkin Aaron J
Published: October 2007

A 5′‐terminal cap is added to most eukaryotic cellular and viral pre‐messenger ribonucleic acids at an early stage of transcription. Capping is essential and modulates several subsequent events in gene expression including RNA splicing, translation and stability. These and other effects involve cap‐binding proteins that recognize the m7GpppN cap structure. Capping proceeds by a similar series of enzymatic steps in a wide range of systems, but differences exist between metazoans and unicellular eukaryotes and viruses, pointing to capping enzymes as potential targets for the development of novel and selective drugs against some fungal, viral and parasitic infections.
Idiotypes
Authors: Uner Aysegul , Gavalchin Jerrie
Published: October 2007

Idiotypes, the unique and characteristic determinants of an immunoglobulin or T cell receptor, can function as antigens. Anti‐idiotypic responses, which include anti‐idiotypic antibody‐producing B cells and idiotype‐specific T cells, form a network of immune cells that regulate their production.
CD
Antigens
Authors: Delves Peter J
Published: October 2007

CD antigens are proteins originally defined as being present on the cell surface of leucocytes but now including some intracellular molecules and molecules present on cells other than leucocytes. Such molecules are assigned a CD number following a consensus reached at regularly held international workshops. CD antigens include a large number of cell surface receptors, signalling molecules and adhesion molecules.
Integrin Superfamily
Authors: Krissansen Geoffrey W , Danen Erik HJ
Published: October 2007

Integrins are a superfamily of cell‐surface adhesion molecules formed from eight different β chains and 18 different α chains that assemble as heterodimers to mediate cell–cell and cell–matrix interactions. As sensors of the microenvironment, they control vital cellular functions such as cell growth, differentiation, programmed death, and motility; developmental processes; and in the adult they mediate tissue maintenance, blood clotting and immunity.
Interleukins
Authors: Meager Anthony , Wadhwa Meenu
Published: October 2007

The interleukins (IL) belong to a category of biologically active proteins, termed cytokines. These proteins are derived mainly from white blood cells and act on white cells, although these criteria are not necessarily exclusive of other cell sources and activities. Interleukins, among other proteins, maintain the haematopoietic and immune systems and control their functions. They have been classified specifically by a designated nomenclature committee of the International Union of Immunological Societies/World Health Organization. In general, numbering of interleukins has followed the order of their discovery and this has led to some anomalies. It has become evident that interleukins can be classified into subgroups or families based on shared structural characteristics, and/ or shared receptor subunits and/or shared chromosomal locations. For example, IL‐1α, IL‐1β, IL‐18 and IL‐33 belong to the ‘IL‐1 family’, IL‐2, IL‐15 and IL‐21 to the ‘IL‐2 family’ (IL‐4, IL‐7, IL‐9 and IL‐13 might also be included as they share at least one receptor subunit with IL‐2 family members), IL‐10, IL‐19, IL‐20, IL‐22, IL‐24, IL‐26, IL‐28 and IL‐29 to the ‘IL‐10 family’, IL‐12, IL‐23 and IL‐27 to the ‘IL‐12 family’. IL‐3 and IL‐5 together with GM‐CSF and IL‐6 and IL‐11 together with several other noninterleukin named cytokines – LIF, OSM, CNTF, CT‐1 – can also be grouped as families of ‘like’ cytokines. The IL‐17 family is comprised of six related proteins (IL‐17A–F), one of which, the murine homologue of IL‐17E, was anomalously designated IL‐25. With hindsight, the remaining interleukins might have been better classified with other biological modifiers. For instance, IL‐8 is clearly a chemokine; IL‐14 and IL‐16 bear scant resemblance to any other interleukins, or other cytokines for that matter.

In the following paper, the molecular characteristics of interleukin proteins, their cognate receptors and intracellular signalling pathways and their biological activities are briefly described. The interactions of particular interleukins in the regulation of immune cell growth, differentiation and function will be illustrated by short sections at the end of the paper covering (1) T‐lymphocyte development and activation and (2) chronic inflammation and autoimmunity.
Infection: Immunological Barriers
Authors: Whitton J Lindsay
Published: October 2007

Microorganisms can infect a host through various portals of entry. The host attempts to counter microbial infection and dissemination using many physical, chemical and immunological weapons.
Immunological Memory
Authors: Zanetti Maurizio
Published: October 2007

Immunological memory is defined functionally as the event that occurs when the immunologically experienced individual reencounters antigen through infection or immunization and develops, as a result, a greater and faster response than after the first encounter.
Promoter Fusions to Study Gene Expression
Authors: Ma Jun
Published: October 2007

Promoter fusions are chimaeric genes designed to have the coding sequence of one gene controlled by the regulatory and promoter sequences of another gene. Promoter fusions are useful tools for studying gene regulation and function and for identifying new genes.
Protein Production for Biotechnology
Authors: Giuliani Sarah E , Landorf Elizabeth V , Collart Frank R
Published: October 2007

Purified proteins are a starting point for many experimental, therapeutic and commercial applications. Developments in biotechnology have generated a collection of resources to enable production of proteins from a variety of sources.
Arthropod‐borne Viruses
Authors: Calisher Charles H
Published: October 2007

Arthropod‐borne viruses (arboviruses) are those that replicate in insects and then can be transmitted by those insects to vertebrates. Arboviral diseases are very common, causing a wide variety of illnesses in humans, livestock and wildlife.
Coltiviruses
Authors: Guirakhoo Farshad , Guirakhoo Susanne M , Monath Thomas P
Published: October 2007

Coltivirus (‘Colti’ from Colorado tick fever (CTF)) (family
Reoviridae
) is a genus of viruses that consist of 12 segments of double‐stranded ribonucleic acid (dsRNA). CTF is the most important tick‐borne human pathogen in the United States of America. Human infections occur after the bite of Colorado tick fever virus (CTFV)‐infected adult ticks, mainly
Dermacentor
spp. First described by Becker in 1930, at least 22 strains of CTFV are known, many of which cause disease in humans.
Cytomegaloviruses
Authors: Livingston Robyn , Chatterjee Archana , Harrison Christopher J
Published: October 2007

The cytomegaloviruses are a common group of viruses that are widely distributed in the animal kingdom, have a complex biology and, in humans, pose a significant threat to immunocompromised individuals and the fetuses of nonimmune mothers.
Influenza Viruses
Authors: Neumann Gabriele , Kawaoka Yoshihiro
Published: October 2007

Influenza viruses cause mild to potentially lethal respiratory disease. Here we summarize the molecular virology of influenza viruses, i.e. the coding strategies, the replication cycle and the functions of the viral proteins.
Animal Viruses Pathogenic for Humans
Authors: Nel Louis H , Weyer Jacqueline
Published: October 2007

Diseases and infections that are readily transmitted between vertebrate animals and man are known as zoonoses. Many of these zoonoses are caused by viruses – some of these are rare, but others are of great epidemiological importance based on high mortality and morbidity and global distribution. New viral zoonoses continue to emerge from all parts of the world, particularly as wildlife and humans come into closer contact, given the present‐day dynamics of global development. Important emerging viral zoonotic diseases include Avian Influenza and severe acute respiratory syndrome (SARS).
Eosinophils
Authors: Wagner Lori , Leiferman Kristin M , Gleich Gerald J
Published: October 2007

The eosinophil is a bone marrow‐derived white blood cell (leucocyte) that is present only in the gastrointestinal tract and lymphatic tissues of healthy individuals. Eosinophils participate in helminth (worm) immunity and in hypersensitivity diseases, such as bronchial asthma and allergies.
Epithelial Cells: Immunological Aspects
Authors: Pastore Saveria , Albanesi Cristina , Girolomoni Giampiero
Published: October 2007

Epithelial cells display their nature of integral, resident components of the innate immune system, and provide a valid defensive line against environmental threats through the expression of a plethora of active mediators, including antimicrobial peptides, cytokines, chemokines and cell membrane molecules. By contrast, epithelial cells can play a relevant role in the pathogenesis of chronic inflammatory disorders (e.g. atopic dermatitis and psoriasis), where the amplification of the inflammatory reactions critically depends on the crosstalk between infiltrating leucocytes and epithelial cells.
Genetic Networks
Authors: Coffman James A , Davidson Eric H
Published: October 2007

Gene expression is regulated by sequence‐specific protein–DNA (deoxyribonucleic acid) interactions that occur within the
cis
‐regulatory domains of genes. Genes that encode sequence‐specific DNA‐binding proteins both regulate and are regulated by the expression of other such genes. A set of genes whose activity is thus linked by sequence‐specific
cis‐trans
regulatory interactions constitutes a genetic network.
Lymphocyte Activation Signals: Transduction
Authors: Kersh Gilbert J
Published: October 2007

Adaptive immunity depends on the transfer of information across the plasma membrane of T and B lymphocytes. This information takes the form of signal transduction pathways that are initiated by the recognition of antigens by specific transmembrane receptors, and result in a complex series of biochemical changes within the cell that ultimately alter cellular function.
Mast Cells
Authors: Kitamura Yukihiko , Oboki Keisuke , Ito Akihiko
Published: October 2007

Mast cell is a type of connective tissue cell but originates from the haematopoietic stem cell. Mast cells function as a major effector of immunoglobulin E‐dependent hypersensitivity reaction.
T Lymphocytes: Cytotoxic
Authors: Gotch Frances M
Published: October 2007

Cytotoxic T lymphocytes are T cells that have the ability to kill other cells. Most are major histocompatibility complex (MHC) Class I restricted CD8 T cells, but CD4 T cells can sometimes kill. Cytotoxic T cells are of great importance in host defence against cytosolic pathogens.
Antigen Presentation to Lymphocytes
Authors: Udono Heiichiro , Wang Jiyang O , Watanabe Takeshi
Published: October 2007

Antigen presentation to T and B lymphocytes by antigen‐presenting cells plays a central role in the initiation and regulation of adaptive immune responses. T cells recognize peptides in the context of major histocompatibility complex (MHC) molecules. By contrast, B cells recognize proteins in a state of solution.
Antigen Recognition by
T
Lymphocytes
Authors: Ferrero Isabel , Michelin Olivier , Luescher Immanuel
Published: October 2007

T lymphocytes (or T cells) are thymus‐derived and are key players in the adaptive cellular immunity. They recognize antigen by means of their T‐cell receptor (TCR), which consist of two chains, and are surface expressed upon association with invariant CD3 units, which mediate TCR signalling. TCR, especially αβ TCR, exhibit a vast diversity, provided by the somatic rearrangement of TCR gene segments. γδ and αβ T cells exhibit important differences regarding tissue localization and antigen recognition. αβ T cells express as coreceptor CD4 or CD8. CD4+ T cells are MHC class II‐restricted and comprise T helper (T
H
) and regulatory (Treg) T cells. CD8αβ+ T cells are MHC class I‐restricted and are predominantly cytotoxic T cells (CTL). γδ T cells constitute as a link between innate and adaptive immunity. They are found frequently in epithelia (e.g. skin and intestine) and recognize nonclassical MHC class Ib molecules and diverse small nonpeptidic compounds in a coreceptor and MHC restriction independent manner.
Xenotransplantation
Authors: Cooper David KC , Ezzelarab Mohamed , Hara Hidetaka
Published: October 2007

The transplantation of organs and tissues across species boundaries is called xenotransplantation. The most likely source of animal organs and cells for transplantation into humans is the pig. Pigs, therefore, have been genetically engineered to provide their tissues with some protection against the human immune response. However, further immunological barriers need to be overcome. Many questions remain regarding the adequate function of pig organs in humans. The safety of xenotransplantation also remains of some concern. Is there a risk of the transfer of a pig infectious microorganism into the community? Present evidence is that this potential risk is low. This potential, however, has legal and regulatory implications.
Plant Response to Water‐deficit Stress
Authors: Bray Elizabeth A
Published: October 2007

When plants do not receive sufficient water they are subjected to a stress called water deficit. Water deficit in the plant disrupts many cellular and whole plant functions, having a negative impact on plant growth and reproduction. Plants have evolved many different mechanisms to deal with the occurrence of this stress as it occurs in their environments. Availability of water is the most important factor in the environment that reduces the production of our crops.
Plant Salt Stress
Authors: Zhu Jian‐Kang
Published: October 2007

Plant salt stress is a condition where excessive salts in soil solution cause inhibition of plant growth or plant death. On a world scale, no toxic substance restricts plant growth more than does salt. Salt stress presents an increasing threat to plant agriculture. Among the various sources of soil salinity, irrigation combined with poor drainage is the most serious, because it represents losses of once productive agricultural land.
C
3
Carbon Reduction Cycle
Authors: Raines Christine A , Lloyd Julie C
Published: October 2007

The C
3
carbon reduction cycle is the primary pathway of carbon fixation in all photosynthetic organisms, reducing carbon dioxide from the atmosphere to form carbohydrates and in higher plants it takes place in the chloroplast stroma.
Protein–DNAInteractions: Polyelectrolyte Effects
Authors: Saecker Ruth M
Published: October 2007

The stability of noncovalent protein–DNA complexes is typically sensitive to the ionic composition of the solution, in a manner that is dependent on the specific ion concentrations and is not a simple ionic strength effect. One important origin of this sensitivity to solution conditions is the polyelectrolyte effect.
Tumour Antigens Recognized by T Lymphocytes
Authors: Van den Eynde Benoît J , Pang Ken C , Chen Weisan
Published: October 2007

Cancer cells bear markers (antigens) that identify them to the immune system, thereby making them targets for destruction by cytolytic T lymphocytes. Therapeutic cancer vaccines designed to exploit our recently gained knowledge of the identity and structure of these antigens are now being tested in clinical trials.
Placental Immune Defences – Protection Against Rejection and Infection
Authors: Liljander Maria , Arvola Marie , Mattsson Ragnar
Published: October 2007

The placenta must not only provide nutrients and take care of fetal waste products, it also needs to protect the fetus from maternal immunological attacks while at the same time transmitting maternal immunoglobulins to ensure protection against infectious agents.