bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Cytochromeb6Complex of Oxygenic Photosynthesis
Authors: Cramer William A. , Yamashita Eiki , Baniulis Danas , Saif Hasan S. 
Published: March 2010

AbstractThe cytochromeb6fcomplex is the central complex in the electron transport chain of oxygenic photosynthesis. It provides the electronic connection between the two photosynthetic reaction centers and generates most of the transmembrane electrochemical proton gradient that is used for ATP synthesis. It is a hetero‐oligomeric 220‐kDa homo‐dimeric complex consisting of 8 polypeptide subunits, 13 transmembrane helical segments, and 7 tightly bound prosthetic groups per monomer. It is one of relatively few hetero‐oligomeric membrane proteins whose crystal structure has been solved to a resolution ≤3.0 Å. Among the seven prosthetic groups per monomer, five have a redox function: twob‐type hemes,bpandbn, on the electrochemically positive and negative sides of the complex, the p‐side heme of cytochromef, a uniquec‐type cytochrome, and a p‐side [2Fe–2S] center, and a unique hemecncovalently bound to the cytochromebsubunit, which interacts electronically with hembn. These groups are arranged to accomplish the oxidation and reduction of plastoquinol/plastoquinone (PQH2/PQ) on the p‐ and n‐sides of the membrane, and thereby accomplish a net transfer of as many as two protons across the membrane per electron transferred through the complex, thus providing the major input to the transmembrane proton electrochemical gradient. The redox reactions of PQ/PQH2occur within the two quinone‐exchange cavities formed by the two monomers of the complex. The p‐side redox reactions are similar to those of the cytochromebc1complex. However, redox reactions on the n‐side are different, partly because of the presence of hemecn.
Geospatial Information in Hydrogeological Studies
Authors: Wojda Piotr , Brouyère Serge , Dassargues Alain 
Published: March 2010

AbstractThe purpose of this article is to make a review of hydrogeological information modeling objectives, techniques, and problems, and finally to propose a solution for data integration and transfer. Hydrogeological data and information management is crucial for efficient integrated water resources administration, protection, and exploitation. To assure an effective management of groundwater resources, a close cooperation and information exchange between different actors at different levels is necessary. The information flux must be optimized between local producers and potential users of hydrogeological data: regional and national institutions, as well as international and transboundary analysts and managers. The paper format of representation and exchange of hydrogeological information has already been replaced by different digital forms. However, an enormous diversity in applied formats and representations makes hydrogeological information extremely difficult to transfer in an automatic way. If this transition is not effective, misinterpretations of hydrogeological data may appear. The proposed solution consists in creating a domain‐specific standard for the hydrogeological information exchange, using recent geomatics advances, taking into consideration appropriate ISO/TC211 and Open Geospatial Consortium (OGC) geographic information standards. Such a new electronic carrier of hydrogeological information facilitates a dialogue between interested parties using web services and inbuilt exchange mechanisms, interdisciplinary collaboration, and international harmonization of environmental sciences.
Mass Spectrometry in Inorganic and Bioinorganic Chemistry
Authors: Becker Johanna Sabine , Becker Julia Susanne 
Published: March 2010

AbstractMass spectrometry (MS) in inorganic and bioinorganic chemistry has been established using sensitive analytical techniques in quite different application fields: the determination of major, minor, and trace element concentrations; for the characterization of surfaces; for precise and accurate isotope ratio measurements; and for the structural analysis of organic and bioorganic compounds. The review gives an overview on different mass spectrometric techniques and their applications
Acid–Base Catalysis by Enzymes
Authors: Kirby Anthony John 
Published: March 2010

Abstract

Proton transfer is the commonest reaction that enzymes perform. Most enzyme reactions go by ionic mechanisms, involving the creation or disappearance of charge. Such reactions are typically acid or base catalysed, but acid and base concentrations are minimal under physiological conditions near pH 7. Enzymes have evolved subtle and highly effective solutions to this problem, involving general acid and general base catalysis by the functional groups available on the side‐chains of amino acids strategically placed in their active sites. General acid and general base catalysis by the same functional groups can be observed, and the relevant mechanisms elucidated, by studying simple systems. But this work typically involves the use of properly designed activated substrates. The extraordinary efficiency of such catalysis in enzyme active sites has not so far been reproduced in model systems, and this remains an active area of investigation.

Key Concepts:

The enzyme active site provides a highly sophisticated reaction vessel, tailored to the needs of the specific reaction and the specific substrate.

General acid and general base catalysis are first‐line support services for the making and breaking of covalent bonds that define the chemistry of metabolic processes.

The unexceptional functional groups available on the side‐chains of amino acids acquire exceptional catalytic proficiency when strategically placed in enzyme active sites.
Glycolytic Enzymes
Authors: Michels Paul AM , Verlinde Christophe LMJ , Fothergill‐Gilmore Linda A 
Published: March 2010

Abstract

All cells must burn fuels to drive the myriad of cellular processes necessary for life. The most important organic fuel is glucose, a stable and soluble sugar that is particularly well suited for its role in biology. Cellular combustion of glucose occurs in 10 well‐controlled steps in which six‐carbon glucose molecules are broken apart (literally ‘glycolysis’) into three‐carbon compounds. In the same process chemical energy is captured through the production of ATP (adenosine triphosphate), the hydrolysis of which powers many cellular processes. The 10 enzymes which catalyse the steps of glycolysis are exceptionally well characterised. They provide a fascinating array of enzymes that have been perfected over long evolution to carry out their tasks swiftly, efficiently and with finely tuned control.

Key concepts:

Glycolysis is an ancient pathway that is present at least in part in all organisms.

Ten enzymes catalyse the reactions of the glycolytic pathway.

Many enzymes occur as isoenzymes in different tissues or in response to different metabolic conditions.

Hexokinase activity is regulated by product inhibition.

A hinge‐bending motion of the two‐lobed structures of hexokinase and phosphoglycerate kinase is induced by substrate binding, and is required to position the substrates correctly for catalysis.

Several reactions of the glycolytic pathway can be catalysed by pairs of nonhomologous enzymes (i.e. glucose‐phosphate isomerase, aldolase, glyceraldehyde‐3‐phosphate dehydrogenase and phosphoglycerate mutase).

Phosphofructokinase occurs as two distantly related types that use different phospho donors: ATP or inorganic pyrophosphate.

Activities of phosphofructokinase and pyruvate kinase are allosterically regulated.

A conserved protein fold of eight parallel β‐strands and eight parallel α helices, first identified in triosephosphate isomerase and therefore known as the ‘TIM barrel’ is found in several glycolytic enzymes and occurs in approximately 10% of all enzymes.

The Rossmann fold that occurs in many nucleotide‐binding proteins was first identified in glyceraldehyde‐3‐phosphate dehydrogenase.

Pyruvate kinase activity is sometimes regulated by posttranslational phosphorylation.
Eukaryotic Replication Fork
Authors: Walther André P 
Published: March 2010

Abstract

In eukaryotic cells, DNA (
deoxyribonucleic acid
) synthesis occurs at specific sites that move through the genome called replication forks. Multiprotein complexes at these forks catalyse the synthesis of two new strands of DNA using parental strands as templates to produce two complete copies of the parental DNA. The eukaryotic replication fork machinery must deal with the chromatin and chromosome structure of eukaryotic genomes, be able to replicate DNA in the context of a complex cell cycle, and be able to deal with the constant threat of mutations that could arise due to replication of damaged DNA, all while trying to efficiently replicate the DNA with high fidelity. The resulting eukaryotic replication fork is a tightly controlled, yet incredibly efficient biological machine capable of synthesizing billions of base pairs of DNA in the span of hours.

Key Concepts:

Eukaryotic DNA replication requires the concerted action of multiple DNA polymerases and accessory factors that replicate the DNA with high efficiency and accuracy.

Eukaryotic chromosomes are replicated in a semidiscontinuous manner by replication forks that coordinate the simultaneous replication of the leading and lagging strands.

The eukaryotic replication machinery is equipped to displace histones that coat chromatin DNA and reconstitute fully functional nucleoprotein chromosomes after DNA replication.
Plant Alkaloids
Authors: Fester Karin 
Published: March 2010

Abstract

Alkaloids are traditionally defined as basic (alkali‐like), nitrogen‐containing organic constituents that occur mainly in plants. The nitrogen in the alkaloid molecule is derived from amino acid metabolism. Since the amino acid skeleton is often largely retained in the alkaloid structure, alkaloids originating from the same amino acid show similar structural features and can be classified according to their biosynthetic origin. The biosynthesis of alkaloids often follows complex pathways and includes stereospecific steps. Alkaloids often have pronounced bioactivities and are therefore thought to play an important role in the interaction of plants with their environment. Alkaloids and extracts of alkaloid‐containing plants have been used throughout human history as remedies, poisons and psychoactive drugs.

Key Concepts

Alkaloids are a heterogeneous class of secondary metabolites.

Alkaloids are defined as basic compounds derived from amino acids, often with heterocyclically bound nitrogen. Pseudoalkaloids are nitrogen‐containing natural products that do not arise from an amino acid core and acquire their nitrogen by transamination of a precursor derived from other biosynthetic pathways.

Alkaloids are biosynthesized via complex pathways that may comprise 20 or more enzymatic steps.

Many alkaloids possess pronounced biological activities, which are often associated with their amine function.

Several alkaloids are used medicinally or provide lead structures for novel synthetic drugs.

Owing to their bioactivities, alkaloids are often toxic to herbivoures. Nevertheless, they may be exploited by specialized species of herbivoures as defence compounds.

Alkaloid‐producing tissue cultures provide an alternative for exploiting slow growing or protected plants. Moreover, they can be utilized for biosynthetic studies and for the commercial production of valuable alkaloids.
Vernalization
Authors: Jean Finnegan E , Helliwell Chris , Sheldon Candice , James Peacock W , Dennis Elizabeth S 
Published: March 2010

Abstract

Vernalization, the promotion of flowering in response to a prolonged period of growth at low temperatures, is an important adaptation of plants growing in regions where harsh winters are followed by relatively short growing seasons. In these plants, flowering is triggered by long days but only after the vernalization requirement has been met. Thus, the requirement for vernalization prevents flowering in the long days of autumn and ensures that flowering occurs in the warmer days of spring and summer, allowing sufficient time for seed development before the onset of the next winter. Various crop plants, including the winter cereals and canola, must be vernalized if they are to initiate flowering and set seed. The key genes controlling the response to vernalization differ between monocots and dicots suggesting that this response arose independently after the divergence of the monocot and dicot lineages.

Key concepts:

Vernalization is the promotion of flowering in response to prolonged periods of low temperatures, such as those experienced in winter.

The physiological properties of vernalization are similar in dicots and monocots but the genes controlling this response differ.

The vernalized state is inherited through mitotic cell divisions; this memory of winter is provided by epigenetic changes to the chromatin of key genes in the vernalization response, although the nature of these changes differs between monocots and dicots.

Epigenetic regulation results in a heritable but potentially reversible change in gene expression that is modulated by changing the accessibility of a gene for transcription.

FLOWERING LOCUS C (FLC)
is a key regulator of vernalization responsiveness in the Brassicaceae but the role of
FLC
homologues in other dicots remains to be elucidated.

The regulation of
FLC
expression is complex and involves both genetic and epigenetic mechanisms and
FLC
has become an important model for studying epigenetic control of plant gene expression.

VERNALIZATION INSENSITIVE 3
(
VIN3
) is induced by cold and the VIN3 protein is incorporated into the Polycomb Repression Complex (PRC2) that regulates
FLC.

Polycomb proteins are conserved across kingdoms and play a role in gene repression in Drosophila,
Caenorhabditis elegans
and mammals.

The vernalized state is reset each generation; resetting occurs at different times depending on the gamete transmitting
FLC
.

An
FLC
orthologue conditions the perennial behaviour of
Arabis alpina
, a relative of
Arabidopsis thaliana
.
Fluorescence Microscopy
Authors: Jacobson Ken 
Published: March 2010

Abstract

Fluorescence microscopy in biomedical research is a light microscope technique designed to view fluorescence emission from a biological specimen. It has become an extremely useful tool to localize genes, messenger
ribonucleic acid
(mRNA) and proteins within live and fixed cells and tissues. Cell biology has been revolutionized by the discovery and applications of
green fluorescent protein
, and its many mutant forms, that can be fused to a cellular protein of interest, making it possible to localize and study the dynamics of that protein in living cells. In addition, the development of other fluorescent reporters, based on small molecule dyes, has made it possible to visualize spatiotemporal variations in intracellular calcium as well as other ions and metabolites and the activity of components in signal transduction networks using specialized biosensors.

Key Concepts

Fluorescence microscopy enables visualization of the emission from fluorescent compounds in various specimens to submicron spatial resolution.

Fluorophores are molecules that emit longer wavelength that emit light after absorption of shorter wavelength light.

Biosensors are fluorophores that report on the location and activity of molecules or ions that, typically, are involved in signalling networks.
Metabolic Pathway Databases
Authors: Ellis Lynda BM 
Published: March 2010

Abstract

Metabolic pathway databases may draw on enzyme, compound and gene databases, but usually go beyond them to show how enzyme reactions link to one another and ultimately form pathways for catabolism, anabolism or other necessary cellular functions. Public metabolic databases may contain information on pathways shared by many organisms; these may omit specialized metabolism. Others may limit themselves to share or unique pathways found in specific organisms, or specialized metabolism. Metabolic pathway databases are a resource for metabolic engineering. Genetic material from microbes, plants and animals is being modified at the present time; these modifications are often based on information mined from a pathway database. Mining of metabolic data is still in its infancy. Based on information stored in today's metabolic databases, it may be possible in the future to predict metabolic pathways for the biodegradation of novel environmental toxins or biosynthesis of needed specialty chemicals.

Key concepts:

Metabolic databases contain information on enzymes, compounds and genes organized in metabolic pathways.

Metabolic databases may contain information on pathways shared by many organisms, or may limit themselves to pathways in specific organisms or to specific types of pathways.

Metabolic databases are a resource for metabolic engineering, which needs information on the genes, enzymes and pathways found in target organisms.
Molecular Dynamics
Authors: Petrenko Roman , Meller Jarosław 
Published: March 2010

Abstract

Molecular dynamics (MD) is a widely used technique for computer simulation of complex systems, modelled at the atomic or some coarse‐grained level. In this article, basic concepts pertaining to MD simulations are systematically introduced and related to the underlying models of physical systems. The principles of the atomic force fields, representation of the environment, the time evolution of the system, as well as the derivation of kinetic and thermodynamic properties of interest from MD trajectories are discussed. Applications of MD to biological systems are illustrated by examples of large scale studies on protein structure and dynamics, protein–protein interactions, and drug design. Limitations and several recent extensions of classical MD, including Replica Exchange and Steered MD, are discussed in the context of applications to biological systems as well. Related simulation protocols, including Monte Carlo and free energy methods, are summarized, highlighting complementarity and common principles of these molecular simulation approaches.

Key Concepts

Computer simulations can be used to facilitate and complement experimental studies of biomolecular systems.

Empirical force fields describe interatomic interactions in the system and enable efficient computation of forces in MD simulations.

MD is routinely used to study biological macromolecules and their environment.

A physical quantity can be measured using MD simulations by taking an arithmetic average over instantaneous values of that quantity obtained from MD trajectories.

Other simulation methods, such as Monte Carlo, enhanced sampling and free energy methods, are often being used in conjunction with MD and its extensions.

Slow processes can be studied computing the relative free energies of different states.

MD and related methods can be applied to systems comprising millions of atoms, providing unique insights into complex biological systems.
Nucleic Acid Backbone Structure Variations: Peptide Nucleic Acids
Authors: Nielsen Peter E 
Published: March 2010

Abstract

Synthetic analogues and mimics of the natural genetic material
deoxyribonucleic acid
(DNA) are potential gene therapeutic (antisense or antigene) drugs. One of these mimics, peptide nucleic acids (PNAs), are chemically closer to peptides and proteins than to DNA, but nonetheless have retained many of the structural properties of DNA. These molecules have found applications as probes in genetic diagnostics and are also being developed into antisense (RNA (
ribonucleic acid
) interference) gene therapeutic drugs, targeting selected genes through sequence‐specific recognition of (messenger or micro)RNA and in the future also antigene applications targeting the double‐stranded DNA of the genes themselves leading to gene silencing or guiding specific gene repair. Finally, the special chemical and structural properties of PNA suggest that these or similar molecules might have played a role in the prebiotic origin of life (on Earth) and also could be interesting components of possible artificial life.

Key concepts:

A range of chemical structures can mimic various functions of our genetic material, the DNA.

Chemical modifications and structural mimics of DNA are useful as genetic diagnostic probes and are being developed into gene therapeutic drugs.

RNA interference drug sequences specifically bind to cellular (messenger or micro)RNA and interfere with (inhibit) their function.

Prebiotic origin of life could have involved peptide nucleic acid molecules as predessors of RNA.
Actin Reorganization in Nerve Morphogenesis
Authors: Singh Ajeet Pratap , Rodrigues Veronica , VijayRaghavan K 
Published: March 2010

Abstract

Anatomists over centuries have described nerve cells which are notable for their diversity of architectures ranging from rather simple cells to highly complex and beautiful shapes. The soma of most neurons have two types of projections – dendrites which receive inputs from the environment or other nerve cells, which specialize in information transfer. The correct shape of a neuron and its connectivity which forms the basis of a functional circuit is crucial for the normal physiology of an animal. Defects in neuronal morphogenesis have been shown to be the cause of several neurological diseases. In this article we focus on a key molecule –
actin
, a component of the cytoskeleton – that forms the basis of cell shape and growth. We discuss how signals from within the cells and from its developmental milieu influence the organization of
actin
which in turn impacts on the shape and function of a nerve cell.

Key Concepts

Actin is enriched in areas of neurons which undergo rapid changes in shape.

Actin dynamics is regulated by multiple upstream signals and intracellular effectors.

Local destabilization of the actin cytoskeleton is a key downstream event during selection of an axon.

Actin dynamics in the growth cone regulates filopodial extension/retraction.

Actin cytoskeleton is highly dynamic in dendritic spines.

Neuronal activity‐dependent spine enlargement is correlated with a shift in F‐/G‐actin equilibrium towards F‐actin.

Rho GTPases are major intracellular regulators of actin dynamics.
Biomechanics of Plant Cell Growth
Authors: Jordan Benjamin M , Dumais Jacques 
Published: March 2010

Abstract

Plant cell growth is an irreversible yielding of the cell wall to the internal turgor pressure of the cell. Plant cells can control their expansion by modulating the structure and material properties of their wall. One major level of control is the distribution and orientation of the stiff cellulose microfibrils within the wall. When aligned, the microfibrils impart the wall with mechanical anisotropy which allows cells to expand preferentially along one direction. Moreover, growth is possible only when the stress in the wall exceeds a critical yield stress, also under cellular control. This article summarizes the key models that have been put forward to account for these aspects of cell growth. We begin with the now classic model by James Lockhart which reconciles the mechanical and hydraulic aspects of cell expansion. We then give an overview of newer modelling efforts to account for the complexity of cell wall mechanics.

Key Concepts:

Plant cell growth is an irreversible change in cell size involving stretching of the cell wall driven by the internal turgor pressure of the cell.

Growth is measured as the relative elemental growth rate (REGR).

The two main modes of cell morphogenesis are tip growth and diffuse growth.

For a cell to grow the cell surface must expand and water must enter the cell. The Lockhart equation encapsulates the balance between these two processes.

Under most circumstances, the rate of cell growth is limited by the extensibility of the cell, wall whereas the resistance to the influx of water is comparatively low (plant cell growth is said to be extensibility limited).

Cellulose microfibrils provide the cell wall with anisotropic mechanical properties which allow cells to expand along a preferred direction.