bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteases: Evolution
Authors: Southan Christopher
Published: October 2007

Human proteases have diverse fold structures, catalytic mechanisms, biochemical functions and evolutionary origins. Most arose by gene duplication, but some arose by horizontal transfer from prokaryotes. Adaptation and diversification of their biological roles have resulted from shifts in substrate specificities, expression patterns and new domain combinations.
Transcriptional Regulation: Evolution
Authors: Wray Gregory A
Published: October 2007

Changes in transcriptional regulation can result from mutations in
cis
(within regulatory sequences) or
trans
(in the structure or expression of transcription factors). Modifications in transcription can have a profound impact on gene function and constitute an important class of evolutionary change within genomes.
Morphological Diversity: Evolution
Authors: Budd Graham
Published: October 2007

Morphology has diversified through the evolutionary process. However, its structure and relationship to the genome are both complex, making its evolution hard to understand.
Fugu
: The Pufferfish Model Genome
Authors: Venkatesh B
Published: October 2007

The pufferfish,
Fugu rubripes
, has the smallest genome among vertebrates. It is a useful model for understanding the structure, function and evolution of vertebrate genomes.
Visual Pigment Genes: Evolution
Authors: Yokoyama Shozo
Published: October 2007

More than 100 visual pigment genes have been cloned from a diverse range of vertebrates. Comparative sequence analyses of these genes and
in vitro
assays of engineered visual pigments have been used to elucidate not only the molecular bases of color vision but also the processes of adaptive evolution at the molecular level.
Myosins
Authors: Sellers James R
Published: October 2007

Myosins are molecular motors that move or interact with actin filaments to perform a variety of functions in cells. The multiple myosin genes in humans contain a conserved motor domain that harbors the machinery needed to interact with actin and hydrolyze ATP. Other functional domains exist to determine the localization and anchoring of the molecule.
Neuropeptides and their Receptors: Evolution
Authors: Hoyle Charles HV
Published: October 2007

Multiple forms of neuropeptides and their receptors have evolved through the processes of genome duplication, gene duplication and point mutation. Some vertebrate peptide lineages have traceable origins in invertebrates, and linkage to homeobox genes may be useful in determining the lineage.
DNA Replication Origins
Authors: Françon Patricia , Méchali Marcel
Published: October 2007

Replication of the genome of any living organism is integral to its maintenance and development. DNA replication starts from a single origin in the genome of simple organisms such as bacteria and small eukaryotic DNA viruses. In complex eukaryotes, such as metazoans, DNA replication starts from thousands of origins spread across the different chromosomes.
Genetic Counseling: Consanguinity and Cultural Expectations
Authors: Karbani Gulshan A
Published: October 2007

Individual and familial responses to the diagnosis of serious genetic disorders are known to vary widely. But in some minority ethnic groups, expectations and norms may further influence these responses and thus render genetic counseling more problematic than usual.
Behavior: Role of Genes
Authors: Järvilehto Timo
Published: October 2007

Much effort in genetics is motivated by the hope that one day human behavior will be explicable in genetic terms. However, the scientific basis of this hope is questionable.
Intelligence, Heredity, and Genes: A Historical Perspective
Authors: Goodey CF
Published: October 2007

The idea of an intelligence specific to humans has not always existed but grew from pre‐modern ideas about their cultural and religious status. Galton's attachment of the term ‘intelligence’ to an existing statistical abstraction (the Gaussian curve) enabled this metaphysical concept to be correlated with the physical phenomenon of genetic material, since both were now apparently measureable. Like intelligence, the ‘nature/nature’ and ‘normal/abnormal’ frameworks dominating cognitive genetics are not trans‐historical but outcomes of the eugenic mind‐set, dependent on it for their validity.
Bioethics: Institutionalization of
Authors: Engelhardt H Tristram , Iltis Ana Smith , Jotterand Fabrice
Published: October 2007

Bioethics is a recognized discipline in the academy, an established practice within the clinic and a source of guidance for healthcare policy. As a complex of theoretical and practical undertakings, bioethics now commands an officially recognized cluster of norm‐setting and behavior‐guiding roles that have become institutionalized elements of the scholarly, clinical and public policy establishment.
Limits of Proteomics: Protein Solubilization Issues
Authors: Rabilloud Thierry
Published: October 2007

Because of their tremendous heterogeneity many proteins are poorly soluble in aqueous solvents. This precludes their analysis by classical proteomics techniques. Technical developments in two‐dimensional electrophoresis as well as the search for alternative techniques are alleviating this major problem.
Protein‐Protein Interaction Maps
Authors: Legrain Pierre
Published: October 2007

The construction of protein–protein interaction maps allows for the study of protein function at a large scale within an organism as well as between organisms. It is particularly useful for protein functional annotations in databases.
Phosphoproteomics
Authors: Veenstra Timothy D , Conrads Thomas P
Published: October 2007

While proteomics aims to globally identify and measure the abundances of proteins, the challenge of phosphoproteomics is to determine globally the phosphorylation status of proteins present in the cell. Advances in mass spectrometry and developments in phosphopeptide enrichment methodologies is enabling high‐throughput global identification and relative quantitation of phosphopeptides.
Protein Glycosylation
Authors: Lisowska Elwira
Published: October 2007

Glycosylation is the most common posttranslational modification of proteins. It is a complex process involving many functional proteins and resulting in a great diversity of structures. The biological role of glycosylation and the molecular and genetic basis of glycosylation disorders have recently been extensively explored.
Protein Structure Prediction and Databases
Authors: Domingues Francisco S , Lengauer Thomas , Sommer Ingolf
Published: October 2007

Three‐dimensional structures of proteins are the key to their molecular function. Traditionally protein structures are determined by experiment. The large set of protein sequences that become available through genomics or proteomics activities calls for computer support of protein structure prediction. Today several databases complement the comparatively small set of protein structures measured by experiment with much larger sets of protein models generated by computer.
Image Analysis Tools in Proteomics
Authors: Voordijk Sonja , Walther Daniel , Bouchet Gérard , Appel Ron D
Published: October 2007

Many proteomics projects rely heavily on the analysis of two‐dimensional electrophoresis gels, a step that is still considered as one of the major bottlenecks in the protein separation/identification process. The latest generation image analysis software supports high‐throughput and large‐scale studies.
Protein Characterization in Proteomics
Authors: Meri Seppo , Baumann Marc
Published: October 2007

Proteomics refers to the comprehensive analysis of proteomes – the protein contents of complex biological mixtures. It includes the separation and identification of proteins, and the identification and analysis of their structure and function using large‐scale methods.
Structural Proteomics: Large‐scale Studies
Authors: Norin Martin , Sundström Michael
Published: October 2007

Structural proteomics or structural genomics is a common term for systematic efforts to functionally annotate protein molecular structures of whole or selected parts of genomes and/or proteomes.
Pattern Searches
Authors: Lisacek Frédérique
Published: October 2007

Common amino acid patterns characterize protein families. The results of automated searches for such patterns are used to qualify protein structure and function.
Eye: Proteomics
Authors: Steely H Thomas , Clark Abbot F
Published: October 2007

Ocular proteomics allows the identification of proteins in diseases of the eye, blindness and aging.
Human Immunodeficiency Virus (HIV) Infection: Genetics
Authors: McNicholl Janet M , Lal Renu B , Kaslow Richard
Published: October 2007

Host genes influence many aspects of the human immunodeficiency virus (HIV) from transmission and infection to disease progression and acquired immunodeficiency syndrome as well as responses to drugs and HIV vaccines.
Mouse
N
‐ethyl‐
N
‐nitrosourea (ENU) Mutagenesis
Authors: Justice Monica J , Northrop Jennifer L
Published: October 2007

Mutagenesis is a powerful tool for understanding gene function and disease that has been used in many organisms from bacteria to fish. The chemical
N
‐ethyl‐
N
‐nitrosourea is being used as a supermutagen in mice to allow forward genetic screens. The addition of a complex mammal such as the mouse to the list of model organisms that have been analyzed by large‐scale mutagenesis will provide new mammalian models of human diseases and will allow an analysis of conserved and divergent evolution among species.
Segmental Duplications and Genetic Disease
Authors: Emanuel Beverly S , Shaikh Tamim H
Published: October 2007

More than 50% of our genome is made up of repetitive DNA elements, which are classified into different categories based on their size, copy number, mechanisms of dispersal and several other factors. Segmental duplications represent one such class of repetitive element. Recently, several genetic diseases have been shown to be the result of chromosomal rearrangements mediated by segmental duplications.
Neural Tube Defects: Genetics
Authors: Kirkpatrick Timothy J , Northrup Hope
Published: October 2007

Neural tube defects comprise complex disorders, annually affecting thousands of pregnancies worldwide. They are hypothesized to be a result of genetic abnormalities and environmental agents, yet the etiology remains puzzling. Research has demonstrated the importance of dietary folic acid in some women for prevention, but many cases still occur.
Male Sex Determination: Genetics
Authors: Ostrer Harry
Published: October 2007

The key event in male sex determination is the transmission of a Y chromosome from father to offspring. In the developing gonad, the sex‐determining gene on the Y chromosome,
SRY
, triggers the expression of other genes that cause the gonad to develop as a testis. Hormones secreted by the developing testis influence the differentiation of male internal and external genitalia and other somatic features.
Kinetochore: Structure, Function and Evolution
Authors: Kitagawa Katsumi
Published: October 2007

Kinetochores are complexes of centromere DNA and proteins. Spindle microtubules bind to chromosomes at the kinetochore, and these complexes are required for accurate chromosome segregation during mitosis. The human kinetochore is a supramolecular complex of DNA and proteins that is involved in various mitotic activities.
Language and Genes
Authors: Tomblin J Bruce
Published: October 2007

The development of spoken language involves the acquisition of a complex system of knowledge that is generally believed to depend on biological systems that are genetically influenced.
Roma (Gypsies): Genetic Studies
Authors: Kalaydjieva Luba , Morar Bharti
Published: October 2007

The Roma, also known as Gypsies, are a transnational founder population, resembling a mosaic of socially and genetically divergent groups. Common origins from a small group of related founders result in sharing of maternal and paternal lineages and of ancient disease‐causing mutations across endogamous Romani groups in different countries. Genetic differentiation between groups, with an impact on genetic epidemiology, is the product of bottleneck events, random genetic drift and differential admixture, and correlates with the migrational history of the Roma in Europe.
Ohno, Susumu
Authors: Wolf Ulrich
Published: October 2007

Ohno Susumu (1928–2000) was a Korean‐American geneticist, who studied the role of genes in evolution and sex determination.
Darlington, Cyril Dean
Authors: Ruse Michael
Published: October 2007

Darlington, Cyril Dean (1903–1981) British cytologist who worked on the formation of the sex cells.
Hamilton, William Donald
Authors: Ruse Michael
Published: October 2007

William Donald Hamilton (1936–2001) was an evolutionist, theorist and field naturalist who explored the genetic relationship between close relatives.
Blocks of Limited Haplotype Diversity
Authors: Morton Newton E
Published: October 2007

A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. Haplotype blocks may be as short as 2 kb or more than 150 kb, depending both on block definition and the spacing of LD cold spots, which tend to be shorter than blocks. Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of polymorphisms defining the haplotype. To be useful in genetic analysis, the haplotype should be shorter than a typical block.
Levan, Albert
Authors: Hultén Maj A , Fredga Karl
Published: October 2007

Albert Levan (1905–1998) was a Swedish cytogeneticist who, in collaboration with Joe Hin Tjio, identified the correct number of chromosomes in humans.
RNAInterference (RNAi) andMicroRNAs
Authors: Hannon Gregory J
Published: October 2007

In 1990, an experiment designed to alter floral pigmentation inPetuniasowed the seeds of what has since become a major new field of biology. Efforts to understand the mechanisms that underlie double‐stranded RNA‐induced (dsRNA) gene silencing are now bearing fruit of many varieties. It is clear that a conserved biological response to dsRNA, known variously as RNA interference (RNAi) or posttranscriptional gene silencing, mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, such as transposons and RNA viruses, and regulates the expression of protein‐coding genes. In addition, RNAi has been cultivated as a means to experimentally manipulate gene expression. In the near future, the use of RNAi to probe gene function at a whole‐genome scale is likely to yield a rich harvest, not only providing insights into basic biological processes but also the tools to identify more rapidly therapeutic targets for numerous human diseases.
Chlorophyll Metabolism
Authors: Eckhardt Ulrich , Grimm Bernhard
Published: October 2007

The two pathways for chlorophyll biosynthesis and catabolism of plants are located in distinct cellular compartments. While the entire biosynthesis of chlorophyll from the first committed metabolic precursor, 5‐aminolaevulinic acid, occurs in plastids, chlorophyll breakdown starts in plastids and the final non‐fluorescent breakdown products are deposited in vacuoles. The current understanding about both pathways in a diverse range of photosynthetic organisms including photosynthetic bacteria, algae and higher plants is outlined in the following report. It is quite obvious that the photosynthetic organisms evolved a complex control of these two pathways to enable specific adaptation to various environmental conditions.
Abiotic Stress
Authors: Bohnert Hans J
Published: October 2007

Plants, being sessile organisms, are exposed to external factors that can be stressful in such a way that growth, development, and reproduction or the yield of crops become compromised. Expanding extensive physiological studies, the last decade has seen a focus on genes and biochemical pathways that determine whether plants are sensitive or tolerant to the many different stress factors: heat, cold and freezing, drought, salinity, flooding or oxidizing agents. Recently, most emphasis is being directed towards an understanding of the mechanisms through which plants recognize external conditions, and on the signailing pathways that initiate protective reactions.
Abscission
Authors: Roberts Jeremy A , González‐Carranza Zinnia H
Published: October 2007

The abscission of organs takes place at discrete sites and at specific times during the life cycle of a plant. These observations suggest that the abscission zone comprises a layer of positionally differentiated cells that undergo separation from their neighbours in response to precise developmental and environmental cues. By studying mutants of
Arabidopsis
that exhibit an attenuated capacity to shed their floral organs, it has been possible to identify a number of genes that may play a role in both the differentiation of abscission zone cells and the timing of organ shedding. The possible applications of this knowledge to agricultural and horticultural species are discussed.
Auxin
Authors: Hobbie Lawrence J
Published: October 2007

The plant hormone auxin is an important regulator of many processes in plants, including pattern formation during early development, elongation and branching of roots and shoots, development of vascular tissues and responses to light and gravity. Our increasingly detailed knowledge of the pathways of auxin synthesis, inactivation, transport and cellular signalling will facilitate control of plant growth and development.
Resistance to Bacterial Pathogens in Plants
Authors: Ade Jules , Innes Roger W
Published: October 2007

To successfully infect a plant, pathogens must overcome three layers of defense: (1) preformed physical barriers; (2) a cell‐surface‐based surveillance system that detects conserved pathogen molecules and (3) an intracellular surveillance system that detects effector proteins injected into host cells. Bacterial plant pathogens overcome the first layer either by invading through natural openings and wounds, and/or by secreting hydrolytic enzymes that break down surface layers. Bacteria typically overcome the second layer by injecting effectors that interfere with defense signaling. Bacteria overcome the third layer either by modifying or eliminating existing effectors, or by evolving new effectors that suppress defense activation.
Brassinosteroids
Authors: Li Jia , Gou Xiaoping
Published: October 2007

Brassinosteroids (BRs) are specific phytosteroids necessary for ordinary plant growth and development. BRs share similar chemical structures with animal steroidal hormones, but show a distinctive signal perception mechanism. The importance of BRs is illustrated by the typical phenotypes of mutants with lesions in key biosynthetic or signalling proteins. These mutants exhibit severe dwarfism, curled and round leaves, considerably delayed senescence, reduced male fertility, altered light‐regulated developmental programmes, changed responses to abiotic and biotic stresses and modified gene expression profiles. Extensive studies within the last three and a half decades have resulted in a comprehensive picture of BRs, from their nearly completed biosynthesis and physiological functions, to their mechanisms of action.
Fitness Costs of Plant Disease Resistance
Authors: Brown James K M
Published: October 2007

Disease is a major agent of evolution by natural selection because infection by a parasite reduces the fitness of its host, yet all plants suffer from disease. This paradox can be explained if host resistance to disease is most beneficial when most plants are susceptible, and if resistance reduces a plant's fitness in the absence of the parasite. Fitness costs of disease resistance may arise in several ways: physiological and metabolic costs of defence against parasites, developmental traits which allow plants to escape disease but are sub‐optimal for seed production, and trade‐offs between resistance and responses to other microbes.
Cytokinins
Authors: Riefler Michael , Werner Tomáš , Heyl Alexander
Published: October 2007

Cytokinins are a class of plant growth regulators that play an important role in many physiological and developmental processes in the plant, such as regulation of cell division, leaf senescence, nutrient uptake and pathogen resistance. Recent years have witnessed rapid progress in our understanding of several aspects of cytokinin biology, especially cytokinin signalling and metabolism.
Endoreduplication and Cell‐size Control in Plants
Authors: Breuer Christian , Sugimoto‐Shirasu Keiko
Published: October 2007

Endoreduplication involves replication of chromosomal deoxyribonucleic acid (DNA) without intervening mitoses. Endoreduplication and resulting high ploidy have often been correlated with an increase in cell size. Cell size is determined by highly dynamic, intersecting signalling pathways in plants, and the nuclear–cytoplasmic ratio is likely to provide a minimum constraint for this control.
Genetic Control of Leaf Shape
Authors: Koenig Daniel P , Sinha Neelima R
Published: October 2007

Development of a complex organ such as the leaf requires the coordinated action of numerous genetic factors. The advent of molecular genetics has allowed for the elucidation of many components of the genetic network controlling leaf development.
Metabolite Profiling in Plants
Authors: Trethewey Richard N
Published: October 2007

Advances in analytical chemistry, computation and biotechnology have led to the recent development of methodologies for broad metabolite profiling. The study of plant metabolism has been one of the first beneficiaries of these technologies and applications have focused on plant metabolite engineering, functional genomics and physiology. In the future, the greatest value will be generated from metabolite profiling technology in applications that integrate plant sciences with nutrition and human health.
Micro
RNAs
(
mi
RNAs
) and Plant Development
Authors: Wang Wang‐Xia , Gaffney Bobby , Hunt Arthur G. , Tang Guiliang
Published: October 2007

microRNAs (miRNAs) are a novel class of 21–24 nucleotide, endogenous, noncoding small ribonucleic acids (RNAs) that play critical roles in diverse biological processes such as: development, cellular differentiation, cell‐cycle control, apoptosis and oncogenesis. In plants, roles of miRNAs in development have been extensively investigated in recent years. This review highlights and discusses the current knowledge about the roles of microRNAs in leaf development, patterning and polarity, floral identity and flower development, developmental phase transition and flowering time, shoot and root development, vascular development and hormone signalling for plant development.
Nitric Oxide Signalling in Plants
Authors: Vandelle Elodie , Zaninotto Federica , Delledonne Massimo
Published: October 2007

Small, simple and highly toxic, nitric oxide (NO) is a gas with a broad chemistry that involves an array of interrelated redox forms with different chemical reactivities. Named ‘Molecule of the Year’ in 1992, NO is now considered a ‘do it all’ molecule that plays a crucial role during the entire lifespan of the plant.
Plant Peptide Signals
Authors: Sakagami Youji
Published: October 2007

The number of plant peptide signal molecules has been increasing and is expected to increase further in the near future. Some peptides have well determined structures, are processed from precursor polypeptides, receive posttranslational modification and interact with their specific receptors. Others are only known from their precursor genes that are suspected to encode biologically active peptides.
The Plant Cell Cycle and Its Control
Authors: Kuijt Suzanne , Schnittger Arp
Published: October 2007

Plants need to accurately amplify their genetic material and equally distribute it between the two daughter cells in order to propagate and develop. This is achieved in an ordered sequence of events which compose the cell cycle. Cell‐cycle regulation is of primary importance for plant development due to the intricate connection between cell proliferation and differentiation, and the subsequent production of cells by the meristems. Control of cell division is also a major way by which plants are able to respond to an ever‐changing environment. While the theme of cyclin‐dependent kinase regulation through the cell cycle is conserved in plants, the cell‐cycle control of multicellular plants also presents a few specializations, most prominently, the large cyclin families and the plant‐specific class of B‐type CDKs.
Plant Centromeres
Authors: Vershinin Alexander V
Published: October 2007

The centromere functions are conserved among all eukaryotes but different organisms have strikingly different centromeric deoxyribonucleic acids (DNAs). Currently in molecular terms, the functional centromere can be defined as a domain of the chromosome where DNA sequences interact with the kinetochore components – proteins. A fundamental feature of all the studied centromeres is a specialized histone H3 variant known as centromeric histone (CENH3). Adaptive evolution of the molecular components contributed to the epigenetic modulation of centomere activity.
Plant Circadian Rhythms
Authors: McWatters Harriet G , Eriksson Maria E
Published: October 2007

Circadian clocks are found in most eukaryotic organisms. By allowing anticipation of daily and seasonal changes they enable coordination of metabolism and life cycle with the natural rhythms of the environment. Plant circadian rhythms are generated by a series of interlocking feedback loops of ribonucleic acid (RNA) and protein expression that respond to environmental cycles of light and temperature. They control essential processes in the plant's development, such as the transition to flowering or growth cessation.
Polar Auxin Transport
Authors: Courseau Isabelle Bohn , Traas Jan
Published: October 2007

Auxin is a plant hormone involved in a wide range of processes. It is transported from cell to cell by a process known as polar auxin transport (PAT), which plays a major role in plant development and physiology.
Root Apical Meristems
Authors: Lee Ji‐Young , Benfey Philip N
Published: October 2007

Root apical meristems are populations of cells at the root tip that divide and form all the tissues of the root. The fate of divided cells is determined by positional signals. The iterative process of cell division, elongation and differentiation promotes root growth. An important aspect of growth is balancing the rate of cell division and differentiation, which is regulated by the quiescent centre.
Shoot Branching and Plant Architecture
Authors: Bennett Tom A , Crawford Scott R , Ward Sally P , Leyser Ottoline
Published: October 2007

A major component of postembryonic shoot development is the formation of secondary axes of growth which originate from axillary meristems located in the axil of leaves. The activity of axillary meristems is tightly regulated by the integration of environmental and genetic inputs, giving rise to the multifarious plant architectures seen in nature.
Starch Biosynthesis and Degradation in Plants
Authors: Smith Alison M
Published: October 2007

Starch is the main form in which plants store carbon. The glucose polymers that constitute the semi‐crystalline starch granule are synthesized by the concerted actions of well‐conserved classes of isoforms of starch synthase and starch‐branching enzyme, via a process that also requires the debranching enzyme isoamylase. The degradation of the granule proceeds via different pathways in different types of starch‐storing tissues.
Sulfur Metabolism in Plants
Authors: Kopriva Stanislav
Published: October 2007

Sulfur is an essential element found in plants in a variety of compounds with many different functions. Sulfur nutrition is important for plant defence against biotic and abiotic stress and for the quality of crops.
Systemic Signalling in Plant Development
Authors: Jackson David
Published: October 2007

Plants are sessile organisms that communicate extensively with their environment to fine‐tune their growth and development. Perception of environmental stimuli often leads to the production of systemic signals that control the development of distant organs and tissues.
Root‐nodule Symbiosis: Molecular Basis of Nodule Formation
Authors: Oldroyd Giles
Published: October 2007

Nutrient availability is a major limitation to plant growth. Legumes have entered into a symbiotic interaction with nitrogen‐fixing rhizobial bacteria that provide the plant with a source of nitrogen. The legume/rhizobial symbiosis is globally important for introducing nitrogen into biological systems. Legume crops are used in sustainable agricultural processes to naturally enrich the soil for nitrogen. Our understanding of the molecular mechanisms that underlie this interaction is expanding and we are beginning to understand the means by which the molecular dialogue occurs between the plant and the bacteria. The signalling pathway in the plant, that is responsible for the recognition of the bacterial signal Nod factor, appears to have evolved in part from a pre‐existing signalling pathway necessary for the establishment of the mycorrhizal symbiosis. Further research in this field may help to apply this symbiosis more broadly in agriculture.
Transcriptional Profiling in Plants
Authors: Hannah Matthew A , Hincha Dirk , Altmann Thomas
Published: October 2007

With appropriate design and data analysis, transcriptional profiling (i.e. the multiparallel analysis of expression of a large number of genes) is a reliable and powerful method to investigate developmental or physiological processes in plants, in particular the responses to genetic and environmental perturbation. Furthermore, its utility is broadened by the public availability of many experiments, which has led to the development of novel tools for determining gene function that are of direct and immediate use to the plant biology community.
Oxidative Stress and Redox Signalling in Plants
Authors: Mühlenbock Per , Karpinska Barbara , Karpinski Stanislaw
Published: October 2007

Plants are due to their constitution unable to escape from environmental stress and are constantly at the risk of being exposed to several stress factors simultaneously that usually are associated with oxidative stress. We are presenting some genetic, molecular and physiological examples that plants functionally integrate varieties of intra‐ and intercellular signalling in response to such stresses. It is concluded that fine control of cellular redox homeostasis as a function of the interaction of hormones and reactive oxygen species (ROS) signalling is important for integrated regulation of plant defence and acclimatory responses.
NK Cell Receptors
Authors: Tian Zhigang , Zhang Cai
Published: October 2007

Natural killer (NK) cell effector functions are regulated by integrated signals across the array of stimulatory and inhibitory receptors engaged upon interaction with target cell surface ligands. A delicate balance between activating and inhibiting receptors determines the outcome of NK cell activation.
Natural Killer
T
Cells
Authors: Bezbradica Jelena S , Van Kaer Luc , Joyce Sebastian
Published: October 2007

Natural killer T (NKT) cells are innate lymphocytes whose functions are regulated by self and foreign glycolipid antigens presented by the antigen‐presenting, major histocompatibility complex (MHC)‐like molecule CD1d. Activation of NKT cells
in vivo
results in rapid release of copious amounts of effector cytokines and chemokines with which they regulate innate and adaptive immune responses to pathogens, certain types of cancers and self antigens. Hence, CD1d and NKT cells are potential targets in vaccine concoctions and for immunotherapies against autoimmune diseases.
Autoimmune Disease: Mechanisms
Authors: Fairweather DeLisa
Published: October 2007

The immune system provides protection against infectious organisms and repairs tissue damage induced by infections or physical damage. Autoimmune disease occurs when the immune response inflicts damage to tissues in the body.
Interaction Networks of Proteins
Authors: Date Shailesh V , Chen Guang
Published: October 2007

Proteins are often the ultimate expression of information encoded in the DNA (deoxyribonucleic acid). Proteins interact with other proteins, nucleic acids, and a variety of small molecules to affect cellular function. Such interactions assume the form of a vast network, portions of which are activated in a spatial and temporal manner. Understanding the makeup, properties and behaviour of this network promises to reveal many important details of the biology of organisms, ultimately helping better our knowledge of molecular and biochemical events that take place at the cellular level.
Protein Production in Mammalian Cells
Authors: Hacker David L , Wurn Florian M
Published: October 2007

Mammalian cells are an important host for the production of clinically relevant recombinant proteins. The most widely used approach for this purpose is to establish a cell line with an actively expressed recombinant gene stably integrated in its genome. Alternatively, protein can be transiently produced in cells for a few days immediately after deoxyribonucleic acid (DNA) transfer without the necessity of recombinant gene integration.
Expression Tags for Protein Production
Authors: Hu Su‐Ming , Wang Andrew H‐J , Wang Ting‐Fang
Published: October 2007

The fusion of a protein of interest to an expression tag(s), called the fusion‐protein approach, has been utilized in the forefront of modern biology and medicine for structural and functional analysis.
Gene Synthesis for Protein Production
Authors: Stewart Lance
Published: October 2007

Synthetic gene production is an enabling technology for improved protein production since it can be used to produce totally novel gene sequences that are optimized for codon usage and other sequence features anticipated to facilitate improved protein expression in defined expression systems. Computer aided gene design algorithms of increasing sophistication, allow researchers to exploit the degeneracy of the genetic code to engineer expression optimized synthetic gene sequences and the overlapping oligonucleotides needed to manufacture the desired synthetic gene by polymerase chain reaction (PCR) methods. Low cost synthetic gene production is ushering in a new era of synthetic biology for improved protein production.
Tandem Affinity Purification (
TAP
) Tags
Authors: Damasceno Cynthia Maria Borges , Rose Jocelyn Kenneth Campbell
Published: October 2007

Tandem affinity purification (TAP) tagging is a method to purify multimeric protein complexes that can be used under essentially physiological conditions. This technique allows subsequent protein identification by mass spectrometry or functional analysis of the proteins post‐purification. The TAP method has already been used to help elucidate large networks of interacting proteins in several organisms.
Disordered Proteins
Authors: Dunker A Keith
Published: October 2007

Disordered proteins and disordered protein regions fail to form specific three‐dimensional (3D) structure as monomers under physiological conditions, existing instead as dynamic structural ensembles. These dynamical proteins and regions often carry out biological function. Just as amino acid sequence codes for 3D structure, amino acid sequence also codes for the failure of a protein or regions to form specific structure. A major goal in the coming years will be to understand sequence‐to‐function relationships for disordered proteins.
Susceptibility to Malaria, Genetics of
Authors: Berghout Joanne , Gros Philippe
Published: October 2007

Malaria has exerted a strong, selective pressure on many genes in the human genome, leading to the development and retention of several alleles which confer a proctective advantage against blood‐stage infection. Many of these polymorphisms, including sickle cell anaemia and the thalassaemias, are in the haemoglobin genes, but other mutations have been found in metabolism and immune response. Since many interacting genes are involved in the host response to malaria, animal models have been extremely useful in helping to identify and understand the host–parasite interaction.
Inflammatory Bowel Disease, Genetics of
Authors: Lees Charles W , Ho Gwo‐Tzer , Satsangi Jack
Published: October 2007

Genetic studies of the chronic inflammatory bowel diseases, Crohn disease (CD) and ulcerative colitis (UC), represent a paradigm for complex disease genetics having seen several notable breakthroughs. Indeed, the discovery of NOD2/CARD15 as a CD susceptibility gene in 2001 was the first in a complex genetic disorder. In this review, we detail the genetic epidemiology in inflammatory bowel disease, genome‐wide linkage and association studies, and candidate genes highlighting the insights they have provided into disease pathogenesis and therapeutics.
The Genetics of Neuronal Channelopathies
Authors: Ma Shaochun , Gargus John Jay
Published: October 2007

A channelopathy is a new mechanism of disease involving dysfunction of ion pumps and channels. Monogenic forms of common neuronal disease phenotypes – such as seizures, ataxia and migraine – have been demonstrated to be produced by mutation of such genes. The mutation serves to produce a constitutionally hyperexcitable tissue that is susceptible to periodic decompensations recognized as disease. There are suggestions that similar mechanisms are at play in the common polygenic forms of these diseases, and that an understanding of these a etiological genes hold the potential to lead to new diagnostics and therapeutics.
Bardet‐Biedl Syndrome, an Oligogenic Disease
Authors: Liu Yangfan , Zaghloul Norann A , Katsanis Nicholas
Published: October 2007

Bardet‐Biedl syndrome (BBS) is a rare multisystemic disorder characterized by defects in renal function, obesity, mental retardation, retinal degeneration and polydactyly. The disease is transmitted primarily in an autosomal recessive fashion but can also exhibit oligogenic inheritance. Twelve BBS genes have been identified to date. Based on localization and functional studies of their protein products, the underlying cause of the disease phenotype is defects in ciliary function which accounts for the pleiotropic nature of the disease. Though it is still unclear exactly how these genes function in cellular signalling pathways, evidence suggests that they are important in a number of fundamental pathways, including the Wnt signalling pathway.
Inherited Disorders of Glycosylation
Authors: Sparks Susan E
Published: October 2007

Glycosylation is an essential process by which sugars are attached to proteins and lipids. Complete lack of glycosylation is not compatible with life. Because of the widespread functions of glycosylation, inherited disorders of glycosylation are multisystemic.
TRP
Channels
Authors: Liman Emily R
Published: October 2007

The first member of the transient receptor potential (TRP) ion channels was identified as a key component of phototransduction in the fly photoreceptor. Since that time, 28 mammalian members of the family have been identified, many of which play important roles in sensory physiology. Most remarkably, some of these channels are directly gated by temperature.
Dynamic Clamp
Authors: Preyer Amanda J , Butera Robert J
Published: October 2007

The dynamic clamp technique uses the membrane voltage measured from an electrically excitable cell to solve computational ion channel models running in real time. The current resulting from these simulations is then injected into the cell in a feedback configuration to create ionic currents that can simulate intrinsic ionic currents within single cells or synaptic currents to create networks of cells.
Anaerobes
Authors: Oren Aharon
Published: October 2007

A diverse world of microorganisms still inhabits anaerobic environments on Earth, and these obtain their energy by fermentation or by anaerobic respiration, in which electron acceptors other than molecular oxygen drive the oxidation of organic compounds. We also know phototrophic and chemoautotrophic processes that function in the absence of oxygen. Collaboration of different groups of microorganisms can lead to degradation of complex organic matter also under anaerobic conditions, with carbon dioxide or a mixture of carbon dioxide and methane as the main products.
Clostridia
Authors: Dürre Peter
Published: October 2007

Clostridia are strictly anaerobic or moderately aerotolerant bacteria, gaining ATP mostly by substrate‐level phosphorylation. A variety of compounds can be degraded and a number of different fermentation pathways are employed. Sophisticated methods for culturing and genetic manipulation are established. Several pathogenic species belong to the genus, however, some of the toxins are used in therapy, research and cosmetic industry. Biotechnologically important are clostridial enzymes, the clostridial solvent production and cancer therapy by recombinant clostridial endospores.
Giant Bacteria
Authors: Schulz‐Vogt Heide N , Angert Esther R , Garcia‐Pichel Ferran
Published: October 2007

For almost all bacteria it is convenient to be very small, but a few highly specialist groups of bacteria have evolved to be orders of magnitude larger than ordinary bacteria.
Mycobacteria: Biology
Authors: Sidders Ben , Stoker Neil G
Published: October 2007

The bacterial genus
Mycobacterium
contains more than 120 members, several of which are extremely successful pathogens of man and animals including the agents of tuberculosis and leprosy. All mycobacteria are aerobic, nonmotile, nonspore forming, Gram‐positive bacteria with a high genomic guanine + cytosine (GC) content. They possess a thick cell wall that contains unique lipids, called mycolic acids, which confer a characteristic acid‐fast staining property and make the genus hardy and resistant to antimicrobials and host defences.
Streptomycetaceae: Phylogeny, Ecology and Pathogenicity
Authors: Lodders Nicole , Kämpfer Peter
Published: October 2007

The family Streptomycetaceae contains three genera, with the genus
Streptomyces
being the best known and most diverse of these three genera. Members of this family are adapted to a wide range of environmental conditions and habitats, and they show a variety of colony – and cell morphological characteristics. Species of the family Streptomycetaceae produce a multitude of bioactive compounds and are able to degrade polymers and other materials used by humans, including rubber and plastics. Only few pathogenic species are known.
Histidine Triad (
HIT
) Superfamily
Authors: Brenner Charles
Published: October 2007

Histidine triad (HIT) enzymes are an ancient superfamily of nucleotide hydrolases and transferases that catalyse mechanistically similar but biologically distinct reactions on nucleotide‐containing substrates in pathways important for cellular growth, apoptosis and deoxyribonucleic acid (DNA), ribonucleic acid (RNA) and carbohydrate metabolism. Four branches of HIT enzymes function as nucleotide hydrolases. These enzymes include homologues and paralogues of histidine triad nucleotide‐binding (Hint) protein, fragile histidine triad (Fhit) protein, Aprataxin and scavenger decapping protein (Dcps). One diverse branch of the HIT superfamily contains nucleotide transferases and phosphorylases related to galactose‐1‐phosphate uridylyltransferase (GalT), AppppA phosphorylase, adenylylsulfate:phosphate adenylyltransferase (APAT), adenosine diphosphate (ADP)‐glucose phosphorylase, and Vtc2, the guanosine diphosphate (GDP)‐
l
‐galactose phosphorylase. This review provides tools to discern the identities and the probable functions of new HIT enzymes from their sequences.
Radical
S
‐adenosylmethionine (
SAM
) Superfamily
Authors: Farrar Christine E , Jarrett Joseph T
Published: October 2007

A large superfamily of enzymes use
S
‐adenosylmethionine (SAM) to generate high‐energy carbon radicals as intermediates in a variety of metabolic and biosynthetic reactions. Despite the diverse reactions catalysed, members of the SAM radical superfamily share a similar structural topology that facilitates the mechanistically important interaction of SAM with an iron–sulfur cluster.
Genetics and Judaism
Authors: Leavitt Frank J
Published: October 2007

Jewish Law (
Halacha
) rarely gives definitive answers nor is it the only source of Jewish thought. A Jewish philosophical–theological attitude may be more useful than
Halacha
when approaching new questions, such as problems in the ethics of genetics, which were not foreseen by the ancient Rabbis. Jewish mysticism (Kabala) is no less essential. An approach based on these three sources –
Halacha
, philosophical–theological thought and Kabala – in the context of specific debates, such as those over genetically modified organisms (GMOs), gene therapy, genetic screening, etc., can be valuable both in themselves and as illustrations of applications of a method.
Insurance Discrimination in the UK – Life Insurance and Genetic Risk
Authors: Needs Jacqueline
Published: October 2007

Life Insurers in the UK have operated within a moratorium on the use of predictive genetic test results since 2001. Prior to this, controversy surrounded the use and interpretation of genetic tests by insurers and led to pressure for legislation to prevent discrimination. The original moratorium applied for five years until November 2006; in March 2005 an extension to the moratorium was announced for a further five years until November 2011. The article explains the events which led to the moratorium, the difficulties of underwriting genetic test results and monitoring the activities of insurers during the moratorium. Research of adverse selection and discrimination is discussed, with reference to the UK, Europe and United States.
Viral Vectors for Gene Therapy
Authors: Philpott Nicola J
Published: October 2007

Viruses can be engineered to deliver genetic material to cells without causing disease. Viral gene therapy vectors have therapeutic use in the treatment of hereditary disease, infectious diseases and cancer as well as for vaccine development.
Cover Picture: Micro/Nano Fabrication of Periodic Hierarchical Structures by Multi‐Pulsed Laser Interference Structuring (Adv. Eng. Mater. 10/2007)
Authors: Lasagni A. , Manzoni A. , Mücklich F.
Published: October 2007

The figure shows periodic hierarchical structures resulting from the combination of interfering laser beams, and laser‐induced periodical surface structure (LIPSS) fabricated on an Al layer over Au‐substrate More details can be found in the paper by A. Lasagni, A. Monzoni, F. Mücklich on page 872.
Steady‐State and Transient Behavior of Organic Electrochemical Transistors
Authors: Bernards D. A. , Malliaras G. G.
Published: October 2007

In recent years, organic electrochemical transistors (OECTs) have emerged as attractive devices for a variety of applications, particularly in the area of sensing. While the electrical characteristics of OECTs are analogous to those of conventional organic field effect transistors, appropriate models for OECTs have not yet been developed. In particular, little is known about the transient characteristics of OECTs, which are determined by a complex interplay between ionic and electronic motion. In this paper a simple model is presented that reproduces the steady‐state and transient response of OECTs by considering these devices in terms of an ionic and an electronic circuit. A simple analytical expression is derived that can be used to fit steady‐state OECT characteristics. For the transient regime, comparison with experimental data allowed an estimation of the hole mobility in poly(3,4‐ethylenedioxythiophene) doped with poly(styrene sulfonate). This work paves the way for rational optimization of OECTs.