bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blocks of Limited Haplotype Diversity
Authors: Morton Newton E 
Published: October 2007

Abstract
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.
RNAInterference (RNAi) andMicroRNAs
Authors: Hannon Gregory J 
Published: October 2007

AbstractIn 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

Abstract
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

Abstract
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

Abstract

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.
Resistance to Bacterial Pathogens in Plants
Authors: Ade Jules , Innes Roger W 
Published: October 2007

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
Metabolite Profiling in Plants
Authors: Trethewey Richard N 
Published: October 2007

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
Root Apical Meristems
Authors: Lee Ji‐Young , Benfey Philip N 
Published: October 2007

Abstract
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

Abstract
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

Abstract
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.
Root‐nodule Symbiosis: Molecular Basis of Nodule Formation
Authors: Oldroyd Giles 
Published: October 2007

Abstract
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

Abstract
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

Abstract
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.
Natural Killer
T
Cells
Authors: Bezbradica Jelena S , Van Kaer Luc , Joyce Sebastian 
Published: October 2007

Abstract

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.
Interaction Networks of Proteins
Authors: Date Shailesh V , Chen Guang 
Published: October 2007

AbstractProteins 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

Abstract
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.
Gene Synthesis for Protein Production
Authors: Stewart Lance 
Published: October 2007

Abstract
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

Abstract
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

AbstractDisordered 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

Abstract
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

Abstract
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

Abstract
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

AbstractBardet‐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.
TRP
Channels
Authors: Liman Emily R 
Published: October 2007

Abstract
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

Abstract
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.