bluuebunny/crossref_metadata_2025 huggingface dataset:
From cell membrane to nucleotides: The phosphate regulon in Escherichia coli
Authors: Torriani Annamaria
Published: February 2005

Most of the essential cellular components, like nucleic acids, lipids and sugars, are phosphorylated. The phosphate equilibrium in Escherichia coli is regulated by the phosphate (Pi) input from the surrounding medium. Some 90 proteins are synthesized at an increased rate during Pi starvation and the global control of the cellular metabolism requires cross‐talk with other regulatory mechanisms. Since the Pi concentration is normally low in E. coli's natural habitat, these cells have devised a mechanism for synthesis of about 15 proteins to accomplish two specific functions: transport of Pi and its intracellular regulation. The synthesis of these proteins is controlled by two genes (the phoB‐phoR operon), involving both negative and positive functions. PhoR protein is a histidine protein kinase, induced in Pi starvation and is a transmembrane protein. It phosphorylates the regulator protein PhoB which is also Pi starvation‐induced. The PhoB phosphorylated form binds specifically to a DNA sequence of 18 nucleotides (the pho Box), which is part of the promoters of the Pho genes. The genes controlled by phoB constitute the Pho regulon.

The repression of phoA (the gene encoding alkaline phosphatase) by high Pi concentrations in the medium requires the presence of an intact Pst operon (pstS, pstC, pstA, pstB and phoU) and phoR. The products of pstA and pstC are membrane bound, whereas the product of pstS is periplasmic and PstB and PhoU proteins are cytoplasmic. The function of the PhoU protein may be regulated by cofactor nucleotides and may be involved in signaling the activation of the regulon via PhoR.
Transvection and long‐distance gene regulation
Authors: Pirrotta Vincenzo
Published: February 2005

Numerous genes contain regulatory elements located many tens of kilobases away from the promoter they control. Specific mechanisms must be required to ensure that such distant elements can find and interact with their proper targets but not with extraneous genes. This review explores the connections between transvection phenomena, the activation of domains of homeotic gene expression, position effect variegation and silencers. These various examples of long‐distance effects suggest that, in all cases, related forms of chromatin packaging may be involved.
Cholinesterases preceding major tracts in vertebrate neurogenesis
Authors: Layer Paul G.
Published: February 2005

The role of acetylcholinesterase (AChE) in neuro‐transmission in well known. But long before synapses are formed in vertebrates, AChE is expressed in young postmitotic neuroblasts that are about to extend the first long tracts. AChE histochemistry can thus be used to map primary steps of brain differentiation. Preceding and possibly inducing AChE in avian brains, the closely related butyrylcholinesterase (BChE) spatially fore‐shadows AChE‐positive cell areas and the course of their axons. In particular, before spinal motor axons grow, their corresponding rostral sclerotomes and myotomes express BChE, and both their neuronal source and myotomal target cells express AChE. Since axon growth has been found inhibited by acetylcholine, it is postulated that both cholinesterases can attract neurite growth cones by neutralizing the inhibitor. Thus, the early expression of both cholinesterases that is at least partially independent from classical cholinergic synaptogenesis, sheds new light on the developmental and medical significance of these enzymes.
Two‐way signalling through the Lfa‐1 lymphocyte adhesion receptor
Authors: Dustin Michael L.
Published: February 2005

T lymphocyte recognition of foreign antigens and migration throughout the body require the regulated adhesion of lymphocytes to diverse types of cells and to the extracellular matrix. The lymphocyte adhesion ‘receptor’ LFA‐1, a member of the integrin family, interacts with ICAM‐1 and other counter‐receptors to mediate adhesion. The LFA‐1/ICAM‐1 interaction is regulated by signals transmitted from the cytoplasm to the extracellular space. Conversely, LFA‐1 transmits signals from the extracellular space to the cytoplasm to regulate T lymphocyte activation. The observed properties of LFA‐1 and related adhesion ‘receptors’ are incorporated into a general model for adhesion during immune surveillance and recognition of foreign antigens.
Targeting of proteins into the eukaryotic secretory pathway: Signal peptide structure/function relationships
Authors: Nothwehr Steven F. , Gordon Jeffrey I.
Published: February 2005

Much progress has been made in recent years regarding the mechanisms of targeting of secretory proteins to, and across, the endoplasmic reticulum (ER) membrane. Many of the cellular components involved in mediating translocation across this bilayer have been identified and characterized. Polypeptide domains of secretory proteins, termed signal peptides, have been shown to be necessary, and in most cases sufficient, for entry of preproteins into the lumen of the ER. These NH2‐ terminal segments appear to serve multiple roles in targeting and translocation. The structural features which mediate their multiple functions are currently the subject of intense study.
Problems And Paradigms: Golgi complex beads and the transition region
Authors: Locke Michael
Published: February 2005

Secretory proteins and membranes move in transfer vesicles from the rough endoplasmic reticulum through the transitional region to the outer saccule of the Golgi complex. In both arthropod and vertebrate cells, the GC beads are a characteristic structural component of the transitional region. The beads are particles about half the size of ribosomes arranged equidistantly from one another and the smooth face of the ER. In an active GC, the beads are in rings through which the ER membrane emerges to form transfer vesicles. The beads may be part of the energy‐dependent step required for the movement of proteins along the secretory pathway, since they lose their ring arrangement under conditions that lower cellular ATP. The beads are organizers for Golgi complexes in the sense that they are the first recognizable components of new GCs as they arise from ER. Arthropod GC beads, but not those of vertebrates, can be visualized through their reaction with bismuth in vivo and in fixed tissue. Useful paradigms for traffic between the ER and the GC need to combine structural and biochemical information. Insect fat body, with its readily resolvable bismuth‐stained beads and easily fractionated cell components may have particular value for this problem.
Baker's yeast, the new work horse in protein synthesis studies: Analyzing eukaryotic translation initiation
Authors: Linder Patrick , Prat Annik
Published: February 2005

The possibility of combining powerful genetic methods with biochemical analysis has made baker's yeast Saccharomyces cerevisiae the organism of choice to study the complex process of translation initiation in eukaryotes. Several new initiation factor genes and interactions between components of the translational machinery that were not predicted by current models have been revealed by genetic analysis of extragenic suppressors of translational initiation mutants. In addition, a yeast cell‐free translation system has been developed that allows in vivo phenotypes to be correlated with in vitro biochemical activities. We summarize here the current view of yeast translational initiation obtained by these approaches.
DNA polymerase epsilon: The latest member in the family of mammalian DNA polymerases
Authors: Syväoja Juhani E.
Published: February 2005

DNA polymerase epsilon is a mammalian polymerase that has a tightly associated 3′→5′ exonuclease activity. Because of this readily detectable exonuclease activity, the enzyme has been regarded as a form of DNA polymerase delta, an enzyme which, together with DNA polymerase alpha, is in all probability required for the replication of chromosomal DNA. Recently, it was discovered that DNA polymerase epsilon is both catalytically and structurally distinct from DNA polymerase delta. The most striking difference between the two DNA polymerases is that processive DNA synthesis by DNA polymerase delta is dependent on proliferating cell nuclear antigen (PCNA), a replication factor, while DNA polymerase epsilon is inherently processive. DNA polymerase epsilon is required at least for the repair synthesis of UV‐damaged DNA. DNA polymerases are highly conserved in eukaryotic cells. Mammalian DNA polymerases alpha, delta and epsilon are counterparts of yeast DNA polymerases I, III and II, respectively. Like DNA polymerases I and III, DNA polymerase II is also essential for the viability of cells, which suggests that DNA polymerase II (and epsilon) may play a role in DNA replication.
Integrins and tumor invasion
Authors: Dedhar Shoukat
Published: February 2005

Cell–extracellular matrix interactions are important in the process of tumor cell invasion and metastasis. In particular, the interactions of tumor cells with basement membranes of tissue epithelial, as well as vascular endothelial, cells are likely to represent key steps in the metastatic process. The interactions between cells and the connective tissue matrix are mediated by a large family of cell surface receptors, the integrins, which represent multiple receptors the integrins, which represent multiple receptors for extracellular matrix and basement membrane components. Here, I review recent progress in elucidating the roles of integrins in tumor cell invasion. Altered expression of this large family of receptors on invasive tumor cells, as compared with non‐invasive cells, may represent a fundamental step in the progressive expression of the invasive phenotype.
Growth cone inhibition – an important mechanism in neural development?
Authors: Davis Jamie A. , Cook Geoffrey M. W.
Published: February 2005

Since the growth cone was first described a century ago by Cajal, considerable effort has been directed towards understanding the mechanisms responsible for its guidance. Traditionally, attention has focussed on the role of adhesive molecules in determining neural development. Recently, it has become apparent that inhibitory interactions may play a crucial part in axonal navigation. A common feature of inhibition seen in three model systems (peripheral nerve segmentation, retinotectal mapping and CNS/PNS segregation) is a collapse of the motile structures of the growth cone. It is increasingly clear that the identification of molecular mechanisms of inhibition, as well as those of adhesion, will be of fundamental importance to understanding neural development.
Swimming against the tide: Chemotaxis in Agrobacterium
Authors: Shaw Charles H.
Published: February 2005

Chemotaxis in bacteria is an excellent model for signal transduction processes. In Agrobacterium tumefaciens, the causative agent of crown gall tumour on wounded plants, it is a vital part of the organism's biology. A chromosomally‐determined chemotaxis system causes the bacterium to be attracted into the rhizosphere by chemoattractants in plant exudates. By interfacing with this system, the multifunctional products of two Tiplasmid encoded genes, virA and virG, allow the sensing of specific wound phenolics such as acetosyringone. This attracts Ti‐plasmid harbouring A. tumefaciens to wound sites, where the higher acetosyringone concentrations lead to virA and virG‐mediated induction of the vir‐genes. The products of the induced genes, act in concert to effect transfer of the T‐DNA to the plant cell.
Assembly and intracellular transport of snRNP particles
Authors: Andersen Janet , Zieva Gary W.
Published: February 2005

The assembly of the major small nuclear ribonucleoprotein (snRNP)d̊ particles begins in the cytoplasm where large pools of common core proteins are preassembled in several RNA‐free intermediate particles. Newly synthesized snRNAs transiently enter the cytoplasm and complex with core particles to form pre‐snRNP particles. Subsequently, the cap structure at the 5/end of the snRNA is hypermethylated. The Resulting trimethylguanosine (TMG) cap is an integral part of the nuclear localization signal for snRNP particles and the pre‐snRNP particles are rapidly transported into the nucleus. SnRNP particles mature when snRNA‐specific proteins complex with the particles, in some cases, just before or during nuclear transport, but in most instances after the particles are in the nucleus. In addition, U6 snRNA hybridizes with U4 snRNA to form a U4/U6 snRNP in the nucleus. The transport signals are retained on the snRNP particles and proteins since existing particles and proteins enter the reformed nucleus after mitosis.
The neuronal growth cone as a specialized transduction system
Authors: Strittmatter Stephen M. , Fishman Mark C.
Published: February 2005

Neuronal growth and remodelling are guided by both intracellular gene programs and extracellular stimuli. The growth cone is one site where the effects of these extrinsic and intrinsic factors converge upon the mechanical determinants of cell shape. We review the growth cone as a transduction device, converting extracellular signals into mechanical forces. A variety of soluble, extracellular matrix and membrane bound molecules control growth cone behavior. In addition, GAP‐43 is discussed as a possible component of the Intraneuronal gene program which modulates growth cone activity. The GTP‐binding protein, Go, is a major growth cone membrane protein that may transduce signals not only from outside the cell, but from within as well. This may provide a molecular site in the growth cone for the coordination of a genetic growth program with environmental signals.
Development of the mammalian gonad: The fate of the supporting cell lineage
Authors: McLaren Anne
Published: February 2005

Sex determination in mammals is mediated via the supporting cell lineage in the fetal gonad. In the very early stages of gonadal development, the fate of the supporting cell population is critically dependent on the expression of the male‐determining gene on the Y chromosome. If this gene is absent or fails to be expressed, or is expressed too late or in too small a number of supporting cells, all supporting cells (XX or XY) differentiate as pre‐follicle cells and development proceeds along the female pathway. Supporting cells in which the male‐determining gene is expressed in a timely manner differentiate as pre‐Sertoli cells; given sufficient such cells, testis cords form and development proceeds in a male direction. If XX supporting cells are also present, a few may be recruited into the pre‐Sertoli population and participate in testis cord formation. The subsequent fate of pre‐follicle cells depends critically on interaction with the germ cell population in the developing gonad: absence of germ cells may lead to partial masculinization of the gonad, and/or to disappearance of the supporting cell component.
Gap genes and gradients – The logic behind the gaps
Authors: Hülskamp Martin , Tautz Diathard
Published: February 2005

Gap genes stand at the top of the zygotic segmentation hierarchy in Drosophila. Their expression domains are set up by a combination of maternal regulatory signals and interactions among themselves. In addition, these regulatory pathways are partially redundantly specified by the maternal and zygotic genomes, or by multiple zygotic gene products. The gap genes code for transcription factors which exert their function by foming short‐range morphogenetic gradients; differential concentrations of these transcription factors can either act as activators or as repressors for the expression domains of neighbouring genes. It is possible to view the gap genes as a system of genes that subdivides the embryo by forming an activation‐repression cascade proceeding from anterior towards posterior.
Catalytic function of DNA topoisomerase II
Authors: Osheroff Neil , Zechiedrich E. Lynn , Gale Kevin C.
Published: February 2005

Although the genetic code is defined by a linear array of nucleotides, it is the three‐dimensional structure of the double helix that regulates most of its cellular functions. Over the past two decades, it has become increasingly clear that aspects of this three‐dimensionality which reflect topological relationships within the double helix (i.e., superhelical twisting, knotting, or tangling) influence virtually every facet of nucleic acid physiology. In vivo, DNA topology is modulated by ubiquitous enzymes known as topoisomerases. The type II enzyme essential to the eukaryotic cell and is required for unlinking daughter chromosomes and maintaining chromosome structure. Moreover, topoisomerase II also has been identified as the primary cellular target for several widely used antineoplastic drugs. Before the physiological functions of topoisomerase II can be effectively dissected or its drug interactions fully exploited, it is imperative to understand the mechanism by which this important enzyme arries out its catalytic cycle.
Mapping replication origins in yeast chromosomes
Authors: Brewer Bonita J. , Fangman Walton L.
Published: February 2005

The replicon hypothesis, first proposed in 1963 by Jacob and Brenner(1), states that DNA replication is controlled at sites called origins. Replication origins have been well studied in prokaryotes. However, the study of eukaryotic chromosomal origins has lagged behind, because until recently there has been no method for reliably determining the identity and location of origins from eukaryotic chromosomes. Here, we review a technique we developed with the yeast Saccharomyces cerevisiae that allows both the mapping of replication origins and an assessment of their activity. Two‐dimensional agarose gel electrophoresis and Southern hybridization with total genomic DNA are used to determine whether a particular restriction fragment acquires the branched structure diagnostic of replication initiation. The technique has been used to localize origins in yeast chromosomes and assess their initiation efficiency. In some cases, origin activation is dependent upon the surrounding context. The technique is also being applied to a variety of eukaryotic organisms.
Calcium channels and signal transduction in plant cells
Authors: Johannes Eva , Brosnan James M. , Sanders Dale
Published: February 2005

An increasing number of studies indicate that changes in cytosolic free Ca2+ ([Ca2+]c) mediate specific types of signal transduction in plant cells. Modulation of [Ca2+]c is likely to be achieved through changes in the activity of Ca2+ channels, which catalyse passive influx of Ca2+ to the cytosol from extracellular and intracellular compartments. Voltage‐sensitive Ca2+ channels have been detected in the plasma membranes of algae, where they control membrane electrical properties and cell turgor. These channels are sensitive to 1,4‐dihydropyridines, which in animal cells specifically affect one class of voltage‐regulated plasma membrane Ca2+ channel. Ca2+‐permeable channels with different pharmacological properties have been found in the plasma membrane of higher plants. Recent evidence suggests the existence of two discrete classes of Ca2+ channel co‐resident in the vacuolar membrane (tonoplast) of higher plants. The first is gated by inositol 1,4,5‐trisphosphate, and bears a number of similarities to its animal counterpart which is located in the endoplasmic reticulum (ER). The second tonoplast Ca2+ channel is voltage‐operated. However, the specific roles of these tonoplast channels in signal transduction have yet to be elucidated.
Multidrug resistant transgenic mice as a novel pharmacologic tool
Authors: Mickisch Gerald H. , Pastan Ira , Gottesman Michael M.
Published: February 2005

Multidrug resistance resulting from expression of an energy‐dependent drug efflux pump encoded by the human MDR1 gene is a major impediment to effective cancer therapy. Pharmacologic intervention aimed at inhibiting this multidrug transporter should improve existing chemotherapy of human cancer, but drug development has been delayed by the difficulty and expense of developing valid animal models. Using recombinant DNA technology, a transgenic mouse has been engineered whose bone marrow is protected from the toxic effects of chemotherapy by expression of the MDR1 gene. This animal system allows the rapid screening of drugs which inhibit the multidrug transporter and heralds a new era of using transgenic animals for pharmacologic screening.
The role of cell death genes during development
Authors: Schwartz Lawrence M.
Published: February 2005

During development, large numbers of cells die by a process known as programmed cell death. This loss of cells plays a number of important roles, including the sculpting of the body form and the removal of vestigial tissues. Data obtained from a variety of organisms has suggested that a cell's ‘decision’ to die is a differentiative event, requiring the activation of specific sets of genes. Several putative ‘cell death’ genes have recently been cloned, and one has been identified as the product of the polyubiquitin gene. Accumulation of ubiquitin has been observed not only during programmed cell death, but also in several neurodegenerative disorders, including Alzheimer's Disease.
New enzymes for old: Redesigning the coenzyme and substrate specificities of glutathione reductase
Authors: Perham Richard N. , Scrutton Nigel S. , Berry Alan
Published: February 2005

A set of amino acid side chains that confer specificity for the coenzyme NADPH and the substrate glutathione in the flavoprotein disulphide oxidoreductase, glutathione reductase, has been identified. Systematic replacement of these amino acid residues in the coenzyme‐binding site switches the specificity of the enzyme from its natural strong preference for NADPH to a marked preference For NADH. The amino acids replaced all lie in a structural motif within the dinucleotide‐binding domain of the protein. Since this domain is a feature common to most dehydrogenases (reductases) that use nicotinamide coenzymes, it may be that the coenzyme specificities of all such enzymes can be manipulated in this way. Similarly, amino acid residues involved in the selective recognition of trypanothione by trypanothione reductase, an enzyme related to glutathione reductase and exclusive to trypanosomatids, were identified. Suitable mutation of the corresponding residues in E. coli glutathione reductase switched its substrate specificity towards trypanothione. A better understanding of the substrate specificity of these enzymes could open up a route to the chemotherapy of trypanosomal infections.
Transfer of yeast artificial chromosomes from yeast to mammalian cells
Authors: Huxley Clare , Gnirke Andreas
Published: February 2005

Human DNA can be cloned as yeast artificial chromosomes (YACs), each of which contains several hundred kilobases of human DNA. This DNA can be manipulated in the yeast host using homologous recombination and yeast selectable markers. In relatively few steps it is possible to make virtually any change in the cloned human DNA from single base pair changes to deletions and insertions. In order to study the function of the cloned DNA and the effects of the changes made in the yeast, the human DNA must be transferred back into mammalian cells. Recent experiments indicate that large genes can be transferred from the yeast host to mammalian cells in tissue culture and that the genes are transferred intact and are expressed. Using the same methods it may soon be possible to transfer YAC DNA into the mouse germ line so that the expression and function of genes cloned in YACs can be studied in developing and adult mammalian animals.
Lethal chromosomal deletions in the mouse, a model system for the study of development and regulation of postnatal gene expression
Authors: Gluecksohn‐Waelsch Salome , Defranco Donald
Published: February 2005

Mechanisms involved in the regulation of development and its genetic control are receiving ever‐increasing attention in studies of mammalian developmental genetics. The potential success of such studies is strongly enhanced by the availability of suitable systems of analysis. Such a system was identified in a series of radiation‐induced chromosomal deletions at and around the albino (c) locus of the mouse associated with cell type‐specific effects on liver differentiation. Their detailed study has aided the analysis of possible machanisms of cell type‐specific gene expression. As summarized in this review, the experimental results strongly suggest that specific trans‐acting developmental regulatory genes are concerned with the differentiation of hormone‐inducible expression of a cluster of hepatocyte specific structural genes mapping in different parts of the genome.
Mitosis‐specific phosphorylation of caldesmon: Possible molecular mechanism of cell rounding during mitosis
Authors: Yamashiro Shigeko , Matsumura Fumio
Published: February 2005

One of the profound changes in cellular morphology during mitosis is a massive alteration in the organization of microfilament cytoskeleton. It has been recently discovered that nonmuscle caldesmon, an actin and calmodulin binding microfilament‐associated protein of relative molecular mass Mr = 83000, is dissociated from microfilaments during mitosis, apparently as a consequence of mitosis‐specific phosphorylation. cdc2 kinase, which is a catalytic subunit of MPF (maturation or mitosis promoting factor), is found to be responsible for the mitosis‐specific phosphorylation of caldesmon. Because caldesmon is implicated in the regulation of actin myosin interactions and/or microfilament organization, these results suggest that cdc2 kinase directly affects microfilament re‐organization during mitosis.
Transduction of plant signal molecules by the Rhizobium NodD proteins
Authors: Györgypal Zoltan , Kiss György Botond , Kondorosi Adam
Published: February 2005

The regulatory NodD proteins of Rhizobium bacteria mediate the activation of a gene set responsible for symbiotic nodule formation by plant signal molecules. Here we discuss the signal recognition and gene activation properties of NodD and present a model summarizing the current knowledge on NodD action.
Gene targeting and gene trap screens using embryonic stem cells: New approaches to mammalian development
Authors: Joyner Alexandra L.
Published: February 2005

Mouse embryonic stem cell lines offer an attractive route for introducing rare genetic alternations into the gene pool since the cells can be pre‐screened in culture and the mutations then transmitted into the germline through chimera production. Two applications of this technique seem ideally suited for a genetic analysis of development are enhancer and gene trap screens for loci expressed during gastrulation and production of targeted mutations using homologous recombination. These approaches should greatly increase the number of mouse developmental mutants available and help to elucidate the genetic hierarchy controlling embryogenesis.
The kinetics of mammalian gene expression
Authors: Hargrove James L. , Hulsey Martin G. , Beale Elmus G.
Published: February 2005

When rates of transcription from specific genes change, delays of variable length intervene before the corresponding mRNAs and proteins attain new levels. For most mammalian genes, the time required to complete transcription, processing, and transport of mRNA is much shorter than the period needed to achieve a new, steady‐state level of protein. Studies of inducible genes have shown that the period required to attain new levels of individual mRNAs and proteins is related to their unique half‐lives. The basis for this is a physical principle that predicts rates of accumulation of particles in compartmental systems. The minimum period required to achieve a new level is directly proportional to product half‐lives because rates of decay control the ratio between the rate of synthesis and the concentration of gene products at steady state. This kinetic model suggests that sensitivity of gene products to degradation by ribonucleases and proteinases is an important determinant of the time scale of gene expression.
Reversible histone modification and the chromosome cell cycle
Authors: Morton Bradbury E.
Published: February 2005

During the eukaryotic cell cycle, chromosomes undergo large structural transitions and spatial rearrangements that are associated with the major cell functions of genome replication, transcription and chromosome condensation to metaphase chromosomes. Eukaryotic cells have evolved cell cycle dependent processes that modulate histone:DNA interactions in chromosomes. These are; (i) acetylations of lysines; (ii) phosphorylations of serines and threonines and (iii) ubiquitinations of lysines. All of these reversible modifications are contained in the well‐defined very basic N‐ and C‐ terminal domains of histones. Acetylations and phosphorylations markedly affect the charge densities of these domains whereas ubiquitination adds a bulky globular protein, ubiquitin, to lysines in the C‐terminal tails of H2A and H2B. Histone acetylations are strictly associated with genome replication and transcription; histone H1 and H3 phosphorylations correlate with the process of chromosome condensation. The subunits of histone H1 kinase have now been shown to be cyclins and the p34CDC2 kinase product of the cell cycle control gene CDC2. It is probable that all of the processes that control chromosome structure:function relationships are also involved in the control of the cell cycle.
Methylation, mutation and cancer
Authors: Jones Peter A. , Rideout William M. , Shen Jiang‐Cheng , Spruck Charles H. , Tsai Yvonne C.
Published: February 2005

The fifth base in human DNA, 5‐methylcytosine, is inherently mutagenic. This has led to marked changes in the distribution of the CpG methyl acceptor site and an 80% depletion in its frequency of occurrence in vertebrate DNA. The coding regions of many genes contain CpGs which are methylated in sperm and serve as hot spots for mutation in human genetic diseases. Fully 30–40% of all human germline point mutations are thought to be methylation induced even though the CpG dinucleotide is under‐represented and efficient cellular repair systems exist. Importantly, tumor suppressor genes such as p53 also contain methylated CpGs and these serve as hot spots for mutations in some, but not all, human cancers. Comparison of the spectrum of mutations present in this gene in different human cancers allows for predictions to be made on the molecular mechanisms of tumorigenesis.
The rel family of proteins
Authors: Rushlow Chris , Warrior Rahul
Published: February 2005

The rel family of proteins can be defined as a group of proteins that share sequence homology over a 300 amino acid region termed the rel domain. The rel family comprises important regulatory proteins from a wide variety of species and includes the Drosophila morphogen dorsal, the mammalian transcription factor NF‐kB, the avian oncogene v‐rel, and the cellular proto‐oncogene c‐rel. Over the last two years it has become apparent that these proteins function as DNA‐binding transcription factors, and that their activity is regulated at the level of subcellular localization.
Accessory protein function in the DNA polymerase III holoenzyme from E. coli
Authors: O'Donnell Mike
Published: February 2005

DNA polymerases which duplicate cellular chromosomes are multiprotein complexes. The individual functions of the many proteins required to duplicate a chromosome are not fully understood. The multiprotein complex which duplicates the Escherichia coli chromosome, DNA polymerase III holoenzyme (holoenzyme), contains a DNA polymerase subunit and nine accessory proteins. This report summarizes our current understanding of the individual functions of the accessory proteins within the holoenzyme, lending insight into why a chromosomal replicase needs such a complex structure.
Transgenic animal studies on the evolution of genetic regulatory circuitries
Authors: Cavener Douglas R.
Published: February 2005

The ability to transfer genes from one species to another provides a powerful method to study genetic regulatory differences between species in a homogeneous genetic background. A survey of several transgenic animal experiments indicates that the vast majority of regulatory differences observed between species are due to differences in the cis‐acting elements associated with the genes under study. A corollary is that in almost all cases the host species provides the necessary regulatory proteins for expression of the transgenes in specific tissues in which the endogenous homolog is not expressed. Although the details of the cis‐acting differences are unknown for most cases, it appears that these differences may consist of the acquisition or loss of unique elements or subtle variation of conserved elements. It is unknown whether much of this variation is directly related to adaptive evolution. The identification of the promoter enhancer elements responsible for these differences is an important first step in examining the functional significance of this variation.
Cancer predisposition in bloom's syndrome
Authors: Sullivan Neil F. , Willis Anne E.
Published: February 2005

This article focusses upon defining those factors which may contribute to the pathogenesis of cancer. The molecular basis of tumour etiology is discussed with reference to cancer predisposing syndromes, and in particular to the human inherited disease, Bloom's sysdrome. In Bloom's syndrome, patients are predisposed to a wide variety of malignant disease. We propose a model in which overexpression of the ubiquitous c‐myc proto‐oncogene contributes to this process.
Problems and paradigms: Induction mechanism of a single gene molecule: Stochastic or deterministic?
Authors: Ko Minoru S. H.
Published: February 2005

A new field of gene expression regulation research is emerging that has previously been overlooked. This new area is concerned with distinguishing the expression of a single gene from the averaged expression of many gene copies within the cell population. This paper reviews research focused on individual genes in inducible gene expression systems. The main experimental strategy is to measure the gene expression level of a single cell containing a single reporter gene molecule. In contrast to the commonly held belief, gene induction is found to be stochastic under certain conditions. The possible mechanisms and implications are discussed.
Genes and genomes: Carrier detection of deletions in female relatives of X‐linked disorders by non‐isotopic in situ hybridisation
Authors: Adinolfi M. , Stone S. , Moralli D.
Published: February 2005

Recent studies suggest that a non‐isotopic in situ hybridisation (NISH) approach can be successfully employed to investigate the carrier status of female relatives in families of selected patients with Duchenne muscular dystrophy (DMD) or Hunter syndrome, whose diseases are due to a specific X chromosome deletion.

Whilst the majority of metaphase spreads from normal females show specific hybridisation signals on both X chromosomes when tested with either dystrophin or Hunter gene‐derived probes, only one X chromosome in each metaphase spread will show the relevant hybridisation complex in female carriers of deletions involving the dystrophin or Hunter gene.

Thus, the NISH method can be a valuable diagnostic tool for the detection of the carrier status of female relatives of patients with X chromosome deletions.
Position effect variegation and chromatin proteins
Authors: Reute Gunter , Spierer Pierre
Published: February 2005

Variegated phenotypes often result from chromosomal rearrangements that place euchromatic genes next to heterochromatin. In such rearrangements, the condensed structure of heterochromatin can spread into euchromatic regions, which then assume the morphology of heterochromatin and become transcriptionally inactive. In position‐effect variegation (PEV) therefore, gene inactivation results from a change in chromatin structure. PEV has been intensively investigated in the fruitfly Drosophila, where the phenomenon allows a genetic dissection of chromatin components. Consequently, many genes have been identified which, when mutated, act as dominant modifiers (suppressors or enhancers) of PEV. Data available already demonstrate that genetic, molecular and developmental analysis of these genes provides an avenue to the identification of regulatory and structural chromatin components, and hence to fundamental aspects of chromosome structure and function.
Mucins: Structure, function, and associations with malignancy
Authors: Devine Peter L. , McKenzie Ian F. C.
Published: February 2005

Mucins are a family of high molecular weight, highly glycosylated glycoproteins found in the apical cell membrane of human epithelial cells from the mammary gland, salivary gland, digestive tract, respiratory tract, kidney, bladder, prostate, uterus and rete testis. Increased synthesis of the core protein and alterations in the carbohydrates attached to these glycoproteins are believed to play important roles in the function and proliferation of tumour cells. Aberrant glycosylation leads not only to the production of novel carbohydrate structures, but also to the exposure of the core peptide. These novel epitopes may be candidates for diagnosis or therapy, by using either synthetic mucin fragments as vaccines, or monoclonal antibody‐based reagents which detect these structures.
Genes and genomes: Reverse genetics of caenorhabditis elegans
Authors: Plasterk Ronald H. A.
Published: February 2005

It is somewhat ironic that animals that are the prime choice for detailed genetic analysis, such as the fruit fly and the nematode, have thus far been largely refractory to reverse genetic analysis. Their detailed genetic map, and small genome size have made them subjects of ambitious genome analysis projects, but there is still no strategy to introduce desired changes into their genomes by homologous recombination. Some alternative approaches have recently become available; this review describes possibilities and unsolved problems for reverse genetics in the nematode Caenorhabditis elegans. The transposon Tc1 could prove to be very useful for the isolation of knock out mutants, and possibly also for introduction of more subtle alterations.
Challenges: Cell transplantation and gene therapy in muscular dystrophy
Authors: Morgan Jennifer E. , Partridge Terence A.
Published: February 2005

Duchenne's muscular dystrophy (DMD), which affects 1/3500 live male births, involves a progressive degeneration of skeletal and cardiac muscle, leading to early death. The protein dystrophin is lacking in DMD and present, but defective, in the allelic, less severe, Becker muscular dystrophy and is also missing in the mdx mouse. Experiments on the mdx mouse have suggested two possible therapies for these myopathies. Implantation of normal muscle precursor cells (mpc) into mdx skeletal muscle leads to the conversion of dystrophin‐negative fibres to ‐positive, with consequent improvement in muscle histology. Direct injectidn of dystrophin cDNA into skeletal or cardiac muscle also gives rise to dystrophin‐positive fibres. Although both appear promising, there are a number of questions to be answered and refinements to be made before either technique could be considered possible as treatments for myopathies in man.
Recombinant neuromuscular synapses
Authors: Phillips William D. , Merlie John P.
Published: February 2005

The developing neuromuscular junction has provided an important paradigm for studying synapse formation. An outstanding feature of neuromuscular differentiation is the aggregation of acetylcholine receptors (AChRs) at high density in the postsynaptic membrane. While AChR aggregation is generally believed to be induced by the nerve, the mechanisms underlying aggregation remain to be clarified. A 43‐kD protein (43k) normally associated with the cytoplasmic aspect of AChR clusters has long been suspected of immobilizing AChRs by linking them to the cytoskeleton. In recent studies, the AChR clustering activity of 43k has, at last, been demonstrated by expressing recombinant AChR and 43k in non‐muscle cells. Mutagenesis of 43k has revealed distinct domains within the primary structure which may be responsible for plasma membrane targeting and AChR binding. Other lines of study have provided clues as to how nerve‐derived (extracellular) AChR‐cluster inducing factors such as agrin might activate 43k‐driven postsynaptic membrane specialization.
The genetic control of tissue polarity in Drosophila
Authors: Adler Paul N.
Published: February 2005

The cuticular surface of Drosophila is decorated by parallel arrays of polarized structures such as hairs and sensory bristles; for example, on the wing each cell produces a distally pointing hair. These patterns are termed [tissue polarity]. Several genes are known whose activity is essential for the development of normal tissue polarity. Mutations in these genes alter the orientation of the hair or bristle with respect to neighboring cells and the body as a whole. The phenotypes of mutations in these genes allows them to be placed in three phenotypic groups. Based on their behavior in genetic mosaics, it has proved possible to determine that individual genes are required either for the generation of an intercellular polarity signal and/or the transduction of that signal to the cytoskeleton.
The molecular and cell biology of anion transport by bacteria
Authors: Maloney Peter C.
Published: February 2005

This article summarizes the study of anion exchange mechanisms in bacteria. Along with defining at least two different families of anion exchange, an examination of such carrier‐mediated antiport reactions has led to techniques that considerably broaden the scope of biochemical methods for examining membrane proteins. Such advances have been exploited to show that anion exchange itself forms the mechanistic base of an entirely new kind of proton pump, one which may shed light on a variety of bacterial events, including methanogenesis. Perhaps most important, the study of exchange provided the final link in a chain of evidence pointing to a structural [rhythm] that seems to characterize membrane carriers. These three issues ‐ a biochemical tool, a new proton pump, and a common structural rhythm ‐ are briefly examined in the context of their origins in the analysis of bacterial anion exchange.
Differentiation and proliferation in mouse embryonal carcinoma cells
Authors: Sleigh Merilyn J.
Published: February 2005

How cell commitment and differentiation are controlled in the early stages of embryogenesis is a problem that has long fascinated developmental biologists. Retinoic acidinduced differentiation of embryonal carcinoma cells in culture provides a model in which these questions can be explored. Recent work has yielded exciting insights into the central series of molecular changes which drives the commitment of these cells to formation of a new phenotype. Interacting with the key molecules in this central pathway is a variety of transcription factors, many of which show changes in availability and/or activity during differentiation. In various combinations, these modulate the activities of genes involved in both cell proliferation and in the production of extracellular matrix and other proteins characteristic of differentiated cells.
RNA editing: Exploring one mode with apolipoprotein B mRNA
Authors: Chan Lawrence
Published: February 2005

RNA editing is a newly described genetic phenomenon. It encompasses widely different molecular mechanisms and events. According to the specific RNA modification, RNA editing can be broadly classified into six major types. Type II RNA editing occurs in plants and mammals; it consists predominantly in cytidine to uridine conversions resulting from deamination/transamination or transglycosylation, although in plants other mechanisms have not been excluded. Apolipoprotein B mRNA editing is the only well‐documented editing phenomenon in mammals. It is an intranuclear event that occurs posttranscriptionally, coincident with splicing and polyadenylation. Recent observations indicate that the tissue‐ and sequence‐specific process is mediated by an enzyme that has separate domains for editing and sequence recognition. The presence of apolipoprotein B mRNA editing activity in tissues that do not produce the protein suggests that other RNAs may be edited and RNA editing may be a genetic phenomenon of general biological importance to the cell.
Steel factor and c‐Kit receptor: From mutants to a growth factor system
Authors: Morrison‐Graham Kathleen , Takahashi Yoshiko
Published: February 2005

Mutations within the Steel and Dominant Spotting loci of mice have led to the recent identification of a growth factor/receptor system required for the normal development of germ cells, pigment cells and hematopoietic cells. Interactions between the products of these genes, Steel factor and c‐Kit respectively, have now been demonstrated to influence various developmental processes, including survival, proliferation, and/or differentiation of cells in a tissue specific manner. In addition, our current understanding of the molecular basis of various Steel and Dominant Spotting alleles coupled with the emerging information on the expression pattern of steel factor and c‐kit transcripts during development, is now beginning to explain the pleiotropic affects of these mutations.
In pursuit of the functions of the Wnt family of developmental regulators: Insights from Xenopus laevis
Authors: Moon R. T.
Published: February 2005

Wnts are a recently described family of secreted glycoproteins related to the Drosophila segment polarity gene, wingless, and to the proto‐oncogene, int‐1. Wnts are thought to function as developmental modulators, with signalling distances of only a few cell diameters. In Xenopus, at least six Wnts, including Xwnts‐1, ‐3A, and ‐4, are expressed initially in the developing central nervous system, with some regions expressing multiple Xwnts. Xwnt‐8 is expressed by mid‐blastula stage, in ventral and lateral mesoderm. Xwnt‐5A mRNAs are stored in the egg, and later are expressed throughout the embryo in both ectoderm and mesoderm, but with a pronounced enrichment in the head and tail. Recent studies in Xenopus have pursued the diverse roles of Xwnts in early development, the mechanisms by which Xwnts signal information between cells, and the cell physiological responses to Xwnt signals.
SV40 DNA replication intermediates: Analysis of drugs which target mammalian DNA replication
Authors: Snapka Robert M. , Permana Paskasari A.
Published: February 2005

The simian virus 40 chromosome, a model for the mammalian replicon, is a uniquely powerful system for the study of drugs and treatments which target enzymes of the mammalian replication apparatus. High resolution gel electrophoretic analysis of normal and aberrant viral replication intermediates can be used effectively to understand the molecular events of replication failure. These events include breakage of replication forks, aberrant topoisomerase action, failure to separate daughter chromosomes, protein‐DNA crosslinking, single and double strand DNA breakage, alterations in topology and inactivation of replication intermediates. The SV40 replication system can also be used to study the recombinational events which often follow drug‐induced replication failure.