bluuebunny/crossref_metadata_2025_split huggingface dataset:
The FEN‐1 family of structure‐specific nucleases in eukaryotic dna replication, recombination and repair
Authors: Lieber Michael R. 
Published: February 2005

AbstractUnlike the most well‐characterized prokaryotic polymerase, E. Coli DNA pol I, none of the eukaryotic polymerases have their own 5′ to 3′ exonuclease domain for nick translation and Okazaki fragment processing. In eukaryotes, FEN‐1 is an endo‐and exonuclease that carries out this function independently of the polymerase molecules. Only seven nucleases have been cloned from multicellular eukaryotic cells. Among these, FEN‐1 is intriguing because it has complex structural preferences; specifically, it cleaves at branched DNA structures. The cloning of FEN‐1 permitted establishment of the first eukaryotic nuclease family, predicting that S. cerevisiae RAD2 (S. pombe Rad13) and its mammalian homolog, XPG, would have similar structural specficity. The FEN‐1 nuclease family includes several similar enzymes encoded by bacteriophages. The crystal structures of two enzymes in the FEN‐1 nuclease family have been solved and they provide a structural basis for the interesting steric requirements of FEN‐1 substrates. Because of their unique structural specificities, FEN‐1 and its family members have important roles in DNA replication, repair and, potentially, recombination. Recently, FEN‐1 was found to specifically associate with PCNA, explaining some aspects of FEN‐1 function during DNA replication and potentially in DNA repair.
Nip and tuck at the neuromuscular junction: A role for proteases in developmental synapse elimination
Authors: Chang Qiang , Balice‐Gordon Rita J. 
Published: February 2005

AbstractDuring late embryonic and early postnatal development, synaptic connections are extensively modified so that some functional connections are weakened and eliminated from a neural circuit while others are strengthened and maintained. The mechanisms that underlie synapse elimination are beginning to be understood from studies of the neuromuscular junction. A recent paper(1) provides some intriguing insights into the role proteases may play in the developmental disassembly of neuromuscular synapses.
Cyclins, cyclin‐dependent kinases and differentiation
Authors: Gao Chun Y. , Zelenka Peggy S. 
Published: February 2005

AbstractCyclin‐dependent kinases and their regulatory subunits, the cyclins, are known to regulate progression through the cell cycle. Yet these same proteins are often expressed in non‐cycling, differentiated cells. This review surveys the available information about cyclins and cyclin‐dependent kinases in differentiated cells and explores the possibility that these proteins may have important functions that are independent of cell cycle regulation.
The pheromonal role of cuticular hydrocarbons in Drosophila melanogaster
Authors: Ferveur Jean‐François 
Published: February 2005

AbstractPheromones play a curcial role in mate stimulation and discrimination. In the fruit fly Drosophila, the most abundant cuticular hydrocarbons act as sex pheromones during courtship behavior. There are several active molecules and they compose a sex‐ and species‐specific pheromonal bouquet. Different species from the Drosophila melanogaster subgroup have adopted alternative systems of chemical mate recognition. Recent exploration of these interspecific variations, and of intraspecific variations, has led to the characterization of genes and to the mapping of structures that process the production and perception of chemical messages.
Telomeres, not the end of the story
Authors: Gotta Monica , Cockell Moira 
Published: February 2005

AbstractTranscription in organisms as diverse as yeast and mammals is subject to chromosomal position effects that result in heritable and variegated patterns of gene expression. Two recent studies have employed a reversible protein‐DNA crosslinking method to identify the structural components of heterochromatin in budding yeast(1,2). The results show that a complex containing the proteins Rap1, Sir2p, Sir3p and Sir4p is physically associated with nucleosomes at telomere proximal regions, but that the repressive chromatin structure extended by Sir3p overexpression has a different composition.
The evolution of sex determination in isopod crustaceans
Authors: Rigaud Thierry , Juchault Pierre , Mocquard Jean‐Pierre 
Published: February 2005

AbstractSex is determined by non‐Mendelian genetic elements overriding the sex factors carried by the heterochromosomes in some species of terrestrial isopods. A bacterium Wolbachia and a non‐bacterial feminizing factor (f) can both force chromosomal males of Armadillidium vulgare to become phenotypic functional females. The f factor is believed to be a genetic element derived from the Wolbachia genome that becomes inserted into the host nuclear genome. The feminizing factors can be considered to be selfish genetic elements because they bias their host's sex ratio to increase their own transmission. New sex‐determining genes are selected (genes resisting the feminizing effects, or the transmission of feminizing elements) as a consequence of the conflict between these elements and the rest of the host's genome. These events drive the sex‐determining mechanisms to evolve, and may explain the polymorphism of sex factors and the poor differentiation of the heterochromosomes in isopods.
A crystal milestone: The structure of regulated Src
Authors: Superti‐Furga Giulio , Gonfloni Stefania 
Published: February 2005

AbstractThe viral and cellular forms of the Src protein tyrosine kinases take a prototypic role in oncology and signal transduction research, by virtue of being holders of an impressive number of ‘firsts’. Our understanding of the biochemistry and physiology of Src has therefore always been used as a reference for our general advancement in the field of protein phosphorylation and growth control. The recent solution of the crystal structure of two members of the Src family(1,2) represents a milestone in these disciplines and, as usual, provides a general lookout post for developments to come.
Evolution of the multi‐tubulin hypothesis
Authors: Wilson Patricia G. , Borisy Gary G. 
Published: February 2005

AbstractMicrotubules are organized into diverse cellular structures in multicellular organisms. How is such diversity generated? Although highly conserved overall, variable regions within α‐ and β‐tubulins show divergence from other α‐ and β‐tubulins in the same species, but show conservation among different species. Such conservation raises the question of whether diversity in tubulin structure mediates diversity in microtubule organization. Recent studies probing the function of β‐tubulin isotypes in axonemes of insects(1) suggest that tubulin structure, through interactions with extrinsic proteins, can direct the architecture and supramolecular organization of microtubules.
A regulatory switch involving a Clp atpase
Authors: Lazazzera Beth A. , Grossman Alan D. 
Published: February 2005

AbstractClp ATPase chaperone proteins are found in procaryotes and eucaryotes. Recently, ClpC of Bacillus subtilis was found to be part of a regulatory switch(1). ClpC, in combination with the MecA and ComS proteins, regulates the activity of a transcription factor, ComK, which is necessary for the development of genetic competence (the ability to bind and take up exogenous DNA). The complex of ClpC:MecA:ComK renders ComK inactive. Interaction between ComS and the ternary complex releases active ComK. This regulatory switch controls ComK activity in response to cell density signals that affect production of ComS. Regulated interaction between Clp ATPases and target proteins might prove to be widespread.
Dorso‐ventral limb polarity and origin of the ridge: On the fringe of independence?
Authors: Zeller Rolf , Duboule Denis 
Published: February 2005

AbstractMolecular and developmental studies of limb pattern formation have recently gained widespread attention. The fact that vertebrate limbs are amenable to both genetic and embryological manipulations has established this model system as a valuable paradigm for studying vertebrate development. Limb buds are polarised along all three major axes and the establishment of the dorso‐ventral (DV) polarity is dependent upon cues localised in the trunk, where a DV ectodermal interface is produced by confrontation of dorsal and ventral identities. By analogy to Drosophila imaginal disc development, this interface has been proposed to determine and position an ectodermal organising centre, the Apical Ectodermal Ridge (AER), controlling limb bud outgrowth. Recent fate mapping studies(1) and studies of genes regulating DV limb polarity(2‐6), AER formation(7,8) and differentiation(9) suggest, however, that DV patterning and AER induction, though coordinately regulated during limb bud outgrowth, may early on be more dissociated than expected.
A telomerase mutant defective in sister chromatid separation at mitosis
Authors: Nakaseko Yukinobu , Yanagida Mitsuhiro 
Published: February 2005

AbstractThe telomere is a functional domain of the chromosome, located at the extreme ends, and is essential for normal chromosome stability. Chromosomes lacking telomeres are inherited improperly, and mutations in the telomeric repeat sequences are thought to lead to senescence and possibly to cancer. The molecular mechanisms maintaining chromosomes by telomeres, however, have been unclear. Results recently reported by Kirk et al.(1) offer an insight into new telomerase function. They have identified a novel telomerase mutation that blocks sister chromatid separation in mitosis.
The SCL/TAL1 gene: Roles in normal and malignant haematopoiesis
Authors: Robb Lorraine , Begley C. Glenn 
Published: February 2005

AbstractSCL (TAL1/TCL5) is a member of the helix‐loop‐helix family of transcription factors. Originally identified because of its involvement in a tumour‐specific chromosomal translocation, overexpression of the SCL gene is the most common molecular abnormality found in human T cell leukaemia. Transgenic models have now formally demonstrated that overexpression of SCL within the T cell lineage is capable of causing malignant transformation. Gene targeting experiments have revealed that the SCL gene is crucial for the development of primitive haematopoiesis in the mouse and is also required for the generation of all adult haematopoietic lineages. Biochemical studies have indicated some of the proteins which interact with SCL and this has refined the hypotheses concerning the mechanisms by which SCL plays a role in leukaemogenesis and haematopoietic development.
Why are Hox genes clustered?
Authors: Mann Richard S. 
Published: February 2005

AbstractThe evolutionarily conserved genomic organization of the Hox genes has been a puzzle ever since it was discovered that their order along the chromosome is similar to the order of their functional domains along the antero‐posterior axis. Why has this colinearity been maintained throughout evolution? A close look at regulatory sequences from the mouse Hox clusters(1,2) suggests that enhancer sharing between adjacent Hox genes may be one reason. Moreover, characterizing the activity of one of these mouse enhancers in Drosophila(2) illustrates that despite many similarities, not all Hox clusters are built in the same way.
Epithelial stem cells
Authors: Jones Philip H. 
Published: February 2005

AbstractNew molecular markers for epidermal stem cells have enabled their isolation both in vitro and from the epidermis lying between hair follicles. Micro‐dissection experiments have localised a second population of stem cells within hair follicles. Epidermal stem cells have a patterned distribution in vivo. The patterning can be reconstituted in vitro, showing that it is generated by interactions between keratinocytes and that the differentiation of epidermal stem cells is regulated by signals from other keratinocytes. Recent evidence from transgenic mice suggests that stem cell behaviour in the gut may be regulated by similar cell‐cell interactions in vivo. Candidate genes for mediating these interactions are the homologues of Drosophila cell fate patterning genes such as Notch and Wingless and the Cadherin family of cell‐cell adhesion molecules. The roles of stem cells and of mutations of the Patched gene in epithelial carcinogenesis are discussed.
Regulation of gene expression in developing epidermal epithelia
Authors: Byrne Carolyn 
Published: February 2005

AbstractSkin is one of the most thoroughly studied epithelia and can be used as a model for transcriptional control of epithelial differentiation. In particular, the stages of epidermal development and differentiation from a simple epithelium are well characterized. Temporal gene expression during development can be used to assign roles for transcription factors in epidermal differentiation. Approaches to understanding transcriptional regulation in epidermis include extensive promoter analysis and expression studies, in some cases coupled to functional studies. This work has not produced any consensus about the importance of any particular factor or class of factors in epidermal specification. There is, as yet, nothing similar to the myo D family of tissue‐specific and cell‐type determining factors in epidermis. These studies, however, have revealed much about control of the differentiation process in epidermis. Most recently, there has been a suggestion that epithelial transcription can be influenced directly by the status of the adhesion complexes at the cell surface, providing a direct link between one of the distinguishing features of the epithelial state and gene transcription.
Epithelial apoptosis
Authors: Metcalfe Anthony , Streuli Charles 
Published: February 2005

AbstractApoptosis is an essential part of the normal cellular phenotype repertoire. In the absence of appropriate survival factors, apoptosis is activated through specific signalling cassettes. Epithelia form distinctive three‐dimensional cohesive structures that depend on adhesive interactions in order for these tissues to carry out their specialised roles, such as secretion and reproduction. The cellular programme that triggers apoptosis in epithelial cells has not yet been shown to differ from that in other cell types, yet the unique characteristics of epithelia endow them with specific determinants for survival. In particular, cell‐matrix and cell‐cell interactions are required to prevent entry of epithelial cells into apoptosis, and soluble factors that have profound effects on epithelia, such as steroid hormones or hepatocyte growth factor, also influence their survival. The regenerative capacity of certain epithelia is controlled by intrinsic expression of survival genes within stem cell populations, and may regulate the susceptibility of different epithelial tissues to undergo carcinogenesis.
Problems and paradigms: Morphogens and pattern formation
Authors: Neumann Carl , Cohen Stephen 
Published: February 2005

AbstractMorphogen gradient theories have enjoyed considerable popularity since the beginning of this century, but conclusive evidence for a role of morphogens in controlling multicellular development has been elusive. Recently, work on three secreted signalling proteins, Activin in Xenopus, and Wingless and Dpp in Drosophila, has stongly suggested that these proteins function as morphogens. In order to define a factor as a morphogen, it is necessary to show firstly, that it has a direct effect on target cells and secondly, that it affects the development of target cells in a concentration‐dependent manner. With these criteria in mind, the evidence available for a variety of proposed morphogens is discussed. While the evidence is not conclusive in most of the cases considered, there is a strong case in favour of the three proteins mentioned above, which suggests that morphogens are potentially of general importance in controlling the development of multicellular organisms.
Molecular evolution of the vertebrate immune system
Authors: Hughes Austin L. , Yeager Meredith 
Published: February 2005

AbstractAdaptive immunity is unique to the vertebrates, and the molecules involved (including immunoglobulins, T cell receptors and the major histocompatibility complex molecules) seem to have diversified very rapidly early in vertebrate history. Reconstruction of gene phylogenies has yielded insights into the evolutionary origin of a number of molecular systems, including the complement system and the major histocompatibility complex (MHC). These analyses have indicated that the C5 component of complement arose by gene duplication prior to the divergence of C3 and C4, which suggests that the alternative complement pathway was the first to evolve. In the case of the MHC, phylogenetic analysis supports the hypothesis that MHC class II molecules evolved before class I molecules. The fact that the MHC‐linked proteasome components that specifically produce peptides for presentation by class I MHC appear to have originated before the separation of jawed and jawless vertebrates suggests that the MHC itself may have been present at this time. Immmune system gene families have evolved by gene duplication, interlocus recombination and (in some cases) positive Darwinian selection favoring diversity at the amino acid level.
Nuclear calcium and the regulation of the nuclear pore complex
Authors: Perez‐Terzic Carmen , Jaconi Marisa , Clapham David E. 
Published: February 2005

AbstractIn eukaryotic cells the nucleus and its contents are separated from the cytoplasm by the nuclear envelope. Macromolecules, as well as smaller molecules and ions, can cross the nuclear envelope through the nuclear pore complex. Molecules greater than approx. 60 kDa and containing a nuclear localization signal are actively transported across the nuclear membranes, but there has been little evidence for regulatory mechanisms for smaller molecules and ions. Recently, diffusion across the nuclear envelope has been observed to be regulated by nuclear cisternal Ca2+ concentrations. Following depletion of Ca2+ from the nuclear store by inositol 1,4,5‐trisphosphate or Ca2+ chelators, a fluorescent 10 kDa marker molecule was no longer able to enter the nucleus. Distinct conformational states of the nuclear pore complexes depended on the Ca2+ filling state of the nuclear envelope, supporting the assumption that a switch in the conformation of the nuclear pore complex may control the transport of intermediate‐sized molecules across the nuclear envelope. Thus nuclear Ca2+ stores may regulate the conformational state of the nuclear pore complex, and thereby passive diffusion of molecules between the cytosol and the nucleoplasm. The physiological significance of this finding is currently unknown.
Evolution of the spectrin repeat
Authors: Pascual Jaime , Castresana Jose , Saraste Matti 
Published: February 2005

AbstractWe now know that the evolution of multidomain proteins has frequently involved genetic duplication events. These, however, are sometimes difficult to trace because of low sequence similarity between duplicated segments. Spectrin, the major component of the membrane skeleton that provides elasticity to the cell, contains tandemly repeated sequences of 106 amino acid residues. The same repeats are also present in α‐actinin, dystrophin and utrophin. Sequence alignments and phylogenetic trees of these domains allow us to interpret the evolutionary relationship between these proteins, concluding that spectrin evolved from α‐actinin by an elongation process that included two duplications of a block of seven repeats. This analysis shows how a modular protein unit can be used in the evolution of large cytoskeletal structures.
Origin of eukaryotic programmed cell death: A consequence of aerobic metabolism?
Authors: Frade José M. , Michaelidis Theologos M. 
Published: February 2005

AbstractA marked feature of eukaryotic programmed cell death is an early drop in mitochondrial transmembrane potential. This results from the opening of permeability transition pores, which are composed of adenine nucleotide translocators and mitochondrial porins. The latter share striking similarites with bacterial porins, (including down‐regulation of their pore size by purine nucleotides), suggesting a common origin. The porins of some invasive bacteria play a crucial role during their accommodation inside the host cell and this co‐existence resembles the endosymbiotic origin of mitochondria. The above observations suggest that early in eukaryotic evolution, former invaders may have used porin‐type channels to enter their host and to induce its death when the levels of its cytoplasmic purine nucleotides were dropped. The appearance of adenosine nucleotide translocators in the primitive eukaryotes, which permitted usage of the oxidative metabolism of the invaders, provided the basis for the permeability transition phenomena, now linked to the apoptotic process. Bcl‐2‐type molecules, being able to modulate the permeability transition pores by interaction with adenosine nucleotide translocators, may have played an essential role in conferring a means of controlling apoptosis.
Building a plasmodium: Development in the acellular slime mould Physarum polycephalum
Authors: Bailey Juliet 
Published: February 2005

AbstractThe two vegetative cell types of the acellular slime mould Physarum polycephalum ‐ amoebae and plasmodia ‐ differ greatly in cellular organisation and behaviour as a result of differences in gene expression. The development of uninucleate amoebae into multinucleate, syncytial plasmodia is under the control of the mating‐type locus matA, which is a complex, multi‐functional locus. A key period during plasmodium development is the extended cell cycle, which occurs in the developing uninucleate cell. During this long cell cycle, many of the changes in cellular organisation that accompany development into the multinucleate stage are initiated including, for example, alterations in microtubule organisation. Genes have been identified that show cell‐type specific expression in either amoebae or plasmodia and many of these genes alter their pattern of expression during the extended cell cycle. With the introduction of a DNA transformation system for P. polycephalum, it is now possible to investigate the functions of genes in the vegetative cell types and their roles in the cellular reorganisations accompanying development.
Does sex determination start at conception?
Authors: Erickson Robert P. 
Published: February 2005

AbstractRecent molecular studies of mammalian sexual determination have been focused on gene expression in the gonadal ridge at the time of appearance of sexual dimorphism: the critical time defined by the ‘Jost principle’. Three lines of evidence suggest that, instead, sex determination may start shortly after conception: (1) the XY preimplantation embryo usually develops more rapidly than the XX preimplantation embryo (this phenotype has been linked to the Y chromosome and will be termed ‘Growth factor Y’); (2) the gene for testis determination, SRY/Sry, and the closely linked genes ZFY/Zfy and Smcy, are transcribed in the preimplantation embryo; and (3) male and female preimplantation embryos are antigenically distinguishable, indicating sex differences in gene expression. The data to support these assertions are reviewed. Possible relationships of these three phenomena to each other and to sex differentiation are discussed. Similarities in mechanisms of sexual determination between marsupial and eutherian mammals are hypothesized. Problems with interpreting male sexual differentiation as being solely due to testosterone and Müllerian inhibiting substance (MIS) are discussed.