bluuebunny/crossref_metadata_2025_split huggingface dataset:
ThevirFpromoter inShigella: more than just a curved DNA stretch
Authors: Prosseda Gianni , Falconi Maurizio , Giangrossi Mara , Gualerzi Claudio O. , Micheli Gioacchino , Colonna Bianca 
Published: January 2004

SummaryIn the human enteropathogenShigellatranscription ofvirF, the primary regulator of the invasion functions, is strictly temperature‐dependent and is antagonistically mediated by H‐NS and FIS, which bind to specific sites on thevirFpromoter. Here we report on the relevance of DNA geometry to the themoregulation ofvirFand demonstrate that thevirFpromoter hosts a major DNA bend halfway between two H‐NS sites. The bent region has been mutagenizedin vitroto mimic temperature‐induced changes of DNA curvature. Functional analysis of curvature mutants and of promoter constructs in which the two H‐NS sites are phased‐out by a half–helix turn reveals that modifying the spatial relationships between these sites severely affects the interaction of H‐NS with thevirFpromoter, as well as itsin vivoandin vitrotemperature‐dependent activity. The role of promoter curvature as thermosensor is also compatible with the present observation that, with increasing temperature, thevirFbending centre moves downstream at a rate having its maximum around the transition temperature, abruptly unmasking a binding site for the transcriptional activator FIS.
Host processing of branched DNA intermediates is involved in targeted transposition of IS911
Authors: Loot Celine , Turlan Catherine , Chandler Michael 
Published: January 2004

SummaryA simplified system using bacterial insertion sequence IS911 has been developed to investigate targeted insertion next to DNA sequences resembling IS ends. We show here that these IR‐targeted events occur by an unusual mechanism. In the circular IS911 transposition intermediate the two IRs are abutted to form an IR/IR junction. IR‐targeted insertion involves transfer of a single end of the junction to the target IR to generate a branched DNA structure. The single‐end transfer (SET) intermediate, but not the final insertion product, can be detected in an in vitro reaction. SET intermediates must be processed by the bacterial host to obtain the final insertion products. Sequence analysis of these IR‐targeted insertion products and of those obtained in vivo revealed high levels of DNA sequence conversion in which mutations from one IR were transferred to another. These sequence changes cannot be explained by the classic transposition pathway. A model is presented in which the four‐way Holliday‐like junction created by SET is processed by host‐mediated branch migration, resolution, repair and replication. This pathway resembles those described for processing other branched DNA structures such as stalled replication forks.
Molybdate transport and its effect on nitrogen utilization in the cyanobacterium Anabaena variabilis ATCC 29413
Authors: Zahalak Marta , Pratte Brenda , Werth Kelly J. , Thiel Teresa 
Published: January 2004

SummaryMolybdenum is an essential component of the cofactors of many metalloenzymes including nitrate reductase and Mo‐nitrogenase. The cyanobacterium Anabaena variabilis ATCC 29413 uses nitrate and atmospheric N2 as sources of nitrogen for growth. Two of the three nitrogenases in this strain are Mo‐dependent enzymes, as is nitrate reductase; thus, transport of molybdate is important for growth of this strain. High‐affinity transport of molybdate in A. variabilis was mediated by an ABC‐type transport system encoded by the products of modA and modBC. The modBC gene comprised a fused orf including components corresponding to modB and modC of Escherichia coli. The deduced ModC part of the fused gene lacked a recognizable molybdate‐binding domain. Expression of modA and modBC was induced by starvation for molybdate. Mutants in modA or modBC were unable to grow using nitrate or Mo‐nitrogenase. Growth using the alternative V‐nitrogenase was not impaired in the mutants. A high concentration of molybdate (10 µM) supported normal growth of the modBC mutant using the Nif1 Mo‐nitrogenase, indicating that there was a low‐affinity molybdate transport system in this strain. The modBC mutant did not detectably transport low concentrations of 99Mo (molybdate), but did transport high concentrations. However, such transport was observed only after cells were starved for sulphate, suggesting that an inducible sulphate transport system might also serve as a low‐affinity molybdate transport system in this strain.
Chromosome 1 trisomy compromises the virulence of Candida albicans
Authors: Chen Xi , Magee B. B. , Dawson Dean , Magee P. T. , Kumamoto Carol A. 
Published: January 2004

SummaryAlthough increases in chromosome copy number typically have devastating developmental consequences in mammals, fungal cells such as Saccharomyces cerevisiae seem to tolerate trisomies without obvious impairment of growth. Here, we demonstrate that two commonly used laboratory strains of the yeast Candida albicans, CAI‐4 and SGY‐243, can carry three copies of chromosome 1. Although the trisomic strains grow well in the laboratory, Ura+ derivatives of CAI‐4, carrying three copies of chromosome 1, are avirulent in the intravenously inoculated mouse model, unlike closely related strains carrying two copies of chromosome 1. Furthermore, changes in chromosome copy number occur during growth in an animal host and during growth in the presence of growth‐inhibiting drugs. These results suggest that chromosome copy number variation provides a mechanism for genetic variation in this asexual organism.
RcaE is a complementary chromatic adaptation photoreceptor required for green and red light responsiveness
Authors: Terauchi Kazuki , Montgomery Beronda L. , Grossman Arthur R. , Lagarias J. Clark , Kehoe David M. 
Published: January 2004

SummaryThe recent discovery of large numbers of phytochrome photoreceptor genes in both photosynthetic and non‐photosynthetic prokaryotes has led to efforts to understand their physiological roles in environmental acclimation. One receptor in this class, RcaE, is involved in controlling complementary chromatic adaptation, a process that regulates the transcription of operons encoding light‐harvesting proteins in cyanobacteria. Although all previously identified phytochrome responses are maximally sensitive to red and far red light, complementary chromatic adaptation is unique in that it is responsive to green and red light. Here, we present biochemical and genetic evidence demonstrating that RcaE is a photoreceptor and that it requires the cysteine at position 198 to ligate an open chain tetrapyrrole covalently in a manner analogous to chromophore attachment in plant phytochromes. Furthermore, although the wild‐type rcaE gene can rescue red and green light photoresponses of an rcaE null mutant, a gene in which the codon for cysteine 198 is converted to an alanine codon rescues the red light but not the green light response. Thus, RcaE is a photoreceptor that is required for both green and red light responsiveness during complementary chromatic adaptation and is the first identified phytochrome class sensor that is involved in sensing and responding to green and red light rather than red and far red light.
Nucleoid restructuring in stationary‐state bacteria
Authors: Frenkiel‐Krispin Daphna , Ben‐Avraham Irit , Englander Joseph , Shimoni Eyal , Wolf Sharon G. , Minsky Abraham 
Published: January 2004

SummaryThe textbook view of the bacterial cytoplasm as an unstructured environment has been overturned recently by studies that highlighted the extent to which non‐random organization and coherent motion of intracellular components are central for bacterial life‐sustaining activities. Because such a dynamic order critically depends on continuous consumption of energy, it cannot be perpetuated in starved, and hence energy‐depleted, stationary‐state bacteria. Here, we show that, at the onset of the stationary state, bacterial chromatin undergoes a massive reorganization into ordered toroidal structures through a process that is dictated by the intrinsic properties of DNA and by the ubiquitous starvation‐induced DNA‐binding protein Dps. As starvation proceeds, the toroidal morphology acts as a structural template that promotes the formation of DNA–Dps crystalline assemblies through epitaxial growth. Within the resulting condensed assemblies, DNA is effectively protected by means of structural sequestration. We thus conclude that the transition from bacterial active growth to stationary phase entails a co‐ordinated process, in which the energy‐dependent dynamic order of the chromatin is sequentially substituted with an equilibrium crystalline order.
In vivo studies on putative Shine–Dalgarno sequences of the halophilic archaeon Halobacterium salinarum
Authors: Sartorius‐Neef Simone , Pfeifer Felicitas 
Published: January 2004

SummaryThe involvement of Shine–Dalgarno sequences in the translation of mRNA in halophilic archaea was investigated for two gvp genes involved in gas vesicle formation in Halobacterium salinarum PHH1. With the exception of gvpA and gvpO, all reading frames of the p‐gvpDEFGHIJKLM and p‐gvpACNO mRNAs contained upstream of the AUG start codon a putative Shine–Dalgarno (SD) sequence that is complementary to the 3′‐end of the small ribosomal subunit RNA. The importance of the SD sequences of gvpG and gvpH was investigated in Haloferax volcanii transformants, and an alteration of the SD sequence resulted in a reduction of the amount of the GvpG or GvpH protein. For a more quantitative analysis the region upstream of gvpH was fused to the bgaH reading frame encoding an enzyme with β‐galactosidase activity as reporter. Scanning mutagenesis within the mRNA leader demonstrated that mutations adjacent to the putative SD sequence GGAGGUCA did not influence the efficiency of translation, whereas constructs harbouring an altered SD sequence yielded only 5–50% of the β‐galactosidase activities obtained with the wild‐type SD element. A complete mutation of the SD sequence still yielded 20% of the wild‐type activity. Alterations in the spacing of the SD sequence and the translation initiation codon of gvpH indicated that a distance of 4 or 10 nucleotides yielded a similar β‐galactosidase activity as found with the 7 nt spacing of the SD element in wild type, whereas a distance of 1 nt resulted in the loss of translation. A complete deletion of the 5′‐UTR resulting in a leaderless mRNA yielded an enhanced β‐galactosidase activity in transformants implying that the initiation of translation involved a mechanism other than a specific mRNA–rRNA interaction.
Cellulolysis is severely affected in Clostridium cellulolyticum strain cipCMut1
Authors: Maamar Hédia , Valette Odile , Fierobe Henri‐Pierre , Bélaich Anne , Bélaich Jean‐Pierre , Tardif Chantal 
Published: January 2004

SummaryProgress towards understanding the molecular basis of cellulolysis by Clostridium cellulolyticm was obtained through the study of the first cellulolysis defective mutant strain, namely cipCMut1. In this mutant, a 2 659 bp insertion element, disrupts the cipC gene at the sequence encoding the seventh cohesin of the scaffoldin CipC. cipC is the first gene in a large ‘cel’ gene cluster, encoding several enzymatic subunits of the cellulosomes, including the processive cellulase Cel48F, which is the major component. Physiological and biochemical studies showed that the mutant strain was affected in cellulosome synthesis and severely impaired in its ability to degrade crystalline cellulose. It produced small amounts of a truncated CipC protein (P120), which had functional cohesin domains and assembled complexes which did not contain any of the enzymes encoded by genes of the ‘cel’ cluster. The mutant cellulolytic system was mainly composed of three proteins designated P98, P105 and P125. Their N‐termini did not match any of the known cellulase sequences from C. cellulolyticum. A large amount of entire CipC produced in the cipCMut1 strain by trans‐complementation with plasmid pSOScipC did not restore the cellulolytic phenotype, in spite of the assembly of a larger amount of complexes. The complexes produced in the mutant and complemented strains contained at least 12 different dockerin‐containing proteins encoded by genes located outside of the ‘cel’ cluster. The disturbances observed in the mutant and trans‐complemented strains were the result of a strong polar effect resulting from the cipC gene disruption. In conclusion, this study provided genetic evidence that the cellulases encoded by the genes located in the ‘cel’ cluster are essential for the building of cellulosomes efficient in crystalline cellulose degradation.
Use of antisense RNA to modify the composition of cellulosomes produced by Clostridium cellulolyticum
Authors: Perret Stéphanie , Maamar Hédia , Bélaich Jean‐Pierre , Tardif Chantal 
Published: January 2004

SummaryThe enzymatic composition of the cellulosomes produced by Clostridium cellulolyticum was modified by inhibiting the synthesis of Cel48F that is the major cellulase of the cellulosomes. The strain ATCC 35319 (pSOSasrF) was developed to over‐produce a 469 nucleotide‐long antisense‐RNA (asRNA) directed against the ribosome‐binding site region and the beginning of the coding region of the cel48F mRNAs. The cellulolytic system secreted by the asRNA‐producing strain showed a markedly lower amount of Cel48F, compared to the control strain transformed with the empty plasmid (pSOSzero). This was correlated with a 30% decrease of the specific activity of the cellulolytic system on Avicel cellulose, indicating that Cel48F plays an important role in the recalcitrant cellulose degradation. However, only minor effects were observed on the growth parameters on cellulose. In both transformant strains, cellulosome production was found to be reduced and two unknown proteins (P105 and P98) appeared as major components of their cellulolytic systems. These proteins did not contain any dockerin domain and were shown to be not included into the cellulosomes; they are expected to participate to the non‐cellulosomal cellulolytic system of C. cellulolyticum.
Bacillus anthracis requires siderophore biosynthesis for growth in macrophages and mouse virulence
Authors: Cendrowski Stephen , MacArthur William , Hanna Philip 
Published: January 2004

SummarySystemic anthrax infections can be characterized as proceeding in stages, beginning with an early intracellular establishment stage within phagocytes that is followed by extracelluar stages involving massive bacteraemia, sepsis and death. Because most bacteria require iron, and the host limits iron availability through homeostatic mechanisms, we hypothesized that B. anthracis requires a high‐affinity mechanism of iron acquisition during its growth stages. Two putative types of siderophore synthesis operons, named Bacillus anthracis catechol, bac (anthrabactin), and anthrax siderophore biosynthesis, asb (anthrachelin), were identified. Directed gene deletions in both anthrabactin and anthrachelin pathways were generated in a B. anthracis (Sterne) 34F2 background resulting in mutations in asbA and bacCEBF. A decrease in siderophore production was observed during iron‐depleted growth in both the ΔasbA and ΔbacCEBF strains, but only the ΔasbA strain was attenuated for growth under these conditions. In addition, the ΔasbA strain was severely attenuated both for growth in macrophages (MΦ) and for virulence in mice. In contrast, the ΔbacCEBF strain did not differ phenotypically from the parental strain. These findings support a requirement for anthrachelin but not anthrabactin in iron assimilation during the intracellular stage of anthrax.
Evolution of fungal sex chromosomes
Authors: Fraser James A. , Heitman Joseph 
Published: January 2004

SummarySexual reproduction enables organisms to shuffle two parental genomes to produce recombinant progeny, and to purge the genome of deleterious mutations. Sex is conserved in virtually all organisms, from bacteria and fungi to plants and animals, and yet the mechanisms by which sexual identity are established share both conserved general features and are remarkably diverse. In animals, sexual identity is established by dimorphic sex chromosomes, whereas in fungi a specialized region of the genome, known as the mating‐type locus, governs the establishment of cell type identity and differs in DNA sequence between cells of different mating‐types. Recent studies on the mating‐type loci of fungi and algae reveal features shared with the mammalian X and Y chromosomes, suggesting that these represent early steps in the evolution of sex chromosomes.
Transitional Cell Carcinoma of the Renal Pelvis in Two Dogs
Authors: Militerno G. , Bazzo R. , Bevilacqua D. , Bettini G. , Marcato P. S. 
Published: January 2004

SummaryTransitional cell carcinoma (TCC) of the renal pelvis was found in two dogs, a 7‐year‐old male English Setter and a 11‐year‐old female Shetland shepherd. Affected dogs were presented for clinical examination without any specific symptoms but haematuria in case 1 and occurrence of whitish material in the urine of case 2; neoplastic disorders were discovered with ultrasonographic investigation and fine needle aspiration biopsy. Histopathological examination was carried out after nephrectomy and ureterectomy of the affected kidney of both dogs, and confirmed the diagnosis of non‐invasive and low grade TCC in case 1 and of infiltrating TCC in case 2. The clinical, gross, cytological and histopathological features of these rare tumours originating from transitional epithelium of the renal pelvis are reported.
Confirmation by DNA analysis that Contarinia maculipennis (Diptera: Cecidomyiidae) is a polyphagous pest of orchids and other unrelated cultivated plants
Authors: Uechi N. , Tokuda M. , Yukawa J. , Kawamura F. , Teramoto K.K. , Harris K.M. 
Published: January 2004

AbstractThe cytochrome oxidase subunit I gene in mitochondrial DNA of 53 larvae of Contarinia maculipennis Felt from flower buds of various host plants, collected from Hawaii, Japan and Thailand was analysed. Monophyly of the clade including C. maculipennis from Hawaii, Thailand and Japan was supported. There was no sequential variation within the specimens from Hawaii and Japan, which differed from one another by 6 bp (1.37%). Three haplotypes were recognized in specimens from Thailand but differences from Hawaiian and Japanese specimens were small. Overall, there were no differences in the 146 deduced amino acid residues. It is therefore concluded that C. maculipennis is a polyphagous species that can develop on plant hosts representing at least seven botanical families. This pest of Dendrobium flower buds in glasshouses is considered to have entered Hawaii, Florida and Japan from Southeast Asia, and was recently intercepted in the Netherlands. Infestations have established and spread in orchid glasshouses, causing concern about the possibility of more extensive damage to orchids and to crops, such as bitter gourd, grown in close proximity to orchid glasshouses in Japan. The potential usefulness of DNA analysis in determining host plant ranges of morphologically identical cecidomyiid species that are currently identified solely on differences of host plant is emphasized.
Amino acid availability: aspects of chemical analysis and bioassay methodology
Authors: Moughan Paul J. 
Published: January 2004

AbstractIt is important to be able to characterise foods and feedstuffs according to their available amino acid contents. This involves being able to determine amino acids chemically and the conduct of bioassays to determine amino acid digestibility and availability. The chemical analysis of amino acids is not straightforward and meticulousness is required to achieve consistent results. In particular and for accuracy, the effect of hydrolysis time needs to be accounted for. Some amino acids (for example, lysine) can undergo chemical modification during the processing and storage of foods, which interferes with amino acid analysis. Furthermore, the modified amino acids may also interfere with the determination of digestibility. A new approach to the determination of available lysine using a modifiedin vivodigestibility assay is discussed. Research is required into other amino acids susceptible to structural damage. There is recent compelling scientific evidence that bacterial activity in the small intestine of animals and man leads to the synthesis and uptake of dietary essential amino acids. This has implications for the accuracy of the ileal-based amino acid digestibility assay and further research is required to determine the extent of this synthesis, the source of nitrogenous material used for the synthesis and the degree of synthesis net of amino acid catabolism. Although there may be potential shortcomings in digestibility assays based on the determination of amino acids remaining undigested at the terminal ileum, there is abundant evidence in simple-stomached animals and growing evidence in human subjects that faecal-based amino acid digestibility coefficients are misleading. Hindgut microbial metabolism significantly alters the undigested dietary amino acid profile. The ileal amino acid digestibility bioassay is expected to be more accurate than its faecal-based counterpart, but correction of the ileal amino acid flow for amino acids of endogenous origin is necessary. Approaches to correcting for the endogenous component are discussed.
The Sociology of Reproduction
Authors: Macintyre Sally 
Published: January 2004

Book reviews in this article:Sheila Kitzinger and John A. Davis, The Place of Birth.Sheila Kitzinger, Women as Mothers.Sheila Kitzinger, The Good Birth Guide.Ann Oakley, Becoming a Mother.Ann Cartwright, The Dignity of Labour? A Study of Childbearing and Induction.
The Social Context of Psychiatric Care
Authors: Bloor Michael , McKeganey Neil 
Published: January 2004

Book reviews in this article:J. Stuart Whiteley and John Gordon, Group Approaches in Psychiatry.R. D. Hinshelwood and Nick Manning (eds). Therapeutic Communities: Reflections and Progress.David Towell and Clive Harries (eds). Innovation in Patient Care.Steven P. Segal and Uri Aviram, The Mentally Ill in Community‐Based Sheltered Care: A Study of Community Care and Social Integration.
The Blair Government and the Core Executive
Authors: Burch Martin , Holliday Ian 
Published: January 2004

AbstractThe article contests the view that the Blair government has presided over the demise of cabinet government in the UK, and the rise of a kind of British presidentialism. By examining changes made at the very heart of government, chiefly in the Prime Minister's and Cabinet Offices, it argues that change under Labour marks the latest stage in the evolution of Britain's still functioning system of cabinet government. Moreover, recent reforms, like so many before, have been partly prompted by deep-seated administrative factors that have helped to shape the core executive for close to a century. Nevertheless, the article concedes that the Blair reforms do reflect an acceleration of pre-existing trends, with the result that the executive arm of government has been substantially enhanced. This has led to some change in the balance of power both within the core executive and across central government more widely.