bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial cos cleavage of bacteriophage λ concatemers requires proheads and gpFI in vivo
Authors: Sippy Jean , Feiss Michael 
Published: April 2004

SummaryThe development of bacteriophage λ and double‐stranded DNA viruses in general involves the convergence of two separate pathways: DNA replication and head assembly. Clearly, packaging will proceed only if an empty capsid shell, the prohead, is present to receive the DNA, but genetic evidence suggests that proheads play another role in the packaging process. For example, λ phages with an amber mutation in any head gene or in FI, the gene encoding the accessory packaging protein gpFI, are able to produce normal amounts of DNA concatemers but they are not cut, or matured, into unit length chromosomes for packaging. Similar observations have been made for herpes simplex 1 virus. In the case of λ, a negative model proposes that in the amber phages, unassembled capsid components are inhibitory to maturation, and a positive model suggests that assembled proheads are required for cutting. We tested the negative model by using a deletion mutant devoid of all prohead genes and FI in an in vivo cos cleavage assay; in this deleted phage, the cohesive ends were not cut. When λ proheads and gpFI were provided in vivo via a second prophage, cutting was restored, and gpFI was required, results that support the positive model. Phage 21 is a sister phage of λ, and although its capsid proteins share ∼60% residue identity with λ’s, phage 21 proheads did not restore cutting, even when provided with the accessory protein gpFI. Models for the role of proheads and gpFI in cos cutting are discussed.
The push–pull mechanism of bacteriophage Ø29 DNA injection
Authors: González‐Huici Víctor , Salas Margarita , Hermoso José M. 
Published: April 2004

SummaryThe mechanism of bacteriophage DNA injection is poorly understood, often considered a simple process, driven merely by the packing pressure inside the capsid. In contrast to the well‐established DNA packaging mechanism of Bacillus subtilis phage Ø29, that involves a molecular motor formed by the connector and a viral ATPase, nothing is known about its DNA injection into the cell. We have studied this process measuring DNA binding of p6, a viral genome organization protein. The linear DNA penetrates with a right‐left polarity, in a two‐step process. In the first step ∼65% of the genome is pushed into the cell most probably by the pressure built inside the viral capsid. Thus, synthesis of viral proteins from the right early operon is allowed. This step is controlled, probably by bacterial protein(s) that slow down DNA entry. In the second step at least one of the viral early proteins, p17, participates in the molecular machinery that pulls the remaining DNA inside the cell. Both steps are energy‐dependent, as treatment of cells with azide overrides the whole mechanism, leading to a deregulated, passive entry of DNA.
Blockage of methylcitrate cycle inhibits polyketide production in Aspergillus nidulans
Authors: Zhang Yong‐Qiang , Keller Nancy P. 
Published: April 2004

Summary Aspergillus nidulans produces the polyketide toxin sterigmatocystin (ST) of which the biosynthetic and pathway specific regulatory genes compose a stc gene cluster. A previous mutagenesis screen identified 23 mutants defective in production of ST. Five mutants constitute a single locus. Genetic complementation and sequencing analysis revealed the mutant locus to be mcsA encoding methylcitrate synthase that converts propionyl‐CoA to methylcitrate. Feeding downstream products of methylcitrate synthase, methylcitrate and pyruvate, did not restore ST production in mcsA mutants, indicating that loss of methylcitrate cycle products is not the cause of the ST defect. However, propionate, a precursor for propionyl‐CoA, inhibited ST production and induced transcription of mcsA in the wild type. Furthermore, propionate impaired formation of two polyketide spore pigments whereas overexpression of mcsA relieved inhibition of ST production by propionate. Transcription analyses revealed that disruption of mcsA did not affect expression of the specialized fatty acid synthase genes (stcJ and stcK) or polyketide synthase gene (stcA) required for formation of norsolorinic acid (NOR), the first stable intermediate in the ST biosynthetic pathway. Feeding studies showed that NOR but not hexanoic acid (the fatty acid produced by StcJ/StcK and primer unit of StcA) or malonate (source of the extender unit of StcA) restored ST production in the mcsA mutant. We hypothesize that excess buildup of propionyl‐CoA in mcsA mutants interferes with polyketide synthase activity.
The ShdA adhesin binds to the cationic cradle of the fibronectin13FnIII repeat module: evidence for molecular mimicry of heparin binding
Authors: Kingsley Robert A. , Keestra A. Marijke , De Zoete Marcel R. , Bäumler Andreas J. 
Published: April 2004

SummaryIntroduction ofSalmonella entericaserotype Typhimurium into food products results from its ability to persist in the intestine of healthy livestock by mechanisms that are poorly understood. The non‐fimbrial adhesin ShdA is a fibronectin binding protein required for persistent intestinal carriage ofS.Typhimurium. We further investigated the molecular mechanism of ShdA‐mediated intestinal persistence by determining the binding‐site of this receptor in fibronectin. Analysis of ShdA binding to fibronectin proteolytic fragments and to recombinant fibronectin fusion proteins identified the13FnIII repeat module of the Hep‐2 domain as the primary binding site for this adhesin. The13FnIII repeat module of fibronectin contains a cationic cradle formed by six basic residues (R6, R7, R9, R23, K25 and R54) that is a high affinity heparin‐binding site conserved among fibronectin sequences from frogs to man. Binding of ShdA to the13FnIII repeat module of fibronectin and to a second extracellular matrix protein, Collagen I, could be inhibited by heparin. Furthermore, binding of ShdA to the Hep‐2 domain was sensitive to the ionic buffer strength, suggesting that binding involved ionic interactions. We therefore determined whether amino acid substitutions of basic residues in the cationic cradle of the Hep‐2 domain that inhibit heparin binding also abrogate binding of ShdA. Combined substitution of R6S and R7S strongly reduced ShdA binding to13FnIII. These data suggest that ShdA binds the Hep‐2 domain of fibronectin by a mechanism that may mimic binding of the host polysaccharide heparin.
Genes governing swarming in Bacillus subtilis and evidence for a phase variation mechanism controlling surface motility
Authors: Kearns Daniel B. , Chu Frances , Rudner Rivka , Losick Richard 
Published: April 2004

SummaryUndomesticated strains of Bacillus subtilis, but not laboratory strains, exhibit robust swarming motility on solid surfaces. The failure of laboratory strains to swarm is caused by a mutation in a gene (sfp) needed for surfactin synthesis and a mutation(s) in an additional unknown gene(s). Insertional mutagenesis of the undomesticated 3610 strain with the transposon mini‐Tn10 was carried out to discover genes needed for swarming but not swimming motility. Four such newly identified swarming genes are reported, three of which (swrA, swrB, and efp) had not been previously characterized and one of which (swrC) was known to play a role in resistance to the antibacterial effect of surfactin. Laboratory strains were found to harbour a frameshift mutation in the swrA gene. When corrected for the swrA mutation, as well as the mutation in sfp, laboratory strains regained the capacity to swarm and did so as robustly as the wild strain. The swrA mutation was an insertion of an A:T base pair in a homopolymeric stretch of eight A:T base pairs, and readily reverted to the wild type. These findings suggest that the swrA insertion and its reversion take place by slipped‐strand mispairing during DNA replication and that swarming motility is subject to phase variation.
The Pseudomonas siderophore quinolobactin is synthesized from xanthurenic acid, an intermediate of the kynurenine pathway
Authors: Matthijs Sandra , Baysse Christine , Koedam Nico , Tehrani Kourosh Abbaspour , Verheyden Lieve , Budzikiewicz Herbert , Schäfer Mathias , Hoorelbeke Bart , Meyer Jean‐Marie , De Greve Henri , Cornelis Pierre 
Published: April 2004

SummaryTo cope with iron deficiency fluorescent pseu‐domonads produce pyoverdines which are complex peptidic siderophores that very efficiently scavenge iron. In addition to pyoverdine some species also produce other siderophores. Recently, it was shown that Pseudomonas fluorescens ATCC 17400 pro‐duces the siderophore quinolobactin, an 8‐hydroxy‐4‐methoxy‐2‐quinoline carboxylic acid (Mossialos, D., Meyer, J.M., Budzikiewicz, H., Wolff, U., Koedam, N., Baysse, C., Anjaiah, V., and Cornelis, P. (2000) Appl Environ Microbiol 66: 487–492). The entire quinolobactin biosynthetic, transport and uptake gene cluster, consisting out of two operons comprising 12 open reading frames, was cloned and sequenced. Based on the genes present and physiological complementation assays a biosynthetic pathway for quinolobactin is proposed. Surprisingly, this pathway turned out to combine genes derived from the eukaryotic tryptophan‐xanthurenic acid branch of the kynurenine pathway and from the pathway for the biosynthesis of pyridine‐2,6‐bis(thiocarboxylic acid) from P. stutzeri, PDTC. These results clearly show the involvement of the tryptophan‐kynurenine‐xanthurenic acid pathway in the synthesis of an authentic quinoline siderophore.
Genetic evidence that the Vibrio cholerae monolayer is a distinct stage in biofilm development
Authors: Moorthy Sudha , Watnick Paula I. 
Published: April 2004

SummaryBiofilm development is conceived as a developmental process in which free swimming cells attach to a surface, first transiently and then permanently, as a single layer. This monolayer of immobilized cells gives rise to larger cell clusters that eventually develop into the biofilm, a three‐dimensional structure consisting of large pillars of bacteria interspersed with water channels. Previous studies have shown that efficient development of the Vibrio cholerae biofilm requires a combination of pili, flagella and exopolysaccharide. Little is known, however, regarding the requirements for monolayer formation by wild‐type V. cholerae. In this work, we have isolated the wild‐type V. cholerae monolayer and demonstrated that the environmental signals, bacterial structures, and transcription profiles that induce and stabilize the monolayer state are unique. Cells in a monolayer are specialized to maintain their attachment to a surface. The surface itself activates mannose‐sensitive haemagglutinin type IV pilus (MSHA)‐mediated attachment, which is accompanied by repression of flagellar gene transcription. In contrast, cells in a biofilm are specialized to maintain intercellular contacts. Progression to this stage occurs when exopolysaccharide synthesis is induced by environmental monosaccharides. We propose a model for biofilm development in natural environments in which cells form a stable monolayer on a surface. As biotic surfaces are degraded with subsequent release of carbohydrates, the monolayer develops into a biofilm.
The histone‐like nucleoid structuring protein H‐NS represses the Escherichia coli bgl operon downstream of the promoter
Authors: Dole Sudhanshu , Nagarajavel V. , Schnetz Karin 
Published: April 2004

SummarySpecificity of repression by the histone‐like nucleoid structuring protein and pleiotropic regulator, H‐NS, is exceptionally high in case of the Escherichia coli bgl (β‐glucoside) operon. Here we present evidence that H‐NS represses the operon at two levels. The binding of H‐NS to an upstream silencer results in an ∼threefold repression of the catabolite gene regulator protein (CRP) dependent bgl promoter. In addition, H‐NS binds to a silencer region located approximately 600–700 base pairs downstream of the promoter, within the coding region of first gene, bglG, resulting in a ∼sevenfold further decrease of expression. Repression by H‐NS at the downstream silencer requires termination factor Rho and is reduced by translation of the bglG mRNA, but is independent of the promoter. This suggests that H‐NS induces polarity of transcription by acting as a roadblock to the elongat‐ing RNA polymerase. The control of the bgl operon by H‐NS at two levels results in a highly specific repression.
Nuclear localization and interaction of RolB with plant 14‐3‐3 proteins correlates with induction of adventitious roots by the oncogene rolB
Authors: Moriuchi Hiroshi , Okamoto Chiho , Nishihama Ryuichi , Yamashita Ichiro , Machida Yasunori , Tanaka Nobukazu 
Published: April 2004

SummaryThe rooting‐locus gene B (rolB) on the T‐DNA of the root‐inducing (Ri) plasmid in Agrobacterium rhizogenes is responsible for the induction of transformed adventitious roots, although the root induction mechanism is unknown. We report here that the RolB protein of pRi1724 (1724RolB) is associated with Nicotianatabacum14‐3‐3‐like protein ωII (Nt14‐3‐3 ωII) in tobacco bright yellow (BY)‐2 cells. Nt14‐3‐3 ωII directly interacts with 1724RolB protein. Green fluorescent protein (GFP)‐fused 1724RolB is localized to the nucleus. GFP‐fused mutant 1724RolB proteins having a deletion or amino acid substitution are unable to interact with Nt14‐3‐3 ωII and also show impaired nuclear localization. Moreover, these 1724RolB mutants show decreased capacity for adventitious root induction. These results suggest that adventitious root induction by 1724RolB protein correlates with its interaction with Nt14‐3‐3 ωII and the nuclear localization of 1724RolB protein.
Canopy studies on ethylene‐insensitive tobacco identify ethylene as a novel element in blue light and plant–plant signalling
Authors: Pierik Ronald , Whitelam Garry C. , Voesenek Laurentius A. C. J. , De Kroon Hans , Visser Eric J. W. 
Published: April 2004

SummaryPlants growing at high densities express shade avoidance traits as a response to the presence of neighbours. Enhanced shoot elongation is one of the best researched shade avoidance components and increases light capture in dense stands. We show here that also leaf movements, leading to a more vertical leaf orientation (hyponasty), may be crucial in the early phase of competition. The initiation of shade avoidance responses is classically attributed to the action of phytochrome photoreceptors that sense red:far‐red (R:FR) ratios in light reflected by neighbours, but also other signals may be involved. It was recently shown that ethylene‐insensitive, transgenic (Tetr) tobacco plants, which are insensitive to the gaseous plant hormone ethylene, have reduced shade avoidance responses to neighbours. Here, we report that this is not related to a reduced response to low R:FR ratio, but that Tetr tobacco plants are unresponsive to a reduced photon fluence rate of blue light, which normally suppresses growth inhibition in wild‐type (WT) plants. In addition to these light signals, ethylene levels in the canopy atmosphere increased to concentrations that could induce shade avoidance responses in WT plants. Together, these data show that neighbour detection signals other than the R:FR ratio are more important than previously anticipated and argue for a particularly important role for ethylene in determining plant responses to neighbours.
Characterization of heterotrimeric G protein complexes in rice plasma membrane
Authors: Kato Chiyuki , Mizutani Tomohiro , Tamaki Hisanori , Kumagai Hidehiko , Kamiya Takehiro , Hirobe Ayumi , Fujisawa Yukiko , Kato Hisaharu , Iwasaki Yukimoto 
Published: April 2004

SummaryTwo genes in the rice genome were identified as those encoding the γ subunits, γ1 and γ2, of heterotrimeric G proteins. Using antibodies against the recombinant proteins for the α, β, γ1, and γ2 subunits of the G protein complexes, all of the subunits were proven to be localized in the plasma membrane in rice. Gel filtration of solubilized plasma membrane proteins showed that all of the α subunits were present in large protein complexes (about 400 kDa) containing the other subunits, β, γ1, and γ2, and probably also some other proteins, whereas large amounts of the β and γ (γ1 and γ2) subunits were freed from the large complexes and took a 60‐kDa form. A yeast two‐hybrid assay and co‐immunoprecipitation experiments showed that the β subunit interacted tightly with the γ1 and γ2 subunits, and so the β and γ subunits appeared to form dimers in rice cells. Some dimers were associated with the α subunit, because few β, γ1, and γ2 subunits were present in the 400‐kDa complexes in a rice mutant,d1, which was lacking in the α subunit. When a constitutively active form of the α subunit was prepared by the exchange of one amino acid residue and introduced intod1, the mutagenized subunit was localized in the plasma membrane of the transformants and took a free, and not the 400‐kDa, form.
Ophthalmic techniques described by Şerefeddin Sabuncuoğlu (1385−1468 ad)
Authors: Oguz Halit , San Imran , Verit Ayhan , Uzel Ilter 
Published: April 2004

Abstract¸Serefeddin Sabuncuoglu (1385−1468 ad) was a Turkish surgeon who lived in the Ottoman Empire during the fifteenth century, a time of progressive expansion. When in his eighties, he wrote Cerrahiyyetü’l‐Haniyye, which means Imperial Surgery. His book is the first example of an illustrated surgical textbook in the Turkish−Islamic medical literature. The importance of his book rests upon the inclusion of colour miniatures of the surgical procedures, incisional techniques and instruments, all drawn by Sabuncuog˘lu himself. Only three hand‐written copies exist, two of which were originally written by the author and are currently exhibited in Paris and Istanbul. The book was rediscovered in 1936, but some parts of it are still suspected to be missing. At present, the book consists of three chapters divided into 193 known sections. The sections deal with all fields of surgery including ophthalmology, and cite relevant Greek, Arabic and Persian textbooks. In this historical article the sections of Cerrahiyyetü’l‐Haniyye pertinent to ophthalmology are critically reviewed, including a selection of the coloured drawings.
Corneal epithelial cellular dysfunction from benzalkonium chloride (BAC) in vitro
Authors: Cha Seung‐Heon , Lee Jong‐Soo , Oum Boo‐Sup , Kim Chi‐Dae 
Published: April 2004

Abstract Purpose: To investigate the functional and morphological toxicity of benzalkonium chloride (BAC) on corneal epithelial cells in vitro. Methods: Primary corneal epithelial cells were cultured from rabbit cornea. Corneal epithelial cells containing radioactive 51Cr were exposed for 5 min, 10 min, 30 min and 60 min to concentration of BAC 0.001%, 0.005%, 0.01%, 0.05% and 0.1%. Control cells were treated with phosphate buffer solution alone. 51Cr release from epithelial cells into the supernatant was used as an index of epithelial cell lysis. Cell detachment (index of cell dysfunction) was analysed by measuring 51Cr activity in the supernatant and wash fluid. Morphological cell damage was investigated with transmission electron microscopy. Results: With the higher concentration and the longer duration of BAC exposure, corneal epithelial cell lysis was increased significantly (P < 0.05). Cells showed severe damage at BAC concentration over 0.05% during 5 min of exposure. Cell dysfunction appeared markedly at BAC concentrations of 0.005% for 30 min of exposure, but decreased with longer exposure times. There was an increase in significant cytoplasmic damage with longer BAC exposure times, although not with a minimal dose of 0.001%. Disrupted cytoplasmic membranes of corneal epithelial cells appeared at the higher BAC concentration of 0.1%, and at the longer exposure time of 30 min with BAC concentration of at least 0.001%. Conclusions: BAC can induce corneal epithelial dysfunction, which can damage the corneal epithelial barrier. This effect occurs when BAC is used frequently or for periods over 30 min, even when the BAC concentration is low (0.001%).
Clinical Case Notes
Authors: Kumar Nikhil , Zeldovich Alina , Chang Andrew 
Published: April 2004

AbstractA case is reported of a 72‐year‐old man with an intruded scleral buckle presenting 30 years after retinal detachment repair. The lesion was noted incidentally and occupied the superotemporal retinal periphery. The diagnosis was confirmed by B‐scan ultrasonography and external examination of the globe. The patient was treated conservatively. No clinical change was evident after 12 months follow up.
Longevity‐associated mitochondrial DNA 5178 A/C polymorphism is associated with intraocular pressure in Japanese men
Authors: Kokaze Akatsuki , Yoshida Masao , Ishikawa Mamoru , Matsunaga Naomi , Makita Ryuji , Satoh Masao , Sekiguchi Kanako , Masuda Yumi , Uchida Yoshiko , Takashima Yutaka 
Published: April 2004

Abstract Background: Mitochondrial DNA 5178 adenine/cytosine (mt5178 A/C) polymorphism has been reported to be associated with longevity in Japanese individuals, with experimental findings concluding that mt5178 A is an anti‐atherogenic genotype. The aim of this study was to determine whether mt5178 A/C polymorphism influences intraocular pressure (IOP), and its relationship with the development of arteriosclerosis. Methods: Four hundred and forty‐nine male volunteers who had visited a general hospital for medical check‐up between August 1999 and August 2000 were enrolled. Of these, 386 Japanese men who had not undergone any medical treatment for hypertension, ocular hypertension or glaucoma were selected as subjects of this study. After these subjects were genotyped, a cross‐sectional study regarding the relationship between genotype and IOP was conducted. Results: Mean IOP was significantly higher in men with mt5178 C (13.3 mmHg) than in those with mt5178 A (12.7 mmHg) (P = 0.037). This significant difference in mean IOP between the two genotypes remained evident after adjusting for age, body mass index, blood pressure, habitual smoking and habitual drinking. Interactions between mt5178 A/C polymorphism and habitual smoking or daily alcohol consumption with regard to IOP were observed. According to multiple regression analysis, habitual smoking was significantly associated with IOP in men with mt5178 A (P for trend = 0.020), while daily alcohol consumption was significantly associated with IOP in those with mt5178 C (P for trend = 0.021). Conclusion: Longevity‐associated mitochondrial DNA 5178 A/C polymorphism may be associated with IOP in Japanese men.
Clinical Case Note
Authors: Sekhar G Chandra , Onam K Sreelatha , Kunjam Vallam 
Published: April 2004

AbstractPlateau iris syndrome is considered to be a rare entity and has been classified into two subtypes, the complete and the incomplete forms. Herein a case is reported of plateau iris syndrome that had a postmydriatic rise in intraocular pressure (IOP) in one eye (complete syndrome) and no increase in IOP in the other (incomplete syndrome). The pre‐ and post‐mydriasis ultrasound biomicroscopic findings were documented. These findings suggest that incomplete plateau iris syndrome may be caused by a difference in the extent of closure of the angle circumferentially over the 360 degrees of the angle.