bluuebunny/crossref_metadata_2025_split huggingface dataset:
An atypical type II topoisomerase from Mycobacterium smegmatis with positive supercoiling activity
Authors: Jain Paras , Nagaraja Valakunja 
Published: October 2005

SummaryTopoisomerases are essential ubiquitous enzymes, falling into two distinct classes. A number of eubacteria including Escherichia coli, typically contain four topoisomerases, two type I topoisomerases and two type II topoisomerases viz. DNA gyrase and topoisomerase IV. In contrast several other bacterial genomes including mycobacteria, encode for one type I topoisomerase and a DNA gyrase. Here we describe a new type II topoisomerase from Mycobacterium smegmatis which is different from DNA gyrase or topoisomerase IV in its characteristics and origin. The topoisomerase is distinct with respect to domain organization, properties and drug sensitivity. The enzyme catalyses relaxation of negatively supercoiled DNA in an ATP‐dependent manner and also introduces positive supercoils to both relaxed and negatively supercoiled substrates. The genes for this additional topoisomerase are not found in other sequenced mycobacterial genomes and may represent a distant lineage.
Identification of Klebsiella pneumoniae virulence determinants using an intranasal infection model
Authors: Lawlor Matthew S. , Hsu James , Rick Paul D. , Miller Virginia L. 
Published: October 2005

SummaryKlebsiella pneumoniae is a Gram‐negative enterobacterium that has historically been, and currently remains, a significant cause of human disease. It is a frequent cause of urinary tract infections and pneumonia, and subsequent systemic infections can have mortality rates as high as 60%. Despite its clinical significance, few virulence factors of K. pneumoniae have been identified or characterized. In this study we present a mouse model of acute K. pneumoniae respiratory infection using an intranasal inoculation method, and examine the progression of both pulmonary and systemic disease. Wild‐type infection recapitulates many aspects of clinical disease, including significant bacterial growth in both the trachea and lungs, an inflammatory immune response characterized by dramatic neutrophil influx, and a steady progression to systemic disease with ensuing mortality. These observations are contrasted with an infection by an isogenic capsule‐deficient strain that shows an inability to cause disease in either pulmonary or systemic tissues. The consistency and clinical accuracy of the intranasal mouse model proved to be a useful tool as we conducted a genetic screen to identify novel virulence factors of K. pneumoniae. A total of 4800 independent insertional mutants were evaluated using a signature‐tagged mutagenesis protocol. A total of 106 independent mutants failed to be recovered from either the lungs or spleens of infected mice. Small scale independent infections proved to be helpful as a secondary screening method, as opposed to the more traditional competitive index assay. Those mutants showing verified attenuation contained insertions in loci with a variety of putative functions, including a large number of hypothetical open reading frames. Subsequent experiments support the premise that the central mechanism of K. pneumoniae pathogenesis is the production of a polysaccharide‐rich cell surface that provides protection from the inflammatory response.
SapT, a lanthionine‐containing peptide involved in aerial hyphae formation in the streptomycetes
Authors: Kodani Shinya , Lodato Michael A. , Durrant Marcus C. , Picart Francis , Willey Joanne M. 
Published: October 2005

SummaryThe developmentally complex soil microbe Streptomyces tendae secretes a hydrophobic peptide that restored to developmental mutants of S. coelicolor the ability to raise aerial hyphae. The S. tendae peptide, SapT, has a lantibiotic structure and molecular modelling predicts that it is amphiphilic, making it structurally and functionally similar to the SapB peptide produced by S. coelicolor. However, SapT, which bears three β‐methyl lanthionine bridges and one lanthionine bridge and demonstrated limited antibiotic activity, is distinct from SapB. The amphiphilic nature of both SapT and SapB is required for their ability to serve as biosurfactants facilitating the emergence of newly formed aerial hyphae. Remarkably, SapB and SapT, and the fungal hydrophobin SC3 were shown to restore to a SapB‐deficient S. coelicolor mutant the capacity to undergo complete morphogenesis, such that the extracellular addition of protein resulted in sporulation. This suggests that the initiation of aerial growth may also indirectly trigger the signal transduction events needed for differentiation. These data imply that the production of morphogenetic peptides may be common among the streptomycetes, but that while their ability to function as biosurfactants is conserved, their specific lantibiotic structure is not. Finally, the identification of a second lanthionine‐containing morphogenetic peptide suggests that lantibiotic structure and function may be more diverse than previously thought.
Genetics of resistance to cotton leaf curl disease in Gossypium hirsutum
Authors: Rahman M. , Hussain D. , Malik T. A. , Zafar Y. 
Published: October 2005

Twenty‐two cotton varieties were screened for resistance to cotton leaf curl disease (CLCuD), a disease of viral origin, using three procedures: field evaluation, whitefly transmission assay and graft inoculation. Viral infection of cotton varieties was determined by visual symptom assessment as well as dot‐blot and multiplex PCR diagnostic techniques. Crosses were made between the most susceptible variety (S‐12) and highly resistant varieties (CP‐15/2, LRA‐5166 and CIM‐443). All F1 plants of these crosses were resistant, showing dominant expression of the resistance as well as the absence of extrachromosomal inheritance. The F2 plants of the crosses CP‐15/2 × S12, LRA‐5166 × S‐12 and CIM‐443 × S12 exhibited a ratio of 13 resistant (symptomless) to three susceptible (with symptoms). Screening of the F2 generation for virus infection by multiplex PCR further subdivided the resistant class into those exhibiting a high level of resistance (HR; PCR‐negative) and those exhibiting resistance (R; symptomless, yet showing virus replication by PCR analysis). Hence, the final ratio was 3:10:3 (HR:resistant:susceptible). The F3 progeny of susceptible F2 plants segregated for resistance, indicating the probable presence of a suppressor gene (S). These findings are consistent with three genes being involved in G. hirsutum resistance to CLCuD, two for resistance (R1CLCuDhir and R2CLCuDhir) and a suppressor of resistance (SCLCuDhir).
Analysis of the histone H3 gene family in Arabidopsis and identification of the male‐gamete‐specific variant AtMGH3
Authors: Okada Takashi , Endo Makoto , Singh Mohan B. , Bhalla Prem L. 
Published: October 2005

SummaryHistones are major components of chromatin, the protein–DNA complex involved in DNA packaging and transcriptional regulation. Histone genes have been extensively investigated at the genome level in animal systems and have been classified as replication dependent, replication independent or tissue specific. However, no such study is available in a plant system. In this paper we report that there are 15 histone H3 genes in the Arabidopsis genome, including five H3.1 genes, three H3.3 genes and five H3.3‐like genes. A gene structure analysis revealed that gene duplication causes redundancy of the histone H3 genes. The expression of one of the H3 genes, termed AtMGH3/At1g19890, is cell‐specific, being restricted to the generative and sperm cells of Arabidopsis pollen as shown by in situ hybridisation and reporter gene analysis. Thus, we conclude that in Arabidopsis, AtMGH3 is a male‐gamete‐specific histone H3 gene. A T‐DNA insertion line for AtMGH3 revealed decreased expression and ectopic RNA splicing. The T‐DNA insertion lines for AtMGH3/At1g19890 and other H3 genes revealed a normal growth phenotype and reproductive fertility. These findings suggest that other H3 genes are likely to compensate for the T‐DNA‐insertion‐induced loss of a single H3 gene because of the high redundancy of these genes in the Arabidopsis genome. These T‐DNA mutant lines should be useful for accumulating different H3 gene mutations in a single plant and for studying replication‐dependent and replication‐independent H3 genes and the specific role of AtMGH3 in chromatin remodelling and transcriptional regulation during development of male gametes.
Consistent transcriptional silencing of 35S‐driven transgenes in gentian
Authors: Mishiba Kei‐ichiro , Nishihara Masahiro , Nakatsuka Takashi , Abe Yoshiko , Hirano Hiroshi , Yokoi Takahide , Kikuchi Akiko , Yamamura Saburo 
Published: October 2005

SummaryIn this study, no transgenic gentian (Gentiana triflora × Gentiana scabra) plants produced via Agrobacterium‐mediated transformation exhibited transgene (GtMADS, gentian‐derived MADS‐box genes or sGFP, green fluorescent protein) expression in their leaf tissues, despite the use of constitutive Cauliflower mosaic virus (CaMV) 35S promoter. Strikingly, no expression of the selectable marker gene (bar) used for bialaphos selection was observed. To investigate the possible cause of this drastic transgene silencing, methylation‐specific sequences were analysed by bisulfite genomic sequencing using tobacco transformants as a control. Highly methylated cytosine residues of CpG and CpWpG (W contains A or T) sites were distinctively detected in the promoter and 5′ coding regions of the transgenes 35S‐bar and 35S‐GtMADS in all gentian lines analysed. These lines also exhibited various degrees of cytosine methylation in asymmetrical sequences. The methylation frequencies in the other transgene, nopaline synthase (NOS) promoter‐driven nptII, and the endogenous GtMADS gene coding region, were much lower and were variable compared with those in the 35S promoter regions. Transgene methylation was observed in the bialaphos‐selected transgenic calluses expressing the transgenes, and methylation sequences were distributed preferentially around the as‐1 element in the 35S promoter. Calluses derived from leaf tissues of silenced transgenic gentian also exhibited transgene suppression, but expression was recovered by treatment with the methylation inhibitor 5‐aza‐2′‐deoxycytidine (aza‐dC). These results indicated that cytosine methylation occurs exclusively in the 35S promoter regions of the expressed transgenes during selection of gentian transformants, causing transcriptional gene silencing.
Appearance of actin microfilament ‘twin peaks’ in mitosis and their function in cell plate formation, as visualized in tobacco BY‐2 cells expressing GFP–fimbrin
Authors: Sano Toshio , Higaki Takumi , Oda Yoshihisa , Hayashi Tomomi , Hasezawa Seiichiro 
Published: October 2005

SummaryThe actin cytoskeleton of higher plants plays an essential role in plant morphogenesis and in maintaining various cellular activities. In this study we established a tobacco BY‐2 cell line, stably transformed with a GFP–fimbrin actin‐binding domain (ABD) 2 construct, that allows visualization of actin microfilaments (MFs) in living cells. Using this cell line, designated BY‐GF11, we performed time‐sequential observations of MF dynamics during cell‐cycle progression. Detailed analyses revealed the appearance of a broad MF band in the late G2 phase that separated to form a structure corresponding to the so‐called actin‐depleted zone (ADZ) in mitosis. In BY‐GF11, the MF structure at the cell cortex in mitosis appeared to form two bands rather than the ADZ. Measurements of fluorescent intensities of the cell cortex indicated an MF distribution that resembled two peaks, and we therefore named the structure MF ‘twin peaks’ (MFTP). The cell plate formed exactly within the valley between the MFTP at cytokinesis, and this cell‐plate guidance was distorted by disruption of the MFTP by an inhibitor of actin polymerization. These results suggest that the MFTP originates from the broad MF band in the G2 phase and functions as a marker of cytokinesis.
Overexpression of a GRAS protein lacking the DELLA domain confers altered gibberellin responses in rice
Authors: Itoh Hironori , Shimada Asako , Ueguchi‐Tanaka Miyako , Kamiya Noriko , Hasegawa Yasuko , Ashikari Motoyuki , Matsuoka Makoto 
Published: October 2005

SummaryThe rice SLR1 (SLENDER RICE 1) gene encodes a DELLA protein that belongs to a subfamily of the GRAS protein superfamily and that functions as a repressor of gibberellin (GA) signaling. Based on the constitutive GA response phenotype of slr1 mutants, SLR1 has been thought to be the sole DELLA‐type protein suppressing GA signals in rice. However, in rice genome databases we identified two sequences homologous to SLR1: SLR1‐like1 and ‐2 (SLRL1 and ‐2). SLRL1 and SLRL2 contain regions with high similarity to the C‐terminal conserved domains in SLR1, but lack the N‐terminal conserved region of the DELLA proteins. The expression of SLRL1 was positively regulated by GA at the mRNA level and occurred preferentially in reproductive organs, whereas SLRL2 was moderately expressed in mature leaf organs and was not affected by GA. Transformation of SLRL1 into the slr1 mutant rescued the slender phenotype of this mutant. Moreover, overexpression of SLRL1 in normal rice plants induced a dwarf phenotype with an increased level of OsGA20ox2 gene expression and diminished the GA‐induced shoot elongation, suggesting that SLRL1 acts as a repressor of GA signaling. Consistent with the fact that SLRL1 does not have a DELLA domain, which is essential for degradation of DELLA proteins, a level of SLRL1 protein was not degraded by application of gibberellic acid. However, the repressive activity of SLRL1 against GA signaling was much weaker than a truncated SLR1 lacking the DELLA domain. Based on these characteristics of SLRL1, the functional roles of SLRL1 in GA signaling in rice are discussed.
HLA‐A and HLA‐B allele frequencies in a mestizo population from Guadalajara, Mexico, determined by sequence‐based typing
Authors: Leal C. A. , Mendoza‐Carrera F. , Rivas F. , Rodriguez‐Reynoso S. , Portilla‐de Buen E. 
Published: October 2005

AbstractHLA‐A and HLA‐B genes were typed by DNA sequencing in a mestizo population from Guadalajara, Jalisco, Mexico. Thirty‐seven HLA‐A and 51 HLA‐B alleles were observed in 103 samples. The common typical Amerindian alleles (>5%) and haplotypes (≥2.0%) found were A*02010101, *24020101, *310102, B*350101, and *4002, and A*310102‐B*4002, A*240201‐B*350101, and the typical European alleles were A*010101, *29010101, B*1402, B*180101, and A*020101‐B*1402, A*020101‐B*510101, and A*3002‐B*180101. This reflects the blending of the two main parental populations of mestizos: Amerindian and Iberian. Mexicans were found to be relatively closer to the Portuguese than to Spaniards. This proximity may indicate a larger Portuguese influence in Mexicans than previously considered. Present data contribute to the understanding of the genetic structure in Mexico.
Occurrence of two newly named oral treponemes –Treponema parvum and Treponema putidum– in primary endodontic infections
Authors: Rôças I. N. , Siqueira J. F. 
Published: October 2005

Background/aims:  Recent evidence from molecular genetic studies has revealed that oral Treponema species are involved in infections of endodontic origin. This study assessed the occurrence of two newly named oral treponemes − Treponema parvum and Treponema putidum – in primary endodontic infections using a culture‐independent identification technique.Methods:  Genomic DNA was isolated directly from clinical samples, and a 16S rRNA gene‐based nested polymerase chain reaction (PCR) assay was used to determine the presence of T. parvum and T. putidum. Species‐specific primer pairs were developed by aligning closely related 16S rRNA gene sequences. The specificity for each primer pair was validated by running PCR against a panel of oral bacteria and by sequence analysis of PCR products from positive clinical samples.Results:  T. parvum was detected in 52% of the root canals associated with chronic apical periodontitis, in 20% of the cases diagnosed as acute apical periodontitis, and in no abscessed case. In general, T. parvum was detected in 26% of the samples from primary endodontic infections. T. putidum was found in only one case of acute apical periodontitis (2% of the total number of cases investigated).Conclusions:  The devised nested PCR protocol was able to identify both T. parvum and T. putidum directly in clinical samples and demonstrated that these two treponemes can take part in endodontic infections.
Involvement of antigen I/II surface proteins in Streptococcus mutans and Streptococcus intermedius biofilm formation
Authors: Pecharki D. , Petersen F. C. , Assev S. , Scheie A. A. 
Published: October 2005

Background/aim:  Dental diseases are caused by microorganisms organized in biofilms. Streptococcus mutans and Streptococcus intermedius are commensals of the human oral cavity. S. mutans is associated with caries, whereas S. intermedius is associated with purulent infections. Oral streptococci including S. mutants and S. intermedius express a family of surface proteins termed antigen I/II (Ag I/II). Ag I/II is implicated in adhesion; however, its role in biofilm formation has not yet been investigated.Methods:  By using isogenic Ag I/II‐deficient mutants of S. mutans and S. intermedius we studied the influence of Ag I/II on in vitro biofilm formation. Biofilm was quantified in polystyrene microtiter plates and visualized by scanning electron microscopy. Ag I/II expression in planktonic and biofilm cells, as well as in the presence or absence of saliva was investigated by immunoblotting.Results:  In the presence of saliva, the Ag I/II‐deficient mutants formed 65% less biofilm than the wild‐types. In the absence of saliva, no difference was observed in S. mutans, whereas the S. intermedius Ag I/II mutant formed 41% less biofilm. Ag I/II expression was reduced in the presence of saliva. No differences in expression were observed between biofilm and planktonic cells.Conclusion:  The results indicated that Ag I/II may be important during biofilm formation particularly in the presence of saliva. These findings may provide useful information regarding the importance of Ag I/II in biofilm formation and in the search of new strategies to control biofilm‐mediated infections.
Stabilizing the stabilizer: group psychoeducation enhances the stability of serum lithium levels
Authors: Colom F , Vieta E , Sánchez‐Moreno J , Martínez‐Arán A , Reinares M , Goikolea JM , Scott J 
Published: October 2005

Objective:  To determine the effect on the serum lithium levels of a psychoeducational program in patients with bipolar disorder.Method:  This is a subanalysis of data obtained from a larger study on the efficacy of group psychoeducation in the prophylaxis of recurrences in bipolar disorders. Data on plasma lithium levels were obtained at five time points: baseline, 6, 12, 18 and 24 months. Serum lithium levels of patients who had received psychoeduction (psychoeducated) (N = 49) and non‐psychoeducated patients (N = 44) were compared.Results:  Mean serum lithium levels were significantly higher and more stable for the psychoeducation group.Conclusions:  As changes in serum lithium level may be a powerful predictor of recurrence for bipolar patients, the addition of group psychoeducation to standard pharmacological treatment may be beneficial to optimize serum lithium levels and, thereby improve outcome.
A positron emission tomography study of the effects of treatment with valproate on brain 5‐HT2A receptors in acute mania
Authors: Yatham Lakshmi N , Liddle Peter F , Lam Raymond W , Adam Michael J , Solomons Kevin , Chinnapalli Manjunath , Ruth Thomas J 
Published: October 2005

Objective:  To examine the effects of treatment with valproate on brain 5‐HT2A receptors in acute manic patients using positron emission tomography (PET) and [18F]‐setoperone.Methods:  Patients with DSM‐IV bipolar I disorder–manic episode were recruited. Patients were drug free or drug naïve at the time of baseline PET scan. All patients were treated with valproate and one patient received lithium in addition to valproate for 3–5 weeks following which they had a post‐treatment PET scan. The effect of treatment on brain 5‐HT2A receptor binding was determined using statistical parametric mapping (SPM) and region of interest (ROI) analyses. Of the 12 manic patients recruited, seven patients had both baseline and post‐treatment PET scans.Results:  All seven patients improved with treatment and were in remission at the time of the second PET scan. Both SPM and ROI analyses showed that treatment with mood stabilizers had no significant effect on brain 5‐HT2A receptor binding in manic patients.Conclusion:  This study suggests that changes in brain 5‐HT2A receptors are not involved in the antimanic effects of mood stabilizers however, we cannot exclude the possibility of 5‐HT2A receptor involvement in down‐stream signaling pathways.
An emotional Stroop functional MRI study of euthymic bipolar disorder
Authors: Malhi Gin S , Lagopoulos Jim , Sachdev Perminder S , Ivanovski Belinda , Shnier Ron 
Published: October 2005

Objective:  To identify the brain regions associated with emotional processing in euthymic bipolar patients.Methods:  The study examined 12 euthymic bipolar patients using functional magnetic resonance imaging (fMRI) while performing an emotional Stroop (eStroop) task. The task comprised emotionally valent and neutral words presented in alternating blocks that was designed to implicitly induce affect. In conjunction with fMRI, galvanic skin responses (GSR) were measured to monitor arousal.Results:  Euthymic bipolar patients had diminished activation in response to the affective stimuli in both cortical and subcortical brain regions when compared with healthy subjects. In particular, patients had less activation in the left ventral prefrontal cortex suggesting a potential trait deficit. Patients were slower to react than healthy controls, but did not differ with respect to accuracy.Conclusions:  Euthymic bipolar patients are perhaps constrained in their ability to engage affective processing. Diminished ventral prefrontal cortex activation corroborates previous reports of a potential trait deficit, suggesting that ‘all is not well in euthymia’, although the effects of medication cannot be overlooked.
Blood inventory management in the type and screen era
Authors: Pereira A. 
Published: October 2005

Background and Objective  Previous models on the management of hospital blood inventories have mostly dealt with the optimization of variables related to the assigned, cross‐matched inventory. Because the type and screen (T&S) procedure allows blood banks to manage surgical reserves with only unassigned inventories, it becomes necessary to gain insight into the factors that determine the efficiency of this kind of blood inventory.Study Design  Stochastic model that simulates the routine operation of a hospital blood bank inventory over a finite number of days was used. Factors that were analysed for their influence on outdate and shortage rates included the mean (MEAN) and variation (CVAR) in daily transfusion, the remaining shelf life of blood units shipped from the blood supplier (RSL) and the number of days between consecutive shipments (INT).Results  Outdate and shortage rates grew exponentially with CVAR, an effect that could be partially counterbalanced by increasing RSL. The variables, MEAN and INT, had little influence on the inventory, provided that blood stocks shipped from the supplier are targeted at the expected average demand for transfusion and RSL is greater than INT.Conclusions  In hospitals that do not hold cross‐matched inventories, CVAR is the major parameter in determining the blood inventory performance. Hospitals with large CVAR must be supplied with young red blood cell (RBC) units, whereas hospitals with smaller CVAR perform well with older stocks. These results advocate for using each hospital's CVAR as the leader parameter in regional optimization policies based on recycling blood units among participating hospitals.