bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new method to estimate relatedness from molecular markers
Authors: FERNÁNDEZ J. , TORO M. A. 
Published: February 2006

AbstractFour major problems can affect the efficiency of methods developed to estimate relatedness between individuals from information of molecular markers: (i) some of them are dependent on the knowledge of the true allelic frequencies in the base population; (ii) they assume that all loci are unlinked and in Hardy–Weinberg and linkage equilibrium; (iii) pairwise methods can lead to incongruous assignations because they take into account only two individuals at a time; (iv) most are usually constructed for particular structured populations (only consider a few relationship classes, e.g. full‐sibs vs. unrelated). We have developed a new approach to estimate relatedness that is free from the above limitations. The method uses a ‘blind search algorithm’ (actually simulated annealing) to find the genealogy that yield a co‐ancestry matrix with the highest correlation with the molecular co‐ancestry matrix calculated using the markers. Thus (i and ii) it makes no direct assumptions about allelic frequencies or Hardy–Weinberg and linkage equilibrium; (iii) it always provide congruent relationships, as it considers all individuals at a time; (iv) degrees of relatedness can be as complex as desired just increasing the ‘depth’ (i.e. number of generations) of the proposed genealogies. Computer simulations have shown that the accuracy and robustness against genotyping errors of this new approach is comparable to that of other proposed methods in those particular situations they were developed for, but it is more flexible and can cope with more complex situations.
Bacillus subtilis RghR (YvaN) represses rapG and rapH, which encode inhibitors of expression of the srfA operon
Authors: Hayashi Kentaro , Kensuke Tsukahara , Kobayashi Kazuo , Ogasawara Naotake , Ogura Mitsuo 
Published: February 2006

SummaryRap proteins regulate the activity of response regulators including Spo0F, DegU and ComA. We found that overexpression of either RapG or RapH severely downregulated the expression of srfA, which belongs to the ComA regulon. Disruption of those genes, however, showed small effects on srfA expression. These observations suggested that Bacillus subtilis cells possess a repressor for rapG and rapH. To identify candidate repressors we developed a novel transcription factor array (TF array) assay, in which disruptions of 287 genes encoding regulatory proteins were independently transformed into a strain carrying rapH–lacZ and the resultant transformants were grown on agar plates containing Xgal to detect β‐galactosidase activity. We identified a yvaN disruptant which showed a rapH‐overproducing phenotype. DNA microarray analysis of the yvaN mutant suggested that both rapG and rapH were overproduced, leading to inhibition of srfA expression. In a gel retardation assay, purified His‐tagged YvaN specifically bound to promoter sequences of rapG and rapH. Further footprint and gel retardation analyses using various deleted probes uncovered critical sequences for YvaN binding. In addition, a lacZ fusion analysis confirmed the significance of YvaN binding for transcription regulation of rapG and rapH. Thus, YvaN was renamed RghR (rapG and rapH repressor). As the rapH gene is activated by ComK and RapH inhibits comK indirectly, this constitutes an autoregulatory loop modulated by RghR.
Direct repeat‐mediated deletion of a type IV pilin gene results in major virulence attenuation of Francisella tularensis
Authors: Forslund Anna‐Lena , Kuoppa Kerstin , Svensson Kerstin , Salomonsson Emelie , Johansson Anders , Byström Mona , Oyston Petra C. F. , Michell Stephen L. , Titball Richard W. , Noppa Laila , Frithz‐Lindsten Elisabet , Forsman Mats , Forsberg Åke 
Published: February 2006

Summary Francisella tularensis, the causative agent of tularaemia, is a highly infectious and virulent intracellular pathogen. There are two main human pathogenic subspecies, Francisella tularensis ssp. tularensis (type A), and Francisella tularensis ssp. holarctica (type B). So far, knowledge regarding key virulence determinants is limited but it is clear that intracellular survival and multiplication is one major virulence strategy of Francisella. In addition, genome sequencing has revealed the presence of genes encoding type IV pili (Tfp). One genomic region encoding three proteins with signatures typical for type IV pilins contained two 120 bp direct repeats. Here we establish that repeat‐mediated loss of one of the putative pilin genes in a type B strain results in severe virulence attenuation in mice infected by subcutaneous route. Complementation of the mutant by introduction of the pilin gene in cis resulted in complete restoration of virulence. The level of attenuation was similar to that of the live vaccine strain and this strain was also found to lack the pilin gene as result of a similar deletion event mediated by the direct repeats. Presence of the pilin had no major effect on the ability to interact, survive and multiply inside macrophage‐like cell lines. Importantly, the pilin‐negative strain was impaired in its ability to spread from the initial site of infection to the spleen. Our findings indicate that this putative pilin is critical for Francisella infections that occur via peripheral routes.
Flocculation, adhesion and biofilm formation in yeasts
Authors: Verstrepen Kevin J. , Klis Frans M. 
Published: February 2006

SummaryYeast cells possess a remarkable capacity to adhere to abiotic surfaces, cells and tissues. These adhesion properties are of medical and industrial relevance. Pathogenic yeasts such as Candida albicans and Candida glabrata adhere to medical devices and form drug‐resistant biofilms. In contrast, cell–cell adhesion (flocculation) is a desirable property of industrial Saccharomyces cerevisiae strains that allows the easy separation of cells from the fermentation product. Adhesion is conferred by a class of special cell wall proteins, called adhesins. Cells carry several different adhesins, each allowing adhesion to specific substrates. Several signalling cascades including the Ras/cAMP/PKA and MAP kinase (MAPK)‐dependent filamentous growth pathways tightly control synthesis of the different adhesins. Together, these pathways trigger adhesion in response to stress, nutrient limitation or small molecules produced by the host, such as auxin in plants or NAD in mammals. In addition, adhesins are subject to subtelomeric epigenetic switching, resulting in stochastic expression patterns. Internal tandem repeats within adhesin genes trigger recombination events and the formation of novel adhesins, thereby offering fungi an endless reservoir of adhesion properties. These aspects of fungal adhesion exemplify the impressive phenotypic plasticity of yeasts, allowing them to adapt quickly to stressful environments and exploit new opportunities.
Lost in the middle of nowhere: the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans
Authors: Gout Lilian , Fudal Isabelle , Kuhn Marie‐Line , Blaise Françoise , Eckert Maria , Cattolico Laurence , Balesdent Marie‐Hélène , Rouxel Thierry 
Published: February 2006

Summary Leptosphaeria maculans, a Dothideomycete causing stem canker on oilseed rape (Brassica napus), develops gene‐for‐gene interactions with its host plants. To date, nine resistance genes (Rlm1–9) have been identified in Brassica spp. The corresponding nine avirulence genes (AvrLm1–9) in L. maculans have been mapped at four independent loci, thereby revealing two clusters of three and four linked avirulence genes. Here, we report the completion of map‐based cloning of AvrLm1. AvrLm1 was genetically delineated within a 7.3 centimorgan interval corresponding to a 439 kb BAC contig. AvrLm1 is a single copy gene isolated within a 269 kb non‐coding, heterochromatin‐like region. The region comprised a number of degenerated, nested copies of four long‐terminal repeat (LTR) retrotransposons, including Pholy and three novel Gypsy‐like retrotransposons. AvrLm1 restored the avirulent phenotype on Rlm1 cultivars following functional complementation of virulent isolates. AvrLm1 homologues were not detected in other Leptosphaeria species or in known fungal genomes including the closely related species Stagonospora nodorum. The predicted AvrLm1 protein is composed of 205 amino acids, of which only one is a cysteine residue. It contains a peptide signal suggesting extracellular localization. Unlike most other fungal avirulence genes, AvrLm1 is constitutively expressed, with a probable increased level of expression upon plant infection, suggesting the absence of tight regulation of AvrLm1 expression.
Oxidative stress promotes degradation of the Irr protein to regulate haem biosynthesis in Bradyrhizobium japonicum
Authors: Yang Jianhua , Panek Heather R. , O'Brian Mark R. 
Published: February 2006

SummaryThe haem proteins catalase and peroxidase are stress response proteins that detoxify reactive oxygen species. In the bacterium Bradyrhizobium japonicum, expression of the gene encoding the haem biosynthesis enzyme δ‐aminolevulinic acid dehydratase (ALAD) is normally repressed by the Irr protein in iron‐limited cells. Irr degrades in the presence of iron, which requires haem binding to the protein. Here, we found that ALAD levels were elevated in iron‐limited cells of a catalase‐deficient mutant, which corresponded with aberrantly low levels of Irr. Irr was undetectable in wild‐type cells within 90 min after exposure to exogenous H2O2, but not in a haem‐deficient mutant strain. In addition, Irr did not degrade in response to iron in the absence of O2. The findings indicate that reactive oxygen species promote Irr turnover mediated by haem, and are involved in iron‐dependent degradation. We demonstrated Irr oxidation in vitro, which required haem, O2 and a reductant. A truncated Irr mutant unable to bind ferrous haem does not degrade in vivo, and was not oxidized in vitro. We suggest that Irr oxidation is a signal for its degradation, and that cells sense and respond to oxidative stress through Irr to regulate haem biosynthesis.
Characterization of three members of the Arabidopsis carotenoid cleavage dioxygenase family demonstrates the divergent roles of this multifunctional enzyme family
Authors: Auldridge Michele E. , Block Anna , Vogel Jonathan T. , Dabney‐Smith Carole , Mila Isabelle , Bouzayen Mondher , Magallanes‐Lundback Maria , DellaPenna Dean , McCarty Donald R. , Klee Harry J. 
Published: February 2006

Summary Arabidopsis thaliana has nine genes that constitute a family of putative carotenoid cleavage dioxygenases (CCDs). While five members of the family are believed to be involved in synthesis of the phytohormone abscisic acid, the functions of the other four enzymes are less clear. Recently two of the enzymes, CCD7/MAX3 and CCD8/MAX4, have been implicated in synthesis of a novel apocarotenoid hormone that controls lateral shoot growth. Here, we report on the molecular and genetic interactions between CCD1, CCD7/MAX3 and CCD8/MAX4. CCD1 distinguishes itself from other reported CCDs as being the only member not targeted to the plastid. Unlike ccd7/max3 and ccd8/max4, both characterized as having highly branched phenotypes, ccd1 loss‐of‐function mutants are indistinguishable from wild‐type plants. Thus, even though CCD1 has similar enzymatic activity to CCD7/MAX3, it does not have a role in synthesis of the lateral shoot growth inhibitor. Rather, it may have a role in synthesis of apocarotenoid flavor and aroma volatiles, especially in maturing seeds where loss of function leads to significantly higher carotenoid levels.
Identification of AtHD2C as a novel regulator of abscisic acid responses in Arabidopsis
Authors: Sridha Sunandini , Wu Keqiang 
Published: February 2006

SummaryHD2 proteins are plant‐specific histone deacetylases. Little is known about the function of HD2 proteins in plants. In this paper, we report that an Arabidopsis HD2 protein, AtHD2C, is involved in abscisic acid and abiotic stress responses. Analysis of Arabidopsis plants containing the AtHD2C:β‐glucuronidase fusion gene revealed that AtHD2C was constitutive expressed in plants. Furthermore, expression of AtHD2C was repressed by abscisic acid. Over‐expression of 35S:AtHD2C‐GFP in transgenic Arabidopsis plants conferred an abscisic acid‐insensitive phenotype. In addition, 35S:AtHD2C‐GFP transgenic plants displayed reduced transpiration and enhanced tolerance to salt and drought stresses when compared with wild‐type plants. The expression of several abscisic acid‐responsive genes was affected in the 35S:AtHD2C‐GFP plants. Our study provides evidence indicating that AtHD2C can modulate abscisic acid and stress responses.
Post‐transplant lymphoproliferative disorders after lung transplantation: first‐line treatment with rituximab may induce complete remission
Authors: Knoop Christiane , Kentos Alain , Remmelink Myriam , Garbar Christian , Goldman Serge , Feremans Walter , Estenne Marc 
Published: February 2006

Abstract: Background: Post‐transplant lymphoproliferative disorders (PTLD) are potentially lethal complications of solid organ transplantation. We, here, report on our experience with rituximab, an anti‐CD20 monoclonal antibody, as first‐line treatment for PTLD in six lung transplant recipients.Patients and methods: Two of the patients developed PTLD during the first year after transplantation, while four developed late‐onset PTLD. One patient presented with PTLD localized to the graft, one had unilateral cervical lymph nodes, and the others presented with multi‐organ involvement. All patients had diffuse large B‐cell lymphoma. Immunosuppressive therapy was reduced and rituximab was administered at a dose of 375 mg/m2/wk for 4 wk.Results: One patient did not respond to the first two courses of rituximab, received conventional chemotherapy, and achieved complete remission; four patients achieved complete remission after four courses with a median relapse‐free survival of 34 months (range: 14–55); and one patient did not respond and died. The diagnosis of complete remission was established by conventional imaging techniques combined to whole‐body positron emission tomography scan.Conclusions: We conclude that reduction in immunosuppression combined to first‐line treatment with rituximab may induce long‐term complete remission in lung transplant recipients presenting PTLD.
Hepatitis B prophylaxis post‐liver transplant without maintenance hepatitis B immunoglobulin therapy
Authors: Nath Dilip S. , Kalis Ann , Nelson Susan , Payne William D. , Lake John R. , Humar Abhinav 
Published: February 2006

Abstract: Background: We examined outcomes in recipients who underwent a liver transplant for HBV‐induced liver disease and received a protocol for prophylaxis that did not use HBIG maintenance.Results: Between October 2002 and July 2005, a total of 14 liver transplant recipients were identified that met the study criteria. Mean recipient age was 47.6 yr; mean donor age was 37.2 yr. Category of transplant was as follows: cadaveric liver (n=10, 71%), cadaveric split‐liver (n=2, 14%), and cadaveric liver–kidney (n=2, 14%). Liver disease was diagnosed at a mean of 7.3 yr before transplant; three (21%) had a coexisting hepatocellular cancer at the time of transplant. Pre‐transplant, all 14 (100%) recipients were hepatitis B surface antigen (HBsAg) positive, and 11 (79%) were HBV DNA positive (mean viral load of 251.2 pg/mL). Three (21%) were E antigen positive, and one (7%) was D antigen positive. Pre‐transplant, seven patients (50%) were on anti‐viral therapy and there was documented diminution in viral loads after initiating anti‐viral therapy in 3 cases. Three (21%) were hepatitis C virus (HCV) antigen positive and all had low‐RNA titers. With mean follow‐up of 14.1 months, all 14 patients are alive with a functioning graft. Mean ALT, AST and total bilirubin values are currently at 43.2, 32.2, and 0.84, respectively. One recipient remains HBsAg surface antigen positive post‐transplant but has normal lab values. The remaining recipients have no evidence of HBV recurrence by serology and protocol biopsies. The regimen has been well tolerated without the need for drug reduction or discontinuation because of side‐effects.Conclusion: Longer follow‐up is needed, but this regimen may represent an alternative to chronic HBIG maintenance therapy.
Increased ecological amplitude through heterosis following wide outcrossing in Banksia ilicifolia R.Br. (Proteaceae)
Authors: Heliyanto B. , Krauss S. L. , Lambers H. , Cawthray G. R. , Veneklaas E. J. 
Published: February 2006

Abstract
To assess whether wide outcrossing (over 30 km) in the naturally fragmented Banksia ilicifolia R.Br. increases the ecological amplitude of offspring, we performed a comparative greenhouse growth study involving seedlings of three hand-pollinated progeny classes (self, local outcross, wide outcross) and a range of substrates and stress conditions. Outcrossed seedlings outperformed selfed seedlings, with the magnitude of inbreeding depression as high as 62% for seed germination and 37% for leaf area. Wide outcrossed seedlings outperformed local outcrossed seedlings, especially in non-native soils, facilitated in part by an improved capacity to overcome soil constraints through greater root carboxylate exudation. Soil type significantly affected seedling growth, and waterlogging and water deficit decreased growth, production of cluster roots, root exudation and total plant P uptake. Our results suggest that the interaction of narrow ecological amplitude and the genetic consequences of small fragmented populations may in part explain the narrow range of local endemics, but that wide outcrossing may provide opportunities for increased genetic variation, increased ecological amplitude and range expansion.
Babesiosis and blood transfusion: flying under the radar
Authors: Leiby D. A. 
Published: February 2006

Infectious agents of disease continue to plague transfusion medicine as an increasing number of pathogens are described that pose a potential blood safety risk. While the recent focus has been on newly emerged agents, several well‐established pathogens provide timely reminders that other agents continue to pose threats, but invariably ‘fly under the radar’, thereby failing to elicit adequate measures to prevent their transmission by blood transfusion. Perhaps foremost among this group of agents are the Babesia spp., which have been known to cause human disease, in the USA, for close to 40 years. B. microti, B. divergens and several Babesia‐like agents are responsible for a growing number of human babesiosis infections. Concomitantly, in the USA, there has been a sharp rise in the number of transfusion‐transmitted infections of Babesia spp., attributable almost exclusively to B. microti. Despite the obvious public health issues posed by Babesia spp., options for preventing their transmission by blood transfusion remain limited. However, recognition that the Babesia spp. are indeed an ongoing and expanding blood safety threat will probably prove instrumental in the development of viable interventions to limit transmission of these agents.
Preoperative autologous blood donation in primary total knee arthroplasty: a single‐centre experience on 214 consecutive patients
Authors: Franchini M. , Regis D. , Gandini G. , Corallo F. , de Gironcoli M. , Aprili G. 
Published: February 2006

Background and Objectives  Although preoperative autologous blood donation (PABD) is a widespread practice in elective orthopedic surgery, it is controversial whether this procedure avoids allogeneic blood transfusions in patients undergoing total knee arthroplasty (TKA).Patients and Methods  We performed a retrospective study on 214 consecutive patients undergoing PABD before elective primary TKA.Results  Thirty‐eight patients (17·8%) were transfused with autologous red blood cells (RBC), while four of them (10·5% of those requiring transfusions, 1·9% of all patients) also received allogeneic RBC. The transfused patients were, in most cases, female and had significantly lower basal and preoperative haemoglobin levels.Conclusions  Based on the results of this study, PABD is not necessary in most patients undergoing TKA, although older female patients with low basal haemoglobin levels could benefit from a predeposit programme and/or erythropoietin support in order to reduce the risk of exposure to allogeneic blood.
Detection of a new weak A blood‐group allele (Aw11)
Authors: Pruss A. , Heymann G. A. , Braun J. , Kiesewetter H. H. , Salama A. 
Published: February 2006

Background and Objectives  Weak ABO variants may escape tests using unlicensed sera.Materials and Methods  Prior to transfusion, ABO grouping was performed using an automated system and in‐house diluted sera, and manual and bedside test techniques. Genotyping and sequencing were performed using standard methods.Results  Initially, the red blood cells (RBC) of the first‐time blood donor were typed as B, but pretransfusion testing carried out using the bedside test indicated the presence of an additional A phenotype. Serological re‐examination confirmed the bedside test results, and the allele in question was identified, by genotyping, as a new weak A variant (Aw11).Conclusions  The use of CE‐marked and licensed antisera is recommended to avoid ABO mistyping.
Bacterial contamination of platelet concentrates prepared by different methods: results of standardized sterility testing in Germany
Authors: Walther‐Wenke G. , Doerner R. , Montag Th. , Greiss O. , Hornei B. , Knels R. , Strobel J. , Volkers P. , Däubener W. ,   Working party on Bacteria Safety in Transfusion Medicine of the Advisory Board of the German Ministry of Health (Arbeitskreis Blut) , Berlin, Germany
Published: February 2006

Background and Objectives  National guidelines for monitoring the bacterial contamination rate of blood components were introduced in Germany in 1997. The objective of this study was to present and evaluate the results of sterility testing of platelet concentrates (PCs) prepared by different methods.Materials and Methods  The analysis of results of sterility testing of blood component production from transfusion medicine centres in Germany in 1998 and 2001 was based on information collected using standardized questionnaires.Results  The bacterial contamination rates for single‐donor PCs derived from whole blood and apheresis (0·210% vs. 0·156%) were comparable and showed no significant difference. However, pooled PCs produced from four buffy coats using the sterile docking procedure showed a significantly higher bacterial contamination rate compared with single‐donor PCs derived from whole blood and apheresis (0·184% vs. 0·604%).Conclusions  Use of standardized methods for sterility monitoring is sufficient to assess collection and production processes in terms of hygiene and yields reliable data on bacterial contamination rates of blood components. The methods described are suitable for using to analyse the efficiency of newly introduced methods to reduce bacterial contamination rates of blood components (e.g. diversion, bacteria screening and pathogen inactivation).