bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotypic variability in children with growth hormone deficiency associated with posterior pituitary ectopia
Authors: Simon Dominique , Hadjiathanasiou Charalambos , Garel Catherine , Czernichow Paul , Léger Juliane
Published: February 2006

Objective  The cause of posterior pituitary ectopia (PPE) with anterior pituitary hormone deficiencies is unknown. This disease is usually considered sporadic. The objective of this study was to improve the phenotypic characterization of children with PPE and growth hormone deficiency (GHD) to seek insight into the mechanisms underlying abnormal pituitary‐gland development.

Patients and design  Sixty children with GHD and PPE were evaluated in this retrospective chart review (1988–2003).

Results  Known extra‐pituitary birth defects (BD) were present in 31 patients (BD+, 52%) and absent in 29 patients (BD–). Among BD+ patients, seven had well‐defined syndromes (Fanconi anaemia, n = 2; Pallister–Hall, n = 1; Currarino, n = 2; or Stilling–Duane, n = 2) and the other 24 had 53 BDs, mainly involving the brain, eyes and the craniofacial structures (n = 27, 51%) but also affecting the heart, skeleton, kidneys, gastrointestinal tract and skin. Of the 60 patients, seven (12%) were born to consanguineous parents (five sporadic and two familial cases). There were seven (12%) familial cases, with wide variations in clinical presentation, endocrine profiles and magnetic resonance imaging (MRI) findings within families and various patterns consistent with autosomal dominant, recessive or X‐linked transmission.

Conclusion  The high rate of extra‐pituitary BDs and of familial components supports a role for genetic factors in the pathogenesis of this heterogeneous disorder. A detailed record of phenotypic abnormalities in patients with GHD and PPE might produce useful hypotheses for genetic studies.
Ewing's sarcoma of bone: the detection of specific transcripts in a large, consecutive series of formalin‐fixed, decalcified, paraffin‐embedded tissue samples using the reverse transcriptase‐polymerase chain reaction
Authors: Mangham D C , Williams A , McMullan D J , McClure J , Sumathi V P , Grimer R J , Davies A M
Published: February 2006

Aims : (i) To report on the routine use of the reverse transcriptase‐polymerase chain reaction (RT‐PCR) technique on decalcified or non‐decalcified, formalin‐fixed, paraffin‐embedded tissue (FFPET) for translocation detection, with particular emphasis on improved RNA extraction methodology and the use of PCR primers designed to generate small amplicons. (ii) To report on the relative incidences of translocation types and transcript variants in a large, single institution series of Ewing's sarcoma of bone.

Methods and results : Using RT‐PCR to detect specific transcript variants, we analysed FFPET from 54 consecutive cases of Ewing's sarcoma of bone. We used ‘gold standard’ detection methods on corresponding fresh and fresh frozen tissue to validate the technique. We have demonstrated the effective use of RT‐PCR on decalcified and non‐decalcified FFPET samples for sarcoma‐specific translocation detection (96% sensitivity, 100% specificity). Tissue decalcification did not affect the detection rate. The relative incidence of Ewing's sarcoma‐specific translocation types and transcript variants was entirely consistent with previously published data.

Conclusions : With equal effectiveness, RT‐PCR can be applied to both acid decalcified and non‐decalcified FFPET for (Ewing's sarcoma) translocation detection and the technique can be introduced into routine practice in histopathology departments.
Finding of conjunctival melanocytic pigmented lesions within pterygium
Authors: Perra M T , Colombari R , Maxia C , Zucca I , Piras F , Corbu A , Bravo S , Scarpa A , Sirigu P
Published: February 2006

Aims : Conjunctival pigmented lesions have characteristic clinical and histopathological appearances. Melanocytic pigmented lesions commonly occur in the conjunctiva, although they have not been previously reported in pterygium, a common lesion which originates from conjunctiva. Our aim was to evaluate the possibility of an association between pterygium and conjunctival melanocytic pigmented lesions.

Methods and results : A total of 80 samples of pterygium excised from Ecuadorian patients in 2002 were collected. Clinical data were available regarding age, sex, race and place of residence. Histological sections were evaluated for the presence of melanocytic pigmented lesions. Nine cases of conjunctival melanocytic, pigmented lesions within pterygium were found and were classified according to the histopathological criteria previously published for pigmented lesions of the conjunctiva, as naevi and primary acquired melanosis (PAM) with varying degrees of atypia. Five of the nine cases showed primary acquired melanosis without atypia, while two cases had atypia; one case showed features of compound naevus and one lesion was designated as subepithelial naevus.

Conclusions : Our findings suggest that conjunctival melanocytic, pigmented lesions occasionally occur in pterygium. All surgically removed pterygia should undergo careful histopathological examination.
Granular cell tumours of the gastrointestinal tract: expression of nestin and clinicopathological evaluation of 11 patients
Authors: Parfitt J R , McLean C A , Joseph M G , Streutker C J , Al‐Haddad S , Driman D K
Published: February 2006

Aims : Granular cell tumours (GCTs) in the gastrointestinal (GI) tract are rare, with few series reported in the literature. Nestin is a recently identified intermediate filament protein that is expressed in neuroectodermal stem cells and skeletal muscle progenitor cells and has been shown to be expressed in gastrointestinal stromal tumours (GISTs) and GI schwannomas. Herein, we describe the clinicopathological and immunohistochemical features of 11 GI GCTs, introducing nestin as an additional marker that identifies these tumours.

Methods and results : The archives of the departments of pathology at London Health Sciences Centre (London, Ontario) and St Michael's Hospital (Toronto, Ontario) were searched for GCTs occurring in the GI tract, yielding 11 cases. Histological features were assessed and immunohistochemistry was performed with S100 protein, nestin, glial fibrillary acidic protein (GFAP), CD34, desmin, CD117, and inhibin‐α. Charts were reviewed for clinical information. Ages at diagnosis ranged from 31 to 73 years; there were six males and four females. All GCTs were solitary, six in the oesophagus, three in the caecum, one in the rectum and one perianal. Most lesions were discovered incidentally. The size of the GCTs ranged from 4 mm to 30 mm. All were submucosal, typically firm, with a white‐yellow appearance. Histologically, the GCTs showed moderate cellularity, predominantly solid growth with areas of nesting. While lesional cells were mainly plump and polygonal, areas of spindling were present in several tumours, more frequently in the colorectum. Margins were circumscribed. Nuclei were round to oval, with even chromatin and small nucleoli. Mitoses were rare to absent and necrosis was absent in all cases. Staining with periodic acid–Schiff, with diastase predigestion, showed globular and diffuse positivity within the cytoplasm. Moderate to strong expression of S100 protein and nestin was observed in 11 of 11 and seven of seven tumours, respectively. GFAP, CD34, desmin, CD117 and inhibin‐α were negative. While patients were variably managed with resection or observation, all remain clinically well, without disease progression.

Conclusions : Although rare, GI GCTs have characteristic clinicopathological features. Nestin may be a useful immunohistochemical marker for identifying these tumours; the presence of this persistent stem cell cytoskeletal filament within GI GCTs suggests that these lesions may arise from a multipotential stem cell in the GI tract.
Duodenal intraepithelial lymphocytosis during Helicobacter pylori infection is reduced by antibiotic treatment
Authors: Nahon S , De Serre N Patey‐Mariaud , Lejeune O , Huchet F‐X , Lahmek P , Lesgourgues B , Traissac L , Bodiguel V , Adotti F , Tuszynski T , Delas N
Published: February 2006

Aim : To evaluate clinical, biological and immunological features of patients with increased duodenal intraepithelial lymphocytes (IELs), and its relation to Helicobacter pylori (HP) and coeliac disease (CD).

Methods : We have studied all patients accrued over a 4‐year period with increased duodenal IELs. Those patients were recalled for biological and immunological evaluation and a second endoscopy.

Results : Twenty‐three from a total of 639 patients were identified and 17 of them were included in the study. The median duodenal IEL count was 59 per 100 epithelial cells. Twelve (71%) patients were HP+; eight of them received HP eradication. At the second endoscopy the duodenal IEL count was significantly lower 2 months after HP eradication (73 versus 28), while the IEL count was unchanged in those patients seronegative for HP (n = 5) or those in whom it was not eradicated (n = 4) (55 versus 55). No patient had coeliac antibodies, four expressed HLA‐DQ2, lower than in the general population, and the prevalence of CD was 2% (12/639 patients).

Conclusion : In some cases an increased duodenal IEL count may be due to an inappropriate host response to HP. HP screening and eradication should be considered before recommending a gluten‐free diet.
Distinct regulation of CD40‐mediated interleukin‐6 and interleukin‐12 productions via mitogen‐activated protein kinase and nuclear factor κB‐inducing kinase in mature dendritic cells
Authors: Yanagawa Yoshiki , Onoé Kazunori
Published: February 2006

The role of mitogen‐activated protein kinase (MAPK) and nuclear factor κB (NF‐κB) pathways, especially NF‐κB‐inducing kinase (NIK)‐mediated alternative pathway, in CD40‐mediated interleukin (IL)‐6 and IL‐12 productions by immature or mature dendritic cells (DCs) was investigated. Murine myeloid DCs were matured by treatment with lipopolysaccharide. CD40 ligation induced modest or vigorous cytokine productions in immature or mature DCs, respectively. After CD40 ligation, p38 MAPK was significantly activated in either immature or mature DCs. SB203580, a p38 MAPK inhibitor, markedly decreased CD40‐mediated IL‐6 and IL‐12 productions in immature DCs. In mature DCs, SB203580 significantly decreased CD40‐mediated IL‐6 but not IL‐12 production. On the other hand, CD40 ligation induced vigorous activation of the NF‐κB alternative pathway including p100 phosphorylation and subsequent nuclear translocations of p52, a processed form of p100, and RelB in mature but not immature DCs. The CD40‐mediated phosphorylation of p100 was completely abolished in NIK‐mutated mature DCs. The NIK mutation markedly reduced CD40‐mediated IL‐12 but not IL‐6 production by mature DCs. Taken together, we concluded that IL‐6 and IL‐12 productions in response to CD40 ligation were controlled by p38 MAPK and NIK mediated alternative pathway, respectively, in mature DCs.
The impact of sulphur dioxide and oxygen on the behaviour of 2‐furaldehyde in beer: an industrial approach
Authors: Carneiro José Ricardo , Guido Luis Ferreira , Almeida Paulo José , Rodrigues José António , Barros Aquiles Araújo
Published: February 2006

2‐Furaldehyde is often used as an analytical indicator of beer flavour deterioration. Although 2‐furaldehyde itself has a flavour threshold far above levels generally present in beer, it can be used as a good marker of heat damage of beer. A reversed‐phase liquid chromatographic assay, using ultraviolet‐visible detection, was applied to investigate the behaviour of 2‐furaldehyde throughout the brewing process and during extended storage of beer. The impact of storage temperature, sulphur dioxide and oxygen content on the level of 2‐furaldehyde was studied. It was found that the concentration of 2‐furaldehyde markedly increases during wort boiling and is rapidly reduced by yeast during the first hours of fermentation, emphasising the yeast reducing capacity as a determinant factor for the 2‐furaldehyde content found in the final beer. The results obtained suggest that sulphur dioxide and oxygen content play a key role on the 2‐furaldehyde content in packaged beer. 2‐Furaldehyde increase during ageing is oxygen dependent and sulphur dioxide retards its development by possibly protecting beer against the occurrence of oxidative reactions.
Mantram repetition for stress management in veterans and employees: a critical incident study
Authors: Bormann Jill E. , Oman Doug , Kemppainen Jeanne K. , Becker Sheryl , Gershwin Madeline , Kelly Ann
Published: February 2006

Aim.  This paper reports a study assessing the usefulness of a mantram repetition programme.

Background.  Complementary/alternative therapies are becoming commonplace, but more research is needed to assess their benefits. A 5‐week programme teaching a ‘mind–body–spiritual’ technique of silently repeating a mantram – a word or phrase with spiritual meaning – to manage stress was developed. A mantram was chosen by individuals, who were taught to repeat it silently throughout the day or night to interrupt unwanted thoughts and elicit the relaxation response.

Methods.  Participants who attended a 5‐week course were invited to participate in the study. Of those who consented, a randomly selected subset (n = 66) was contacted approximately 3 months after the course for a telephone interview using the critical incident interviewing technique. Participants were asked whether the intervention was helpful or not, and if helpful, to identify situations where it was applied. Interviews were transcribed and incidents were identified and categorized to create a taxonomy of uses. The data were collected in 2001–2002.

Results.  Participants included 30 veterans, mostly males (97%), and 36 hospital employees, mostly females (86%). Mean age was 56 years (sd = 12·94). Fifty‐five participants (83·3%) practiced the technique and reported 147 incidents where the programme was helpful. Outcomes were organized into a taxonomy of incidents using four major categories that included managing: (a) emotions other than stress (51%); (b) stress (23·8%); (c) insomnia (12·9%); and (d) unwanted thoughts (12·3%). A group of raters reviewed the categories for inter‐rater reliability.

Conclusions.  The majority of participants from two distinct samples reported that the mantram programme was helpful in a variety of situations. The critical incident interviewing method was found to be practical, efficient, and thorough in collecting and analyzing data. Such qualitative methods contribute to understanding the benefits of mind–body complementary therapies.
HIV/AIDS knowledge, attitudes and beliefs among Nepalese adolescents
Authors: Mahat Ganga , Scoloveno Mary Ann
Published: February 2006

Aim.  This paper reports an exploration of Nepalese adolescents’ knowledge, attitudes and beliefs of HIV/AIDS.

Background.  Nepal is confronted with an increasing incidence of HIV/AIDS among adolescents and young adults. A priority of nurses and other health professionals in Nepal is the prevention of the spread of HIV infection. The first step in prevention is assessing the HIV/AIDS knowledge, attitudes and beliefs of adolescents.

Methods.  A cross‐sectional correlational design was carried out in 2003 in a private school in Kathmandu, Nepal. A total of 150 adolescents participated in the study. Two instruments were used: a demographic questionnaire and the Youth Survey, which included questions on knowledge, attitudes and beliefs.

Findings.  The majority of the adolescents had a moderate level of overall HIV/AIDS knowledge, but lacked knowledge in the areas of mode of transmission and prevention of HIV/AIDS. Approximately 79% thought that AIDS was a big problem and 67% were afraid of getting AIDS. However, only 16·7% reported that they were likely to get AIDS, and 18·7% did not perceive living in Kathmandu as a risk for HIV/AIDS.

Conclusion.  The findings of this study will help policymakers and healthcare professionals develop a culturally sensitive and needs specific educational programme for urban Nepalese adolescents. The findings may also have lessons for public health and school nurses working in similar contexts. Nurses, and more specifically public health nurses in Nepal, need to play an active role in the development and implementation of educational programs on HIV/AIDS. Research needs to be done in rural as well as urban areas of Nepal on adolescents’ HIV/AIDS knowledge, attitudes and beliefs.
Feasibility and acceptability of providing nurse counsellor genetics clinics in primary care
Authors: Westwood Greta , Pickering Ruth M , Latter Sue , Lucassen Anneke , Little Paul , Karen Temple I.
Published: February 2006

Aim.  This paper reports a pilot study to test the feasibility of providing genetic nurse counsellor clinics in primary care in the United Kingdom, to develop a questionnaire to evaluate patients’ satisfaction with their genetics appointments, and to establish patient and provider costs.

Background.  Genetic counsellors are healthcare professionals with experience in medical genetics and counselling and often have a professional background in nursing, science, genetics, psychology, or public health and work as members of multidisciplinary teams. Professional genetic counsellor accreditation is possible in the United Kingdom, United States of America, Australia and Canada. Increasing referrals to specialist genetics services have precipitated a review of models of service delivery in the United Kingdom.

Methods.  A random half of 74 general practices in three primary care trusts were selected for the study, and the patients registered with these practices and referred to the clinical genetics service, were offered an appointment in primary care with a genetic nurse counsellor. A clinic follow‐up postal questionnaire was developed.

Results.  Between July 2002 and May 2003, 64 appointments were offered to patients referred and registered with the selected general practices, 45 (79%) patients attended their appointment and 34 (77%) returned their follow‐up questionnaire. Total mean satisfaction score was high and patients were most satisfied with the information and affective domains of the appointment. Those referred with a family history of cancer were more satisfied than those referred with a non‐cancer diagnosis. Forty‐eight per cent of patients seen by the genetic nurse counsellor did not need to attend a further appointment with a doctor in secondary care. Patients were satisfied with the travel time and distance to clinic and patient clinic costs were low.

Conclusion.  Patients do attend genetic nurse counsellor clinics in primary care, and are satisfied with the new location. A large cluster randomized controlled trial is now being conducted to obtain a controlled comparison of clinic attendance rates and patients’ satisfaction with clinics in primary vs. secondary care settings.
Geographic patterns of diversity in streams are predicted by a multivariate model of disturbance and productivity
Authors: CARDINALE BRADLEY J. , HILLEBRAND HELMUT , CHARLES DONALD F.
Published: February 2006

Univariate explanations of biodiversity have often failed to account for broad‐scale patterns in species richness. As a result, increased attention has been paid to the development and testing of more synthetic multivariate hypotheses. One class of multivariate hypotheses, founded in successional diversity theory, predict that species richness is jointly influenced by periodic disturbances that create new niche opportunities in space or time, and the production of community biomass that speeds displacement of inferior by superior competitors.

While the joint response of diversity to disturbance and productivity has gained support from theoretical and small‐scale experimental studies, evidence that corresponding patterns of biodiversity occur broadly across natural systems is scarce.

Using a data set that employed standardized methods to sample 85 streams throughout the mid‐Atlantic United States of America, we show that biogeographical patterns of primary producer diversity in stream ecosystems are consistent with the predictions of a multivariate model that incorporates disturbance frequency and community biomass production as independent variables. Periphyton species richness is a concave‐down function of disturbance frequency (mean no. floods year−1) and of biomass production (µg of biomass accrual cm−2 day−1), and an increasing function of their interaction.

Changes in richness across the disturbance × productivity response surface can be related to several predicted life‐history traits of the dominant species.

Our findings complement prior studies by showing that multivariate models which consider interactive effects of community production and ecosystem disturbance are, in fact, candidate explanations of much broader patterns of richness in natural systems. Because multivariate models predict synergistic effects of ecological variables on species diversity, human activities – which are simultaneously altering both the disturbance regime and productivity of streams – could be influencing biodiversity more than previously anticipated.
Herbivore‐induced plant volatiles induce an indirect defence in neighbouring plants
Authors: KOST C. , HEIL M.
Published: February 2006

Many plant species respond to herbivory with increased emission of volatile organic compounds (VOCs): these attract carnivorous arthropods and thereby function as an indirect defence mechanism. Whether neighbouring plants can ‘eavesdrop’ on such airborne cues and tailor their defences accordingly, remains controversial.

We used Lima bean plants (Phaseolus lunatus) to investigate whether herbivore‐induced VOCs induce another indirect defence strategy, i.e. the secretion of extrafloral nectar (EFN) in conspecific plant neighbours, and whether this enhances the defence status of the receiving plant under natural conditions.

EFN secretion was induced by VOCs released from herbivore‐damaged bean tendrils as well as by a synthetic VOC mixture resembling the natural one. One constituent of the herbivore‐induced blend – the green leaf volatile (3Z)‐hex‐3‐enyl acetate – was sufficient to elicit the defence reaction.

A long‐term experiment comparing the defensive effect of EFN alone with the VOC‐mediated effect (EFN induction plus attraction of plant defenders) suggested that Lima bean benefits from both indirect defences. Repeated treatment of tendrils with either an artificial blend of VOCs or with EFN led to the attraction of a higher cumulative number of predatory and parasitoid insects (i.e. ants and wasps) as well as to less herbivore damage and an increased production of inflorescences and leaves.

Our results demonstrate that one indirect defence mechanism can induce another one in conspecific plants, and that Lima bean plants can benefit from this VOC‐induced EFN secretion under natural conditions. Both extrafloral nectaries and the capability to release VOCs upon herbivory are present in many plant taxa and airborne signalling may thus represent a common mechanism for regulating the secretion of EFN in plant parts which face an increased risk of herbivory.
Genetic variation and relationships among eight Indian riverine buffalo breeds
Authors: KUMAR SATISH , GUPTA JALAJ , KUMAR NIRAJ , DIKSHIT KIRTI , NAVANI NAVEEN , JAIN PRADEEP , NAGARAJAN MUNIYANDI
Published: February 2006

Twenty‐seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy–Weinberg equilibrium were observed for 26 locus‐breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of FST index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour‐joining tree constructed from chord distances, multidimensional scaling (MDS) display of FST values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800–2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes.
Effect of disturbances on the genetic diversity of an old‐forest associated lichen
Authors: WERTH SILKE , WAGNER HELENE H. , HOLDEREGGER ROLF , KALWIJ JESSE M. , SCHEIDEGGER CHRISTOPH
Published: February 2006

Lichens associated with old forest are commonly assumed to be negatively affected by tree logging or natural disturbances. However, in this study performed in a spruce‐dominated sylvopastoral landscape in the Swiss Jura Mountains, we found that genetic diversity of the epiphytic old‐forest lichenLobaria pulmonariadepends on the type of disturbance. We collected 923 thalli from 41 sampling plots of 1 ha corresponding to the categories stand‐replacing disturbance (burnt), intensive logging (logged) and uneven‐aged forestry (uneven‐aged), and analysed the thalli at six mycobiont‐specific microsatellite loci. We found evidence for multiple independent immigrations into demes located inburntandloggedareas. Using spatial autocorrelation methods, the spatial scale of the genetic structure caused by the clonal and recombinant component of genetic variation was determined. Spatial autocorrelation of genotype diversity was strong at short distances up to 50 m inloggeddemes, up to 100 m inuneven‐ageddemes, with the strongest autocorrelation up to 150 m forburntdemes. The spatial autocorrelation was predominantly attributed to clonal dispersal of vegetative propagules. After accounting for the clonal component, we did not find significant spatial autocorrelation in gene diversity. This pattern may indicate low dispersal ranges of clonal propagules, but random dispersal of sexual ascospores. Genetic diversity was highest inloggeddemes, and lowest inburntdemes. Our results suggest that genetic diversity of epiphytic lichen demes may not necessarily be impacted by stand‐level disturbances for extended time periods.
Correlates of genetic differentiation and isolation by distance in 17 congenericSilenespecies
Authors: MOYLE LEONIE C.
Published: February 2006

The contemporary pattern of intraspecific genetic variation can indicate the relative role of gene flow and local differentiation in shaping the evolutionary history and future trajectory of a species. To assess the recent influence of contrasting life history and demographic characteristics on genetic structure within a group of closely related species, patterns of genetic differentiation (FSTand related statistics) and isolation by distance (IBD) were compared among 17 congeneric herbaceous plant species. Data came from 35 published studies of 16 species, and a previously unpublished analysis of chloroplast genetic variation in the rare endemicSilene rotundifolia. Among‐population genetic variance was most strongly influenced by the type of genetic marker used; cytoplasmic markers showed larger values than allozyme and anonymous nuclear markers. Other independently significant factors were geographical range size and, for allozyme studies, reproductive system; in particular, endemism and hermaphroditism were associated with higher among‐population genetic variance, whereas large native geographical range and dioecy were associated with lower among‐population variance. Over equivalent spatial scales, dioecious populations also showed weaker IBD than hermaphrodites, perhaps because increased population transience and/or variance in the spatial pattern of gene flow are more closely associated with dioecy in this genus. Invasive populations had both highly variable among‐population genetic variance, and no evidence for IBD, consistent with nonequilibrium conditions. Other analysed factors including predominant pollinator had no discernable influence on genetic structure or patterns of IBD. In general, this comparative approach appears to be valuable for synthesizing the complementary information provided byF‐statistics and IBD, and for indicating the relative importance of particular biological factors in shaping genetic variation within different species of a closely related plant group.
Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation
Authors: KURODA Y. , KAGA A. , TOMOOKA N. , VAUGHAN D. A.
Published: February 2006

The research objectives were to determine aspects of the population dynamics relevant to effective monitoring of gene flow in the soybean crop complex in Japan. Using 20 microsatellite primers, 616 individuals from 77 wild soybean (Glycine soja) populations were analysed. All samples were of small seed size (< 0.03 g), were directly collected in the field and came from all parts of Japan where wild soybeans grow, except Hokkaido. Japanese wild soybean showed significant reduction in observed heterozygosity, low outcrossing rate (mean 3.4%) and strong genetic differentiation among populations. However, the individual assignment test revealed evidence of rare long‐distance seed dispersal (> 10 km) events among populations, and spatial autocorrelation analysis revealed that populations within a radius of 100 km showed a close genetic relationship to one another. When analysis of graphical ordination was applied to compare the microsatellite variation of wild soybean with that of 53 widely grown Japanese varieties of cultivated soybean (Glycine max), the primary factor of genetic differentiation was based on differences between wild and cultivated soybeans and the secondary factor was geographical differentiation of wild soybean populations. Admixture analysis revealed that 6.8% of individuals appear to show introgression from cultivated soybeans. These results indicated that population genetic structure of Japanese wild soybean is (i) strongly affected by the founder effect due to seed dispersal and inbreeding strategy, (ii) generally well differentiated from cultivated soybean, but (iii) introgression from cultivated soybean occurs. The implications of the results for the release of transgenic soybeans where wild soybeans grow are discussed.
Microsatellite analysis of the phylogeography, Pleistocene history and secondary contact hypotheses for the killifish,Fundulus heteroclitus
Authors: ADAMS STEPHANIE M. , LINDMEIER JAMES B. , DUVERNELL DAVID D.
Published: February 2006

The mummichog,Fundulus heteroclitus, exhibits extensive latitudinal clinal variation in a number of physiological and biochemical traits, coupled with phylogeographical patterns at mitochondrial and nuclear DNA loci that suggest a complicated history of spatially variable selection and secondary intergradation. This species continues to serve as a model for understanding local and regional adaptation to variable environments. Resolving the influences of historical processes on the distribution of genetic variation within and among extant populations ofF. heteroclitusis crucial to a better understanding of how populations evolve in the context of contemporary environments. In this study, we analysed geographical patterns of genetic variation at eight microsatellite loci among 15 populations ofF. heteroclitusdistributed throughout the North American range of the species from Nova Scotia to Georgia. Genetic variation in Northern populations was lower than in Southern populations and was strongly correlated with latitude throughout the species range. The most common Northern alleles at all eight loci exhibited concordant latitudinal clinal patterns, and the existence of an abrupt transition zone in allele frequencies between Northern and Southern populations was similar to that observed for mitochondrial DNA and allozyme loci. A significant pattern of isolation by distance was observed both within and between northern and southern regions. This pattern was unexpected, particularly for northern populations, given the recent colonization history of post‐Pleistocene habitats, and was inconsistent with either a recent northward population expansion or a geographically restricted northern Pleistocene refugium. The data provided no evidence for recent population bottlenecks, and estimates of historical effective population sizes suggest that post‐Pleistocene populations have been large throughout the species distribution. These results suggest thatF. heteroclituswas broadly distributed throughout most of its current range during the last glacial event and that the abrupt transition in allele frequencies that separate Northern and Southern populations may reflect regional disequilibrium conditions associated with the post‐Pleistocene colonization history of habitats in that region.
A new method to estimate relatedness from molecular markers
Authors: FERNÁNDEZ J. , TORO M. A.
Published: February 2006

Four 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

Rap 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

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

Yeast 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

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

The 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

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

HD2 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.
Overcoming diabetic gastroparesis en route to kidney transplant
Authors: De Csepel John , Jack Angela , El‐Sabrout Rafik , Butt Khalid
Published: February 2006

Abstract: Gastroparesis is a debilitating condition that affects a significant number of diabetic patients. Some of these patients have end‐stage renal disease and are in need of kidney transplant. Symptoms of gastroparesis include: early satiety, pyrosis, epigastric pain, nausea and vomiting, which may lead to caloric and electrolyte deficiencies as well as significant weight loss. A viable option for diabetic gastroparesis patients who fail first line treatments consisting of dietary changes and gastric prokinetic medications is gastric electrical stimulator (GES) implantation. We present a 41‐yr‐old man and 35‐yr‐old woman with diabetic gastroparesis, who were initially deemed unacceptable candidates for renal transplantation because of marked malnourishment and a concern that they would not be able to tolerate immunosuppressant medications. In less than two yr following GES implantation, each patient underwent a successful kidney transplant.
Accidental transplantation of a kidney with a cystic renal cell carcinoma following living donation: management and 1 yr follow‐up
Authors: Neipp Michael , Schwarz Anke , Pertschy Stefanie , Klempnauer Jürgen , Becker Thomas
Published: February 2006

Abstract: Transmission of cancer is a fatal risk in organ transplantation. We present a case of incidental renal carcinoma in a kidney obtained from a living donor. A 56‐yr‐old father was evaluated for donation for his 28‐yr‐old daughter. An MRT scan revealed two cysts in the right kidney. Right‐sided donor nephrectomy and subsequent transplantation was performed. The wall of the prominent cyst was partially excised prior to transplantation. Histology revealed a high‐grade renal clear cell carcinoma 10 d after transplantation. Following careful evaluation the recipient underwent partial nephrectomy. Immunosuppression was switched to rapamune. The graft function remained stable. Donor and recipient are without evidence of tumor recurrence 1 yr after transplantation. Our policy to obtain the kidney presenting anatomical variations proved to be beneficial for the donor. In case of transmission of cancer partial resection preserving graft function might be justified.