Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce

Phagocytic ability of neutrophils and monocytes in neonates

<p>Abstract</p> <p>Background</p> <p>Infections by a variety of pathogens are a significant cause of morbidity and mortality during perinatal period. The susceptibility of neonates to bacterial infections has been attributed to immaturity of innate immunity. It is considered that one of the impaired mechanisms is the phagocytic function of neutrophils and monocytes. The purpose of the present study was to investigate the phagocytic ability of neonates at birth.</p> <p>Methods</p> <p>The phagocytic ability of neutrophils and monocytes of 42 neonates was determined using the Phagotest flow cytometry method, that assesses the intake of <it>E. Coli </it>by phagocytes, in cord blood and in peripheral blood 3 days after birth. Fifteen healthy adults were included in the study as controls.</p> <p>Results</p> <p>The phagocytic ability of neutrophils in the cord blood of neonates was significantly reduced compared to adults. The 3^rdpostnatal day the reduction of phagocytic ability of neutrophils was no longer significant compared to adults. The phagocytic ability of monocytes did not show any difference from that of adults either at birth or the 3^rdpostnatal day.</p> <p>Conclusions</p> <p>Our findings indicate that the intake of <it>E. Coli </it>by phagocytes is impaired at birth in both preterm and full term neonates compared to adults. This defect is transient, with the phagocytic ability in neonates reaching that of the adults 3 days after birth.</p

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.publishersversionPeer reviewe

A comparative investigation of student teacher and mentor beliefs during teaching practice

This paper presents the results of comparative research focusing on student teachers&apos; beliefs and mentors&apos; beliefs during teaching practice. This research was part of the evaluation of the Teaching Practice course which is offered to final year students of the Faculty of English Studies of the University of Athens within the framework of the Pre-service Teacher Education and Training programme (PREED) that the Faculty offers. Research has repeatedly shown that student teachers have well entrenched beliefs and attitudes about teaching and expectations about the role of the teacher which have been formed on the basis of their own experiences as pupils and images of &quot; good&quot; teachers (apprenticeship of observation). These inherent beliefs are stable and act as filters through which student teachers interpret new information and approach classroom practice. Their beliefs strongly influence their own developing practice and what and how student teachers learn during teacher education programmes. Research has shown that practice teaching experiences may help student teachers in modifying their preconceived ideas about teaching and classroom instruction when encouraged by experienced mentor teachers to confront and reflect on their beliefs. But mentor beliefs need to be compatible with the aims of the pre-service teacher education programme in order to positively influence student teacher beliefs. The research thus sought to investigate the compatibility of student teacher and mentor beliefs and the extent to which these were in line with principles of the Pre-service Teacher Education and Training programme (PRE-ED). Student teachers&apos; and mentor&apos; beliefs were investigated through questionnaires administered to 100 students and their mentors after teaching practice. The results of the questionnaires were particularly revealing as regards the effect of the experienced mentor teachers and the school culture on student teacher&apos;s beliefs and provide useful insights for the design of teacher education programmes. © Common Ground, Evdokia Karavas, Mary Drossou, All Rights Reserved, Permissions

Genome and species relationships in genus Avena based on RAPD and AFLP molecular markers

Species and genome relationships among 11 diploid (A and C genomes), five tetraploid (AB and AC genomes) and two hexaploid (ACD genome) Avena taxa were investigated using amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers. The two primer pairs used for the AFLP reactions produced a total of 354 polymorphic bands, while 187 reproducible bands were generated using ten RAPD primers. Genetic similarities amongst the entries were estimated using the Jaccard and Dice algorithms, and cluster analyses were performed using UPGMA and neighbor joining methods. Principle coordinate analysis was also applied. The highest cophenetic correlation coefficient was obtained for the Jaccard algorithm and UPGMA clustering method ( r=0.99 for AFLP and r=0.94 for RAPD). No major clustering differences were present between phenograms produced with AFLPs and RAPDs. Furthermore, data produced with AFLPs and RAPDs were highly correlated ( r=0.92), indicating the reliability of our results. All A genome diploid taxa are clustered together according to their karyotype. The AB genome tetraploids were found to form a subcluster within the A(s )genome diploids (AFLPs), indicating their near-autoploid origin. The AC genome tetraploids are clustered to the ACD genome hexaploids. Finally, the C genome diploids form an outer branch, indicating the major genomic divergence between the A and C genomes in Avena

Acute Bone Marrow Aplasia Associated with Intravenous Administration of Deferoxamine (Desferrioxamine)

The authors report the clinical course and fatal outcome of a case of acute bone marrow aplasia, after intravenous administration of deferoxamine (desferrioxamine) to a 16-year-old girl with homozygous β-thalassaemia. The type of aplasia was mainly that of a megakaryocytic thrombocytopenia, but the 2 other haemopoetic series were also involved. The absence of any other toxic factors and the quite rapid onset of the bone marrow failure after this type of treatment strongly suggest that intravenous administration of high doses of deferoxamine was the potential toxic factor. © 1990, ADIS Press Limited. All rights reserved

Early abnormal amplitude-integrated electroencephalography (aEEG) is associated with adverse short-term outcome in premature infants

Background: In preterm infants with IVH the electrocortical background activity is affected and there is a correlation between the severity of cerebral injury to the degree of depression, however the usefulness of the early aEEG recordings has hardly been determined. Aim: To identify early aEEG features that could be used as prognostic markers for severe brain injury in prematures. Methods: In 115 infants, 25-32 wk GA, aEEG recordings during the first 72 h of life were correlated with head ultrasound findings. Continuity (Co), sleep-wake cycling (Cy) and amplitude of the lower border (LB) of the aEEG were evaluated by semi-quantitative analysis. Results: The infants were divided into four groups based on head ultrasound findings: A (n = 72, normal), B [n = 16, grades 1-2 intraventricular hemorrhage (IVH)], C (n = 21, grades 3-4 IVH) and D (n = 6, periventricular leukomalacia). 18 infants (16 of group C and 2 of group D) died during hospitalization. Significantly lower values of all aEEG features were found in group C infants. The presence of pathological tracings (burst-suppression, continuous low-voltage, flat trace) or discontinuous low-voltage (DLV), the absence of Cy and LB < 3 mu V in the initial aEEG displayed a sensitivity of 88.9%, 63% and 51.9% respectively, for severe brain injury. Logistic regression of aEEG features and GA to the presence or absence of severe injury revealed that only Co was significantly correlated to outcome. Using this feature 83.19% of cases were correctly classified. Conclusion: Pathological tracings or DLV in the initial aEEG is predictive for poor short-term outcome in premature neonates. (C) 2012 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved

The influence of extrauterine life on the aEEG maturation in normal preterm infants

Objective: To study, the maturational changes of the amplitude-integrated electroencephalogram (aEEG) in preterm infants without neurological disorders and especially the influence of the duration of extrauterine life, over this process. Methods: 96 preterm infants, 25-34 weeks' gestational age (CA) at birth, clinically stable and without ultrasonographic evidence of neurological abnormalities, were studied. The aEEG recordings were obtained within 72 h of life and then weekly until discharge. Four aspects of each tracing (continuity. sleep-wake cycling, bandwidth, and lower border), were evaluated by visual analysis, applying pre-established criteria. Results: We analysed 624 aEEG recordings at postmenstrual age (PMA) of 25-42 weeks. With advanced CA the aEEG becomes more continuous (p: 0.022), it displays definite sleep-wake cycles (p: 0.011), and its bandwidth acquires the mature pattern (p: 0.012). A positive significant interaction of CA and PMA in the evolution of aEEG was found regarding continuity (p: 0.002), sleep-wake cycling (p: 0.002), and bandwidth (p: 0.02). Conclusion: The evolution of the aEEG tracing depends on both CA and PMA. The older the infants at birth the more mature the aEEG pattern. At the same PMA, preterm infants of lower CA display an advanced maturation of the aEEG comparing with others of higher GA. (c) 2009 Elsevier Ireland Ltd. All rights reserved

Axonal sensorimotor neuropathy in patients with ß-thalassaemia

Methods: Thirty six patients with a mean age of 29.2±8.2 years and 17 healthy controls with a mean age of 27.6±9.1 were included in this study. Measurements included the neuropathy symptoms score (NSS), the neuropathy disability score (NDS) as well as nerve conduction studies of two motor (ulnar and peroneal) and two sensory (ulnar and sural) nerves of the right limbs. Results: A mainly sensory axonal polyneuropathy was present in 19 out of 36 patients (52.7%). Eight out of these 19 patients also had abnormal NDS values. The neuropathy correlated significantly with the age of the patients and the hematocrit. However, it did not correlate with the presence of antibodies against HCV, the ferritin levels, or with a history of transfusions, desferrioxamine treatment, or splenectomy. Conclusions: This study showed a high prevalence of a predominantly sensory neuropathy in patients with ß-thalassaemia. The electrophysiological data suggest that the underlying pathology is an axonopathy. Chronic hypoxia of the nerves resulting from severe anaemia may contribute to the pathogenesis of this neuropathy

Axonal sensorimotor neuropathy in patients with beta-thalassaemia

Objective: The purpose of this study was to investigate the prevalence of peripheral neuropathy in patients with beta-thalassaemia. Methods: Thirty six patients with a mean age of 29.2 +/- 8.2 years and 17 healthy controls with a mean age of 27.6 +/- 9.1 were included in this study. Measurements included the neuropathy symptoms score (NSS), the neuropathy disability score (NDS) as well as nerve conduction studies of two motor ( ulnar and peroneal) and two sensory ( ulnar and sural) nerves of the right limbs. Results: A mainly sensory axonal polyneuropathy was present in 19 out of 36 patients (52.7%). Eight out of these 19 patients also had abnormal NDS values. The neuropathy correlated significantly with the age of the patients and the hematocrit. However, it did not correlate with the presence of antibodies against HCV, the ferritin levels, or with a history of transfusions, desferrioxamine treatment, or splenectomy. Conclusions: This study showed a high prevalence of a predominantly sensory neuropathy in patients with beta-thalassaemia. The electrophysiological data suggest that the underlying pathology is an axonopathy. Chronic hypoxia of the nerves resulting from severe anaemia may contribute to the pathogenesis of this neuropathy