Evolutionary analysis of “hagfish amelogenin”

Hagfishes lack mineralized tissues and teeth. Part of a cDNA strand, allegedly from amelogenin, the major gene involved in enamel formation in mammals, has recently been cloned in a hagfish (Slavkin and Diekwish, Anat. Rec., 1996;245:131–150). This cloning is of great interest because it could change the current view about the evolution of mineralized tissues, but no phylogenetic analysis of this piece of DNA has been made by the authors. Phylogenetic analysis of this part of cDNA has been conducted using both phenetic and cladistic methods. The cDNA amplified in hagfish does not fit with a nonmammalian origin but fits well with a degraded rodent sequence. The gene cloned in hagfish is probably of mammalian origin due to contamination during PCR. Anat. Rec. 252:608–611, 1998. © 1998 Wiley-Liss, Inc.     

Comparison of chromosome analysis and chromosomal microarray analysis: what is the value of chromosome analysis in today’s genomic array era?

PurposeChromosomal microarray analysis enables the detection of microdeletions/duplications and has become the standard in clinical diagnostic testing for individuals with congenital anomalies and developmental disabilities. In the era of genomic arrays, the value of traditional chromosome analysis needs to be reassessed.MethodsWe studied 3,710 unrelated patients by chromosomal microarray analysis and chromosome analysis simultaneously and compared the results.ResultsWe found that chromosomal microarray analysis detected the chromosomal imbalances that were identified by chromosome analysis with the exception of six cases (0.16%) that had mosaic abnormalities. Of note, one case showed mosaicism for two abnormal cell lines, resulting in a balanced net effect and a normal chromosomal microarray analysis. Further structural abnormalities such as unbalanced translocations, rings, and complex rearrangements were subsequently clarified by chromosome analysis in 18% of the cases with abnormal chromosomal microarray analysis results. Apparently balanced rearrangements were detected by chromosome analysis in 30 cases (0.8%).ConclusionOur data demonstrate that although chromosomal microarray analysis should be the first-tier test for clinical diagnosis of chromosome abnormalities, chromosome analysis remains valuable in the detection of mosaicism and delineation of chromosomal structural rearrangements.ConclusionGenet Med 2013:15(6):450–457     

Early detection of idiopathic scoliosis – analysis of three screening models

Introduction

The prevalence of lateral curvatures of the spine ranges from 0.3% to 15.3% in the general population. The aim of the study was to develop and compare three different screening tests for idiopathic scoliosis (IS) with respect to their effectiveness and costs.

Material and methods

The Delphi method was used to assess the efficacy of each screening algorithm in detecting IS in the population. An economic analysis was also performed.

Results

Diagnostic Algorithm 1 for IS comprised a screening examination performed by nurses and a general practitioner (GP) with verification by specialists. The unit cost of carrying out diagnostic work-up for IS in Algorithm 1 was €94 per child. The second algorithm involved the use of the moiré computer method, followed by verification by a specialist. The lower unit cost of €86 per child of diagnostic work-up according to Algorithm 2 was due to fewer stages compared to Algorithm 1. The highest effectiveness with the highest costs were found for the third algorithm, with only one stage, a specialist''s consultation (cost €153 per child).

Conclusions

The number of stages in an algorithm does not correlate positively with its efficacy or cost. The recommended scheme is Algorithm 3, where children are examined by rehabilitation specialists or a physiotherapist using a scoliometer and an inclinometer. The use of the apparently most expensive scheme (Algorithm 3) should result in lowering the costs of treatment of established idiopathic scoliosis and, in the long term, prove to be the most cost-effective solution for the health care system.     

Prognostic value of Y deletion analysis: what is the clinical prognostic value of Y chromosome microdeletion analysis?

In many centres, Y chromosome deletion analysis is still not performed routinely and if so, the results are used for genetic counselling but are not considered as having a useful prognostic value. The type of deletion (AZFa, b or c) has been proposed as a potential prognostic factor for sperm retrieval in men undergoing TESE. AZFc deletions and partial AZFb deletions are associated with sperm retrieval in approximately 50% of cases while in the case of a patient with complete AZFb deletion the probability of finding mature spermatozoa is virtually nil. Therefore the extent and position of a Y microdeletion is important (complete or partial). The prognostic value of Y chromosome deletion analysis in cases of oligozoospermia is important when one considers the progressive decrease of sperm number over time in men with AZFc deletions. Cryo-conservation of spermatozoa in these cases could avoid invasive techniques, such as TESE/ICSI, in the future. Male offspring that are conceived by ICSI or IVF techniques from father with oligozoospermia or azoospermia would also benefit from knowledge of their Y status, since the identification of the genetic defect will render future medical or surgical therapies unnecessary. Y microdeletion screening is therefore important, not only to define the aetiology of spermatogenic failure, but also because it gives precious information for a more appropriate clinical management of both the infertile male and his future male child.     

Immunohistochemical analysis of retroperitoneal Müllerian cyst

Retroperitoneal cysts are uncommon diseases, and benign nonneoplastic Müllerian cysts are extremely rare among the known cases. We report a case of a 35-year-old woman with a retroperitoneal Müllerian cyst with the tubal type of epithelium. The patient presented with a large (20 cm in diameter), palpable abdominal mass. This multilocular cystic mass was resected from the retroperitoneum between the descending colon and the left renal fascia. Histologically, it was lined by monolayered low-cuboidal to columnar cells without atypia that resembled tubal epithelium, including cilia. Loose fibrous tissue and incomplete smooth muscle bundles were identified beneath the epithelium of the lining. Immunohistochemical tests showed that the lining cells were strongly positive for cytokeratins (CKs) (polyclonal, 7, 18, CAM 5.2, AE1/AE3), epithelial membrane antigen, cancer antigen 125, progesterone receptor, and estrogen receptor. The lining cells were also occasionally weakly positive for CK5/6. They tested negative for CK20, carcinoembryonic antigen, calretinin, and CD 10.     

Quantitative peptidomic analysis of the cartilage tissues of different ages北大核心

BACKGROUND: There are many studies on the physiological roles of high-molecular-weight protein in cartilage tissue, but low-molecular-weight peptides are rarely investigated. OBJECTIVE: To conduct a quantitative analysis of cartilage tissue peptide in low- and high-age population, and to screen active peptides related to cartilage development from the differential peptides. METHODS: The cartilage tissue samples from six cases of low age (< 3 years old) and eight cases of high age (6-8 years old) population were collected, cartilage peptides analyzed quantitatively by liquid chromatography tandem mass spectrometry, and the differences in the peptide composition between two groups were analyzed by isotope dimethyl labeling method. RESULTS AND CONCLUSION: We identified 588 differential peptides in the cartilage tissues of two groups, which were originated from 428 proteins. Sixteen peptides were present at higher levels in the high-age group (over 4-fold expression), and 6 were present at higher levels in the low-age group (over 4-fold expression). Through analyzing the molecular mass, isoelectric point and gene ontology of the differential peptides, we preliminarily understand the characteristics of cartilage peptides at molecular level, which provides a new perspective for searching more active cartilage peptides. © 2018, Journal of Clinical Rehabilitative Tissue Engineering Research. All rights reserved.     

Genetic analysis of the requirements for α-actinin function

Null -actinin mutations in Drosophila are lethal and produce conspicuous defects in muscle structure and function. Here, we used transgene rescue to examine the requirements for -actinin function in vivo. First, we tested the ability of a cDNA-based transgene encoding the adult muscle isoform of -actinin under control of the heterologous ubiquitin promoter to rescue the lethality of null -actinin mutations. Successful rescue indicated that alternative splicing, which also generates larval muscle and non-muscle isoforms, was not essential for viability and that there were no strict spatial or temporal requirements for -actinin expression. Secondly, chimeric transgenes, with functional domains of -actinin replaced by similar domains from spectrin, were tested for their ability to rescue -actinin mutants. Replacement of either the actin binding domain or the EF hand calcium binding domain yielded inactive proteins, indicating that these conserved domains were not functionally equivalent. Thirdly, the length of -actinin was modified by adding a 114 amino acid structural repeat from -spectrin to the center of the rod domain of -actinin. Addition of this sequence module was expected to increase the length of the native -actinin molecule by at least 15%, yet was fully compatible with -actinin function as measured by rescued lethality and flight. Thus, unexpectedly, the exact length of -actinin was not critical to its function in the muscle Z disk.     

Morphological analysis of the trachea and pattern of breathing in βENaC-Tg mice

Cystic fibrosis (CF) is caused by mutations in the CFTR (cystic fibrosis transmembrane conductance regulator) gene which is a Cl- channel and a regulator of the epithelial Na+ channel (ENaC). We have recently shown that newborn CFTR-deficient mice exhibit abnormalities of the tracheal cartilage leading to altered ventilation (Bonvin et al., 2008). However, the mechanism by which a lack of CFTR causes tracheal cartilage defects remains unknown. The main goal of the present study was to determine whether the development of airway cartilage defects is related to ENac channel dysfunction. We thus performed macroscopic analysis of the trachea and explored ventilatory function in adult βENaC-overexpressing (βENaC-Tg) mice with airway Na+ hyperabsorption and "CF-lung" lung disease, at 2 and 5 month of age. Only minor cartilaginous abnormalities were observed in 8 out of 16 βENaC-Tg mice and in 2 out of 20 littermate controls. Breathing pattern was progressively altered in βENaC-Tg mice as evidenced by a significant decrease in respiratory frequency. Our results suggest that Na+ hyperabsorption alone is not a major contributor to the development of tracheal malformation observed in CF mice and that breathing pattern changes in βENaC-Tg mice likely reflect airflow limitation due to airway mucus obstruction.     

Prognostic value of Y deletion analysis: How reliable is the outcome of Y deletion analysis in providing a sound prognosis?

Y chromosomal microdeletions at the azoospermia factor (AZF) locus have been implicated as one of the major causes of idiopathic male infertility. The availability of intracytoplasmic sperm injection (ICSI) in treating a variety of male infertility has raised the risk of the transmission of Y microdeletions from father to son. In many IVF centres, Y microdeletion analysis has been used as a diagnostic tool for genetic counselling of infertile couples. Presently, the only prognosis that can be derived from Y microdeletion analysis is that the affected male offspring would benefit from proper clinical management of their infertility. Prognoses based on the pattern of Y microdeletions in relation to phenotype are rather subjective and inconclusive because of insufficient data to derive a definitive correlation whose significance can be determined by statistical analysis. Standardization of the number and choice of sequence-tagged sites (STS), whose deletions result in defective spermatogenesis, for the polymerase chain reaction (PCR) analysis of Y microdeletions would enhance its reliability in the interpretation of the results which is crucial for therapeutic decision-making. Furthermore, in-depth understanding of the gene functions in male infertility, especially at the AZF locus, would contribute greatly to the quality of the prognostic value of Y microdeletion analysis.     

Need for enforcement of ethicolegal education – an analysis of the survey of postgraduate clinical trainees

Background  

The number of medical lawsuits in Japan was between 14 and 21 each year before 1998, but increased to 24 to 35 per year after 1999. There were 210 lawsuits during this 10-year period. There is a need for skills and knowledge related to ethics, which is as fundamental to the practice of medicine as basic sciences or clinical skills. in Japan education in ethics is relatively rare and its importance is not yet recognized. Establishing ethics education using legal precedents, which has already been achieved in Western countries, will be a very important issue in Japan. In the present study, a questionnaire survey was conducted among graduate intern doctors, in order to investigate whether ethics education using precedents might have a positive effect in Japan.     

Loss of heterozygosity analysis: Practically and conceptually flawed?

The Knudson "two-hit" hypothesis has provided the rationale for studies that aim to identify tumor-suppressor genes by mapping regions of allelic loss (loss of heterozygosity, LOH). Although LOH has been found in practically all types of tumors, very few such projects have been successful in identifying their tumor-suppressor targets. The prime explanation for this failure is probably that researchers have, in general, been too credulous about the two-hit hypothesis, and too willing to ignore factors such as intratumor heterogeneity, contamination by normal cells, karyotypic complexity, homozygous deletions, gene dosage changes, and polymerase chain reaction artifacts. We suggest ways of minimizing these problems. Unfortunately, there is no guarantee that existing or newer methods, such as genomic microarrays and in situ single-nucleotide polymorphism analysis, will solve the difficulties of LOH analysis. The future prospects for LOH studies are, as ever, uncertain.     

Is detection of schizocytes by computerised image analysis accurate?

Schistocytes result from red cell fragmentation. The identification of the schistocytes is critical for decisions on appropriate management of the patients. Currently, a systematic approach to the counting method remains rewarded. We programmed a computer image analysis device (Q-Win, Leica) in order to detect fragmented red cells. A good correlation between the computer and a well-trained biologist was found after minor modifications of the computer's results. Image analysis should reduced the biologist-to-biologist variation and improve the identification and enumeration of the schistocytes.     

Protein analysis of tissues—current views and clinical perspectives

Proteomics raises high expectations in finding novel and reliable biomarkers for diagnosis, prognosis and therapy prediction. The goal of the 2-day workshop “Protein analysis of tissues—current views and clinical perspectives” was to bring together scientists from multiple areas of protein research interested in tissue analysis.     

Sequence analysis of the 5′ ends of tomato spotted wilt virus N mRNAs

Summary Messenger RNAs transcribed from the tomato spotted wilt virus (TSWV) RNA genome have characteristic extra non-templated heterogeneous sequences at their 5 ends which may be the result of a cap-snatching event involving cellular mRNAs. In order to investigate the genetic origin of these extra sequences and to gain more insight in the process of cap-snatching as performed by TSWV, nucleocapsid protein (N) mRNAs derived from the TSWV S RNA were cloned and sequenced. Twenty clones were obtained which contained 5-proximal sequences of non-viral origin, ranging in length from 12 to 21 nucleotides. None of the sequences analyzed were identical and no base preference at the endonucleolytic site was observed.     

The homology analysis of internal transcribed spacer sequence of ribosomal DNA in common dermatophytes

In order to analyze the sequences of the internal transcribed spacer (ITS) including the 5.8 S ribosomal DNA (rDNA) of common dermatophytes, so as to obtain a rapid and accurate method to identify the species of dermatophytes and to establish the phylogenetic tree of these species to understand their relationship,16 strains of dermatophytes were collected and preliminarily identified by morphological characteristics. General primers for fungi ITS1 and ITS4 were used to amplify the ITS rDNA of each strains with PCR. The PCR products after purification were sequenced directly and were analyzed through internet. In the results,11 strains were identified by means of morphological features, among which 5 strains were Trichophyton,5 strains were Microsporum and 1 was Epidermaphyton, which was consistent with the results by molecular biology. In the 5 unidentifiable strains, 1 strain was proved to be Chrysosporium by molecular biology. These strains studied could be divided into 3 different classes as indicated in the analysis of the phylogenetic tree of the sequences in ITS, which were quite different from those of morphological classification. It is evident from the above observations that the molecular method of analysis on the ITS sequences is a rapid, highly sensitive and accurate approach for the detection of dematophyte species, however, it still exhibits some limitations needing the supplementation with morphological identification.     

Quantitative Poincaré plot analysis of heart rate variability: effect of endurance training

The aim of the study was to evaluate the effectiveness of the Poincaré plot analysis of heart rate variability (HRV) in observing endurance training-induced changes. Four 10-min manoeuvres were performed (supine lying, standing, steady state exercising and subsequent recovery) by eight control subjects before and after a short-term endurance training and by eight subjects trained for at least 3 years. HRV was assessed by traditional time- and frequency-domain indexes, in parallel with the Poincaré plot analysis. In the latter each R-R interval is plotted as a function of the previous one, and the standard deviations of the instantaneous and long-term R-R interval variability are calculated. In our subjects, the Poincaré scatter grams became gradually narrower from supine to exercising, with progressive parasympathetic withdrawal. Short- and long-term endurance training led to higher aerobic power (p<0.05) and ventilatory threshold shifted towards higher power output (p<0.05). All HRV evaluation methods showed that HRV values were higher after training both during supine lying and standing (p<0.05). The Poincaré scatter grams were wider in the trained state. Standard deviations of the Poincaré plot were significantly correlated with the main parameters of the time- and frequency-domain analyses, especially concerning the parasympathetic indicators. These results suggested that Poincaré plot parameters as well as the "width" of the scatter gram could be considered as surrogates of time- and frequency-domain analysis to assess training-induced changes in HRV.     

Prediction of atrial fibrillation recurrence after cardioversion—Interaction analysis of cardiac autonomic regulation

Today atrial fibrillation (AF) is the most common cardiac arrhythmia in clinical practice accounting for approximately one third of hospitalizations and accompanied with a 5 fold increased risk for ischemic stroke and a 1.5 fold increased mortality risk. The role of the cardiac regulation system in AF recurrence after electrical cardioversion (CV) is still unclear.The aim of this study was to investigate the autonomic regulation by analyzing the interaction between heart rate and blood pressure using novel methods of nonlinear interaction dynamics, namely joint symbolic dynamics (JSD) and segmented Poincaré plot analysis (SPPA). For the first time, we applied SPPA to analyze the interaction between two time series. Introducing a parameter set of two indices, one derived from JSD and one from SPPA, the linear discriminant function analysis revealed an overall accuracy of 89% (sensitivity 91.7%, specificity 86.7%) for the classification between patients with stable sinus rhythm (group SR, n = 15) and with AF recurrence (group REZ, n = 12). This study proves that the assessment of the autonomic regulation by analyzing the coupling of heart rate and systolic blood pressure provides a potential tool for the prediction of AF recurrence after CV and could aid in the adjustment of therapeutic options for patients with AF.     

Design and application research of nucleotide sequence analysis system software

INTRODUCTION　　From integrallevel and celllevel,the research of organism and diseasediagnosishave already entered molecular level.Molecular biology is the science to researchstructure and function of organism macromolecule.Based on differentgene code se-…