Prevalence of trachoma in Pernambuco State, Brazil (2014-2015)

To estimate the prevalence of cases of trachoma in the population at social risk aged 1-9 years in Pernambuco State and its mesoregions. This was a cross-sectional study in which secondary data from the National Household Survey on Trachoma (2014-2015) were analyzed. The study covered 96 census tracts distributed across the mesoregions of Pernambuco State (Metropolitan Region of Recife, Zona da Mata, Agreste, Sertao do Sao Francisco and Sertao Pernambucano). The study included all homes with children aged 1-9 years, and all of them were examined for trachoma, using the WHO criteria. Among the total of 7,423 children aged 1-9 years who participated in this survey, 446 presented with active trachoma. Thus, the prevalence of trachoma in Pernambuco State, in children between 1-9 years old was 6.65%, and it was higher among children aged 5-9 years (7.12%) and among girls (7.23%). This result was seen in the majority of the mesoregions studied, except in the Zona da Mata and Sertao do Sao Francisco, where there were higher prevalences in the age group of 1-4 years (5.55%) and among boys (5.90%). A tendency towards a higher prevalence between 1 and 6 years of age was observed. The follicular trachoma continues to be an important public health problem in Pernambuco State. It particularly affects poor people, including those living in urban areas of the State.

A cutoff thyroglobulin value suggestive of distant metastases in differentiated thyroid cancer patients

Serum thyroglobulin is used as part of the early postoperative assessment of differentiated thyroid cancer (DTC) since there is a clear relationship between an increased risk of recurrence and persistent disease after initial treatment and high postoperative stimulated thyroglobulin (ps-Tg) values. Thus, although ps-Tg above 10-30 ng/mL is considered an independent predictor of worse prognosis, the value that is associated with distant metastases is not defined. Thus, this was our objective. We selected 655 DTC patients from a nuclear medicine department database (Irmandade Santa Casa de Misericórdia de São Paulo, Brazil). All patients had received total thyroidectomy and radioactive iodine (RAI) therapy and had ps-Tg values higher than 10 ng/mL with negative anti-thyroglobulin antibodies. Then, we selected patients who presented post-therapy whole-body scan with pulmonary and/or bone uptake but with no mediastinum or cervical uptake. Patients with negative findings on functional imaging or any doubt on lung/bone uptake were submitted to additional exams to exclude another non-thyroid tumor. Of the 655 patients, 14.3% had pulmonary and 4.4% bone metastases. There was a significant difference in ps-Tg levels between patients with and without metastases (P<0.001). The cutoff value of ps-Tg was 117.5 ng/mL (sensitivity: 70.2%; specificity: 71.7%) for those with lung metastasis, and 150.5 ng/mL (sensitivity: 79.3%; specificity: 85%) for those with bone metastasis. The cutoff value for patients with eitherpulmonary or bone metastasis was 117.5 ng/mL (sensitivity: 70.2%; specificity: 83.7%). Our findings demonstrated that ps-Tg could predict distant metastasis in DTC patients. We identified a cutoff of 117.5 ng/mL with a high negative predictive value of 93.7%.

Household Survey of Trachoma among Children Living in Pernambuco, Brazil

This study analyzed the association between individual and household factors and the incidence of trachoma among a population aged between 1 and 9 years in the state of Pernambuco. This was a population-based household study conducted using a population-based sample of residents from 96 census sectors of the 1778 sectors considered to be at social risk in the state. The estimated odds ratio of the univariate analysis presented a confidence interval of 95%. Weights and clusters were adjusted through the Generalized Linear and Latent Mixed Model (GLLAM) method. Trachoma cases were the dependent variable in the multivariate analysis. The independent variables were selected through the stepwise forward method, with an input criterion of 20% (p < 0.20) and an output criterion of 10% (p < 0.10). The prevalence was 6.65%. Trachoma was associated with a female sex, age of 5–9 years, either the absence of use or infrequent use of soap to wash the hands and face, the presence of nasal secretion, a lack of piped water from a public supply system, a greater number of rooms used for sleeping, a greater number of people living in the same household, and a family income of up to one minimum monthly wage. The prevalence of follicular trachoma in Pernambuco was higher than what is recommended by the World Health Organization (WHO).

Thoracoscopy in the management of pediatric empyemas

INTRODUCTION

Thoracoscopy is increasingly being used in the treatment of empyema. This study assesses feasibility, efficacy and safety in children.

MATERIAL AND METHODS

Clinical files of patients who underwent primary thoracoscopy for empyema between 2006 and 2014 were reviewed. Demographic, clinical and surgical data were analyzed and a comparison between the period before (period1) and after (period2) the learning curve was performed.

RESULTS

Ninety-one patients (53 males, 58%) were submitted to thoracoscopy at a median age of 4 years. There were 19 conversions to thoracotomy with a steady decrease of conversion rate until 2009 (period1) and no conversions thereafter (period2). There was no difference in any of the analyzed parameters between patients submitted to thoracoscopy alone and those requiring conversion in period1. Six cases (6.6%) needed redo-operation (five in period2) and thoracotomy was the elected approach in four. Necrotizing pneumonia was present in 60% of the reoperated cases; in other words, in period2 3 out of 9 cases with necrotizing pneumonia required reintervention (p=0.07). Thoracotomy was avoided in sixty-eight (75%) patients (62% in period1 versus 92% in period2, p=0.001).

DISCUSSION AND CONCLUSIONS

Thoracoscopic approach for empyema is feasible and safe avoiding a significant number of thoracotomies after a short learning curve. An increase of reintervention rate should be expected, but throracoscopy alone is effective in the great majority of the cases. Necrotizing pneumonia may be associated with a higher risk of reintervention, as it is a contra-indication to thoracoscopy and probably surgery.

Asthma prevalence and risk factors in early childhood at Northern Portugal

Asthma is the commonest and most important chronic non-infectious disease in childhood and it has become more prevalent in recent years. There is a shortage of studies in relation to early childhood and so, as part of the INAIRCHILD project, this cross-sectional study aimed to assess the prevalence of asthma and its associated risk factors, namely demographic, environmental, psychosocial and clinical factors for infants and preschoolers living in Northern Portugal. Data concerning asthma prevalence were collected through questionnaires based on those from the International Study of Asthma and Allergies in Childhood (ISAAC-derived), the questionnaires were distributed to 1042 children attending the 17 nurseries involved in the INAIRCHILD project (10 in urban and suburban context, and 7 in rural context). The response rate was 48%. Prevalence of asthma based on symptomatology and odds ratio was calculated. Around 52% of the studied children presented at least one of the respiratory symptoms investigated (wheeze, dyspnea and cough) in the absence of upper respiratory infections. The prevalence of asthma was 10.7%, comparable to the figures for Portuguese schoolchildren (6-7 years old) reported by the national Directorate-General of Health, thus showing that an early diagnosis might be possible and helpful for the mitigation of childhood asthma. Environmental context (urban, suburban or rural), gender and family asthma history showed clear associations with asthma prevalence, namely non-rural location, male gender, and having an asthmatic parent were found to be risk factors.

Effectiveness of Different Mechanical Methods on Dentin Caries Removal: Micro-CT and Digital Image Evaluation

PURPOSE

To determine the caries removal effectiveness (CRE) and minimal invasive potential (MIP) of caries excavation methods using digital imaging and microtomography analyses.

METHODS

Twelve human molars with occlusal caries lesions in dentin were randomly divided into three groups (carbide bur, exacavator, and polymer bur). They were sectioned mesiodistally, and standardized digital and computed microtomography x-ray (micro-CT) images were taken from each section before and after caries excavation. On each image, initial carious dentin (IC), prepared cavity (PC), and residual caries (RC) were defined according to visual criteria using ImageJ software. CRE was determined based on the RC/IC ratio, whereas MIP was determined by the PC/IC ratio. Data were analyzed using one-way analysis of variance and Student t-test or with Kruskal-Wallis and Student-Newman-Keuls test. The level of significance was set at 0.05.

RESULTS

For both digital image and micro-CT analysis, the carbide bur showed higher CRE values than the excavator (p=0.0063 and p=0.0263, respectively) and the polymer bur (p=0.0028 and p=0.0005, respectively). The latter two presented similar results (p>0.05). Regarding MIP, for the digital image analysis, the polymer bur was different from the carbide bur (p=0.0030) but was not different from that of the excavator (p=0.1240). For micro-CT analysis, the MIP values of all the groups were significantly different, and the polymer bur was the most conservative method (p<0.05).

CONCLUSIONS

The carbide bur was the most effective method for caries removal but was not completely conservative. The polymer bur and excavator presented low invasive potential but were not able to remove all of the carious dentin.

Impact of different methodologies on the detection of point mutations in routine air-dried fine needle aspiration (FNA) smears

Currently the best method to select suspicious thyroid nodules for surgery is fine needle aspiration (FNA) cytology. However, FNA cytology has some inherent limitations, which can partly be overcome by molecular analysis. Therefore, molecular testing for somatic mutations has emerged as the most promising approach for molecular FNA diagnostics. The objective of this methodological study was to evaluate the feasibility of detecting BRAF, NRAS, HRAS, and KRAS mutations from routine air-dried thyroid FNA smears, and to find an optimal method for detecting these mutations in FNA samples. DNA was extracted from 110 routine air-dried FNA smears and the corresponding surgically obtained formalin-fixed paraffin-embedded tissues. The presence of BRAF, NRAS, HRAS, and KRAS mutations was assessed by real-time PCRs and high resolution melting analysis, and/or pyrosequencing in comparison to real-time PCRs using hybridization probes and fluorescence melting curve analysis. The high-resolution melting-PCRs revealed a significantly lower number of PCR failures and questionable results, and detected more mutations than the PCRs using hybridization probes. The number of PCR failures ranging from 14-16% by high-resolution melting-PCRs could be further reduced to 5-14% by adding pyrosequencing assays. Moreover, pyrosequencing increased the specificity of the assays, up to 98-100%, while the sensitivity ranged between 32-63%. In summary, the mutation detection, especially in air-dried FNA samples, improves when using PCR assays in combination with high resolution melting analysis. Additional improvement can be obtained by subsequent pyrosequencing in comparison to previously described real-time PCRs using hybridization probes and fluorescence melting curve analysis.

Spirometric tests to assess the prevalence of childhood asthma at Portuguese rural areas: influence of exposure to high ozone levels

The study here reported aimed to: i) evaluate the prevalence of childhood asthma at a Portuguese rural area with high ozone concentrations through lung function tests, validating the previously estimated one assessed through questionnaires (similar to those of the ISAAC); ii) compare the achieved prevalence with the one reported at an unexposed area (with low ozone concentrations), aiming to evaluate the influence of exposure to high ozone levels; and iii) determine potential risk factors. Ninety-five of the original 478 children that completed the questionnaires, mentioned to have at least one of asthma symptoms (wheeze, dyspnea or cough) and were therefore evaluated by spirometry. FEV(1) was in average 89.7% for asthmatics and 102.8% for non-asthmatics. For the studied sample the risk was higher for girls with a tendency to be higher from 8 to 10 years old. Lifetime prevalence of childhood asthma at the exposed area was 9.2%. Children living at the exposed area had 3 times higher risk of having asthma than those living at the unexposed area. Considering that ozone concentrations were the main difference between both areas, it can be suggested that ozone pollution increased asthma prevalence. Nevertheless, it should be remarked that further studies should be done to confirm these results.

Fat-soluble vitamins in human lactation

Lactation has three distinct phases: colostrum, transition, and mature, with the quantity of fat-soluble vitamins and carotenoids tending to decline while the total fat content increases. The number of deliveries seems to be directly related to higher concentrations of beta-carotene and vitamin E in colostrum. Little is known about vitamin quantities during the other phases. In the present study, vitamin A and E concentrations during different phases of lactation were measured in primiparous and multiparous mothers to analyze the variation and suitability for the diet of a breastfed child. Phase of lactation and number of deliveries were highly significant for log mean vitamin A while only one phase showed significance for log mean vitamin E. There was a sharp decline in the levels of vitamin A and E in the course of the initial phase of lactation. The variability between measurements declined as colostrum transitioned to mature milk. There were significant measurable inter-group differences in retinol levels in milk obtained during early lactation. Vitamin A and E content can reach 2.5 and 1.4 times of levels recommended intake, respectively.

Role of viruses and atypical bacteria in asthma exacerbations among children in Oporto (Portugal)

BACKGROUND

Upper respiratory tract infections are known to be a significant precipitant of acute asthma exacerbations. The aim of this study was to evaluate seasonal trends and the role of these pathogens in asthma exacerbations in school-aged children from Oporto (Portugal).

METHODS

Nasal aspirates were collected from children aged 6 to 12 years old with asthma exacerbations attended in the Pediatric Emergency Department one day per week from January 1 to December 31, 2003. Demographic data, severity of asthma and asthma exacerbations, and current treatment were recorded. Samples were obtained through nasal wash with 1 ml saline and were processed by immunofluorescence assays (respiratory syncytial virus, adenovirus, parainfluenza and influenza virus), retrotranscription polymerase chain reaction (rhinovirus) and polymerase chain reaction (enterovirus, Chlamydia pneumoniae and Mycoplasma pneumoniae).

RESULTS

In 54 eligible children, 37 nasal samples were obtained. Infectious agents were detected in 78 % of the patients. Rhinovirus was detected in 70.3 %, Mycoplasma pneumoniae in 16.2 %, enterovirus in 10.8 %, and Chlamydia pneumoniae in 2.7 %. Coinfection was identified in 21.6 % of the samples. There was no significant correlation between current treatment status, severity of asthma or exacerbations and the isolated agents. Two distinct peaks of asthma exacerbation were found, 40.5 % in spring and 32.4 % in autumn [corrected] The highest number of cases was recorded in March and the lowest in August and January. Rhinoviruses was detected in 27 % of the cases in autumn and in 24.3 % in spring [corrected]

CONCLUSIONS

These results confirm the previously reported high frequency of rhinovirus detection in asthma exacerbations in children and provide evidence that asthma exacerbations and rhinovirus infections follow a seasonal pattern, occurring mostly in spring and autumn. The findings also underscore the frequency of Mycoplasma pneumoniae detection, and emphasize the importance of this agent as a possible trigger of asthma exacerbations.

[Hypoglycaemia without ketosis. A case report]

INTRODUCTION

Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (LCHADD) is a rare disease, inherited as autosomal-recessive trait, with variable clinical presentation including severe hypoglycaemia, cardiomyopathy, sudden infant death, progressive liver failure, 'Reye like' syndrome, neuromyopathy, muscle weakness and rhabdomyolysis.

CASE REPORT

We report a 3 years old male patient admitted to our emergency department with vomiting, hypotonia and prostration, after a common respiratory infection. The presence of hypoketotic hypoglycaemia and elevated liver enzymes in the admission motivated a metabolic study. We found an abnormal low lactate/pyruvate ratio, decreased serum carnitine and dicarboxylic aciduria leading to the diagnosis of a fatty acid oxidation disorder (LCHADD). The molecular study of HADHA gene revealed homozygosity for the G1528C mutation in the patient DNA, and heterozygosity in both parents.

CONCLUSIONS

The diagnosis of a fatty acid oxidation disorder must be considered in the presence of vomiting associated with excessive prostration specially if there is hypoketotic hypoglycaemia or familiar sudden infant death history. Physicians should be aware about these conditions and for the importance of measuring both glycaemia and ketone bodies during the evaluation of high risk situations.

[Multifocal phakic intraocular lens implant to correct presbyopia]

INTRODUCTION

Presbyopic surgery is considered as the new frontier in refractive surgery. Different solutions are proposed: myopization of one eye, insertion of an accommodative crystalline lens, scleral surgery, the effects of which are still unknown, and finally multifocal phakic implants. We therefore decided to undertake a prospective study under the Huriet law to determine its efficacy and specify the conditions required for an anterior chamber multifocal phakic implant.

MATERIAL AND METHOD

Fifty-five eyes of 33 patients received an anterior chamber foldable multifocal phakic implant. Twenty-one females and 12 males underwent surgery. Initial refraction was between -5D and +5D. The implant's single addition was +2.50. Recuperating a distant uncorrected visual acuity of 0.6 or better and near uncorrected vision of Parinaud 3 or better can be considered a very good postoperative result.

RESULTS

Average follow-up was 42.6+/-18 weeks. Mean postoperative refraction was -0.12+/-0.51 D. Mean postoperative uncorrected visual acuity was 0.78+/-0.20. Postoperative uncorrected visual acuity was Parinaud 2.3+/-0.6. Eighty-four percent of eyes operated on recuperated 0.6 or better without correction and Parinaud 3 or better without correction. Lenses in four eyes were explanted for different reasons, essentially optical, and no severe anatomical complications were observed.

CONCLUSIONS

Placing an anterior chamber multifocal phakic implant to correct presbyopia is an effective technique with good predictability and has the advantage of being reversible in case of intolerance, optical parasite effects or undesired complications. Considering the particularity of this surgery, it is imperative to respect very strict inclusion criteria: anterior chamber depth equal to or above 3.1 mm, open angle, endothelial cell count equal to or above 2000 cells/mm2, absence of an incipient cataract or the slightest evidence of macular alteration.

Étude in vivo de l’accommodation naturelle chez un sujet albinos

Modifications of the anterior segment during accommodation of the eye under examination cannot be studied in a simple and direct way with anterior segment imaging techniques such as Scheimpflug photography, A Scan, B Scan, and UBM. With this equipment, it is necessary to stimulate the fellow eye in order to observe the variations of the analyzed eye. The techniques using ultrasound equipment can only be used with contact systems or with water baths that will modify the anatomical dimensions or the pressure of the anterior segment. With the Scheimpflug photographic technique, geometrical reconstructions are necessary and cannot be used in certain axes. Optical coherence tomography provides the advantage of producing non-contact images of the anterior segment in static and dynamic conditions that are then easy to use. The target of the optical system can be focused and unfocused with negative or positive lenses, thus reproducing the conditions of natural accommodation. With a normal subject, the morphological modifications of the crystalline lens behind the iris screen cannot be studied because the infrared light source used is blocked by the pigment epithelium. The absence of this pigment in an albino subject allowed us to study the modifications of the crystalline lens and the ciliary body during accommodation. In this study, we were able to definitely confirm all the modifications of the anterior segment as described by von Helmholtz in 1855, who, at the time, used very rudimentary optical procedures based on the reflections of a flame on the surface of the crystalline lens.

Analyse du segment antérieur de l’œil avec un tomographe à cohérence optique

PURPOSE

To study the biometric modifications of the anterior segment depending on accommodation and age. To try and define their possible applications in certain fields of anterior segment surgery, in particular in refractive implants.

MATERIAL AND METHOD

Anterior chamber biometry can be very easily studied with 1310-nm wavelength optical coherence tomography. The equipment has a fixation target that can be focused and defocused with negative lenses in order to stimulate natural accommodation. The human anterior chamber was therefore studied during accommodation. We studied 104 eyes of 56 patients aged between 7 and 82 years. Refraction was between +5D and - 5D. A single operator carried out all the measurements. The anterior chamber's horizontal diameter, the anterior chamber's depth, the horizontal pupil diameter and the horizontal radius of curvature of the crystalline lens' anterior pole were measured unaccommodated or after stimulating accommodation.

RESULTS

The different static or dynamic measurements were compared to ametropia, age and accommodation. At rest, the average AC diameter was 12.33 mm, the average AC depth was 3.11 mm and the average pupil diameter was 4.26 mm. On average, for 1 D of accommodation, the crystalline lens anterior pole moved forward by 30 microm. There was a 0.3-mm reduction in its radius of curvature and a 0.15-mm reduction in pupil diameter. Several other measurements are illustrated on graphs.

CONCLUSIONS

The AC OCT is a user-friendly instrument to evaluate the anterior segment and explore the anterior chamber (cornea, iris, crystalline lens, irido-corneal angle). The 1310-nm light wavelength is blocked by pigments preventing exploration behind the iris. However, the AC OCT is capable of providing good-quality images and a better visualization of the anatomical relationships of the anterior segment, even behind an opaque cornea.

Contact entre le cristallin naturel et différents modèles d’implants réfractifs phakes. Étude avec l’OCT de chambre antérieure

Three patients received three different models of phakic implants. With the usual slit-lamp examination method, we were not able to establish whether there was contact between the implants and the natural crystalline lens. Using the anterior chamber optical coherence tomography scanner (AC-OCT), we were able to demonstrate that there was direct contact between the natural crystalline lens and the three different phakic implants. A dynamic study of these contacts was carried out during accommodation. These observations show that examination of the anterior segment with the optical coherence tomography scanner is essential in refractive surgery.

The first green lineage cdc25 dual-specificity phosphatase

The Cdc25 protein phosphatase is a key enzyme involved in the regulation of the G(2)/M transition in metazoans and yeast. However, no Cdc25 ortholog has so far been identified in plants, although functional studies have shown that an activating dephosphorylation of the CDK-cyclin complex regulates the G(2)/M transition. In this paper, the first green lineage Cdc25 ortholog is described in the unicellular alga Ostreococcus tauri. It encodes a protein which is able to rescue the yeast S. pombe cdc25-22 conditional mutant. Furthermore, microinjection of GST-tagged O. tauri Cdc25 specifically activates prophase-arrested starfish oocytes. In vitro histone H1 kinase assays and anti-phosphotyrosine Western Blotting confirmed the in vivo activating dephosphorylation of starfish CDK1-cyclinB by recombinant O. tauri Cdc25. We propose that there has been coevolution of the regulatory proteins involved in the control of M-phase entry in the metazoan, yeast and green lineages.

Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions

Campomelic dysplasia (CD), a human skeletal malformation syndrome with XY sex reversal, is caused by heterozygous mutations in and around the gene SOX9. SOX9 has an extended 5' control region, as indicated by CD translocation breakpoints scattered over 1 Mb proximal to SOX9 and by expression data from mice transgenic for human SOX9-spanning yeast artificial chromosomes. To identify long-range regulatory elements within the SOX9 5' control region, we compared approximately 3.7 Mb and 195 kb of sequence around human and Fugu rubripes SOX9, respectively. We identified only seven and five protein-coding genes in the human and F. rubripes sequences, respectively. Four of the F. rubripes genes have been mapped in humans; all reside on chromosome 17 but show extensive intrachromosomal gene shuffling compared with the gene order in F. rubripes. In both species, very large intergenic distances separate SOX9 from its directly flanking genes: 2 Mb and 500 kb on either side of SOX9 in humans, and 68 and 97 kb on either side of SOX9 in F. rubripes. Comparative sequence analysis of the intergenic regions revealed five conserved elements, E1-E5, up to 290 kb 5' to human SOX9 and up to 18 kb 5' to F. rubripes SOX9, and three such elements, E6-E8, 3' to SOX9. Where available, mouse sequences confirm conservation of the elements. From the yeast artificial chromosome transgenic data, elements E3-E5 are candidate enhancers for SOX9 expression in limb and vertebral column, and 8 of 10 CD translocation breakpoints separate these elements from SOX9.

The myosin light chain kinase gene is not duplicated in mouse: partial structure and chromosomal localization of Mylk

The gene encoding myosin light chain kinase (MYLK) is duplicated on human chromosome 3 (HSA3; 3p13;3q21) and on a chromosome with conserved synteny to HSA3 in most non-human primate species. In human, the functional copy resides on 3q21, whereas the 3p13 site contains a pseudogene. To trace the origin of the duplication, we characterized the mouse gene Mylk. A single sequence corresponding to the functional Mylk was detected. We sequenced a 180-kb bacterial artificial chromosome clone containing the 24 first exons of Mylk; the complete mouse gene is expected to span >200 kb. Comparisons with the draft of the human genome revealed that the sequence and structure of MYLK are conserved in mammals. Fluorescence in situ hybridization (FISH) analysis indicated that the mouse gene localizes to a single site on chromosome 16B4-B5, a region with conserved synteny with HSA3q. Our study provides information on both the structure and the evolution of MYLK in mammals and suggests that it was duplicated after the divergence of rodents and primates.

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies

We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.

Expression of the genes encoding the vasopressin-activated calcium-mobilizing receptor and the dual angiotensin II/vasopressin receptor in the rat central nervous system

The distributions of two newly discovered receptors, the vasopressin-activated calcium-mobilizing receptor (VACM-1) and the dual angiotensin II/vasopressin receptor (AII/AVP), in the central nervous system (CNS) of the rat were determined using reverse transcriptase-polymerase chain reaction and in situ hybridization. The sequence of the rat VACM-1 cDNA was determined and found very homologous to the rabbit and human sequences. Both VACM-1 and AII/AVP receptor genes were widely expressed in the brain, but differed according to the cell type studied. Glial cells were very faintly labelled. The epithelial cells of the choroid plexuses, the ependymal cells and the pia mater were all labelled. Both genes were most active in neurones throughout the CNS. VACM-1 and AII/AVP receptors were detected in neurones previously shown to possess V1a and V1b vasopressin receptors, and/or the AT1 and AT2 angiotensin II receptors in many brain areas. This was the case for the magnocellular neurones of the supraoptic and paraventricular nuclei of the hypothalamus. We suggest that the VACM-1 and AII/AVP receptors may account for the V2-like responses to vasopressin by these neurones which lack a genuine V2 vasopressin receptor.

Evolution of the Gypsy endogenous retrovirus in the Drosophila melanogaster subgroup

We conducted a phylogenetic survey of the endogenous retrovirus Gypsy in the eight species of the Drosophila melanogaster subgroup. A 362-bp fragment from the integrase gene (int) was amplified, cloned, and sequenced. Phylogenetic relationships of the elements isolated from independent clones were compared with the host phylogeny. Our results indicate that two main lineages of Gypsy exist in the melanogaster subgroup and that vertical and horizontal transmission have played a crucial role in the evolution of this insect endogenous retrovirus.

From sequence to chromosome: the tip of the X chromosome of D. melanogaster

One of the rewards of having a Drosophila melanogaster whole-genome sequence will be the potential to understand the molecular bases for structural features of chromosomes that have been a long-standing puzzle. Analysis of 2.6 megabases of sequence from the tip of the X chromosome of Drosophila identifies 273 genes. Cloned DNAs from the characteristic bulbous structure at the tip of the X chromosome in the region of the broad complex display an unusual pattern of in situ hybridization. Sequence analysis revealed that this region comprises 154 kilobases of DNA flanked by 1.2-kilobases of inverted repeats, each composed of a 350-base pair satellite related element. Thus, some aspects of chromosome structure appear to be revealed directly within the DNA sequence itself.

The genome sequence of Drosophila melanogaster

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

Sequence, structure, and evolution of a complete human olfactory receptor gene cluster

The olfactory receptor (OR) gene cluster on human chromosome 17p13.3 was subjected to mixed shotgun automated DNA sequencing. The resulting 412 kb of genomic sequence include 17 OR coding regions, 6 of which are pseudogenes. Six of the coding regions were discovered only upon genomic sequencing, while the others were previously reported as partial sequences. A comparison of DNA sequences in the vicinity of the OR coding regions revealed a common gene structure with an intronless coding region and at least one upstream noncoding exon. Potential gene control regions including specific pyrimidine:purine tracts and Olf-1 sites have been identified. One of the pseudogenes apparently has evolved into a CpG island. Four extensive CpG islands can be discerned within the cluster, not coupled to specific OR genes. The cluster is flanked at its telomeric end by an unidentified open reading frame (C17orf2) with no significant similarity to any known protein. A high proportion of the cluster sequence (about 60%) belongs to various families of interspersed repetitive elements, with a clear predominance of LINE repeats. The OR genes in the cluster belong to two families and seven subfamilies, which show a relatively high degree of intermixing along the cluster, in seemingly random orientations. This genomic organization may be best accounted for by a complex series of evolutionary events.

Genomic sequencing reveals the structure of the Kcnk6 and map3k11 genes and their close vicinity to the sipa1 gene on mouse chromosome 19

In this report we present the analysis of two overlapping mouse cosmid clones that contain the entire Kcnk6, Map3k11 and Pcnxl3 genes, as well as part of the Sipa1 gene. The sequence and genomic organisation of the Kcnk6 and Map3k11 genes are described in detail. Sipa1 and Map3k11, which have independently been mapped with low resolution to the centromeric region of mouse chromosome 19, are shown here to lie close to each other and to the Kcnk6 gene, which has not previously been mapped. This gene cluster maps to the vicinity of the Dancer (Dc) mutation, which involves inner ear abnormalities and circling phenotypes. Since potassium channels have been implicated in deafness disorders, we have analysed the Kcnk6 gene, which encodes a two-P domain potassium channel, in the Dc mutant. No Dc-causing mutation in the Kcnk6 coding region could be identified. However, we detected a polymorphism in the Kcnk6 gene that leads to a C-terminal extension of the encoded protein by eight amino acids.

A genomic region encompassing a cluster of olfactory receptor genes and a myosin light chain kinase (MYLK) gene is duplicated on human chromosome regions 3q13-q21 and 3p13

The olfactory receptor (OR) multigene family is widely distributed in the human genome. We characterize here a new cluster of four OR genes (HGMW-approved symbols OR7E20P, OR7E6P, OR7E21P, and OR7E22P) on human chromosome 3p13 that is contained in an approximately 250-kb region. This region has been physically mapped, and a 106-kb portion containing the OR genes has been sequenced. All the OR sequences are disrupted by frameshifts and stop codons and appear to have arisen through local duplications. A myosin light chain kinase pseudogene (HGMW-approved symbol MYLKP) lies at one end of the OR gene cluster. Sequences spanning the entire region are also present at 3q13-q21, the site of the functional MYLK gene. This region duplicated locally before the divergence of primates, and the two paralogous copies were later separated to sites on either side of the centromere. This study increases our understanding of the evolution of the human genome. The 3p13 cluster is the first example of a tandem array of OR pseudogenes, and duplications of such clusters may account for the accumulation of a large number of pseudogenes in the human genome.

Simple variant t(8;21) acute myeloid leukemias harbor insertions of the AML1 or ETO genes

We report on the molecular characterization of two acute myeloid leukemias (AML), one AML-M1 (patient 1) and one AML-M2 (patient 2) with t(8;21)(p21;q22) and t(8;20)(q22;p13), respectively, at diagnosis. The locations of the breakpoints, 21q22 in patient 1 and 8q22 in patient 2, prompted us to search for a cryptic t(8;21)(q22;q22) and involvement of the AML1 and ETO genes. Dual-color fluorescence in situ hybridization (FISH) using whole chromosome painting probes for chromosomes 8, 20, and 21 confirmed the conventional cytogenetic karyotypes. However, dual-color FISH using appropriate ETO and AML1 probes disclosed an insertion of AML1 into 8q22 on the derivative chromosome 8 in patient 1 and of ETO into 21q22 on one chromosome 21 in patient 2, leading to AML1-ETO fusion signals. Both cases expressed an AML1-ETO transcript, shown by reverse transcriptase polymerase chain reaction and cDNA sequencing. Creation of functional AML1-ETO fusion genes in these two simple variant t(8;21) probably occurred through complex mechanisms, combining translocation and insertion of chromosomal segments.

High gelsolin content of developing oligodendrocytes

The actin-binding protein gelsolin that severs and caps the actin microfilaments under the control of the cytoplasmic free calcium and the membranous phosphatidylinositol 4,5-bisphosphate, is essentially restricted to the oligodendroglia in the central nervous system. Immunocytochemistry showed that gelsolin is an early marker of oligodendrocytes, both in vivo, in the rat cerebellum, and in vitro, in oligodendrocyte culture. We report the early appearance of gelsolin in A2B5-positive precursor oligodendrocyte cells and the specific expression of gelsolin in OL-1-, GC-, and MBP-positive oligodendrocytes in culture. The protein was distributed throughout the cell body and in the branched cell processes of cultured oligodendrocytes, but not in the MBP-positive membrane sheets. Gelsolin is thus cytosolic and not a myelin component. The quantitative study demonstrated that that the cerebellar gelsolin content changes significantly with age, with the maximal value at the age of 21 days, confirming that large amounts of gelsolin are transiently synthesized during development, especially from the first events of myelinogenesis. The results are consistent with gelsolin being involved, through its effects on the actin cytoskeleton, in the motile events occurring during the growth of the oligodendroglial processes towards the axons and the wrapping of the myelin sheaths around the axons.

Conformational stability of human skeletal tropomyosins modified by site-directed mutagenesis

We have used human beta-tropomyosin produced in Escherichia coli and deletion mutants obtained by site-directed mutagenesis to analyse the conformational stability of this molecule under various experimental conditions. Protein engineering has allowed us to answer some questions raised by stability analysis of the wild-type tropomyosin. The complex pattern of denaturation is due neither to heterogeneity of the preparation nor to head-to-tail interactions. The N- and C-termini are not of importance for the thermal stability of the molecule. On the contrary, deletion of the 31 C-terminus amino acids leads to a dramatic decrease of the stability observed in guanidinium chloride. This lowering is interpreted as the participation of one more guanidinium chloride ions to the denaturation equilibrium. Analysis of the stability in presence of organic solvents reveals that acetonitrile and methanol induce opposite effects. Investigation of these effects by three methods (CD, fluorescence and electrophoresis that measure respectively the content in alpha-helix, the contact between the two strands and the strands exchange) leads to the conclusion that strand separation can precede the denaturation of the alpha-helix.

Distribution of gelsolin in the retina of the developing rabbit

The distribution of gelsolin, a calcium-dependent actin-severing and capping protein, in the retina of the developing and adult rabbit was studied. Gelsolin immunoreactivity was found in the photoreceptors and ganglion cells, where it may have a role in neuronal morphogenesis. Only the inner segment of the photoreceptors retained a high gelsolin content in the adult retina, perhaps because the attached outer segment is continuously renewed throughout life. Gelsolin, which is a major component of the rabbit brain oligodendrocytes, was also found in the myelin of the medullary ray region of the rabbit retina. Müller cells in all regions of the rabbit retina also contain gelsolin from early in development to adulthood. Since one of the functions of these cells is to ensheath neuronal elements in the inner plexiform and optic fiber layers, we suggest that gelsolin may play the same role in Müller cells as it does in oligodendrocytes, i.e., sheath formation via its calcium-dependent action on the actin microfilament networks.

Purification and characterization of an exon 2-deleted human beta-tropomyosin constructed by the polymerase chain reaction

We deleted exon 2 in human skeletal beta-tropomyosin (h beta-SK tropomyosin) using an improved adaptation of polymerase chain reaction (PCR) technology. The first PCR product was used to prime the full-length cDNA, leading to an exon 2-deleted h beta-SK tropomyosin. This new protein, des-(39-80)-tropomyosin, could then be expressed in Escherichia coli and purified to homogeneity. At the nucleotide level, the junction between exons 1 and 3 has been precisely made in the PCR product. The mutated protein was purified using high-performance liquid chromatography. Des-(39-80)-tropomyosin revealed new immunological properties but was still recognized by certain antitropomyosin antibodies. Furthermore, the structural characteristics of the mutated tropomyosin fit those of the full-length tropomyosin. This new adaptation of PCR technology appears to be suitable for every kind of mutation inside a cloned DNA molecule, and one mutation primer per mutation is sufficient.

Profilin and profilin mRNA in the cerebellum of the developing rat

Profilin and profilin mRNA concentrations were determined in the cerebellum of the developing rat. Profilin represented nearly 0.1% of total Triton-soluble protein both at birth and at the end of the developmental period. During brain maturation, the profilin concentration was regulated at the transcriptional level. A transient increase of profilin mRNA and profilin was observed at the end of the first postnatal week, a period of intense cell proliferation, neuritic outgrowth and synaptogenesis. We propose that profilin may act by forming, during the critical period of cerebellar development, a reserve pool of monomeric actin that can easily be mobilized in cell regions such as growth cones or synaptic junctions where filamentous actin is highly concentrated.

Purification and characterization of recombinant tropomyosins

The cloning of a cDNA coding for the skeletal human beta-tropomyosin in the bacterial expression vector pKK233-2 is reported. Deletion mutants were also constructed. pCF-T1088 was obtained by elimination of exon 9 and pCF-T1089 was built by deleting 2/3 of the first exon. The recombinant tropomyosins were synthesized in E. coli after induction by IPTG. The mutant proteins were characterized by western blot using antibodies raised against native tropomyosin. The amount of the human protein synthesized in E. coli varies with each mutant, suggesting the involvement of the structure of the protein or of the mRNA on the synthesis or the stability of the recombinant protein. After precipitation of most of the bacterial proteins at 100 degrees C, purification was achieved by high-performance liquid chromatography (HPLC) using TSK-DEAE, hydroxyapatite and reversed-phase columns. The chromatographic behaviour of the mutants were compared. Characterization of the mutated tropomyosins was achieved by tryptic digestion and analysis of the peptide composition by reversed-phase HPLC. A computer program for predicting the retention times of the peptides generated was written. It is shown that it is possible to identify the mutations solely by comparing the chromatogram of the tryptic digest with the profile obtained by computer simulation.

Construction, expression and unexpected regulatory properties of a tropomyosin mutant with a 31-residue deletion at the C-terminus (exon 9)

The cDNA coding for human skeletal muscle beta-tropomyosin was expressed in Escherichia coli to produce an unacetylated beta-tropomyosin. This cDNA was deleted from the sequence corresponding to the exon 9 and expressed in E. coli to produce an unacetylated beta-tropomyosin mutant lacking the C-terminal residues 254-284. The main structural and functional properties of the two isolated proteins, designated tropomyosin-1 and des-(254-284)-tropomyosin, respectively, were characterized in comparison with those of the genuine rabbit skeletal muscle alpha beta-tropomyosin. The folding and thermal stability of the three tropomyosins were indistinguishable. Tropomyosin-1, but not des-(254-284)-tropomyosin, was polymerized in the presence of troponin and did bind to actin in the presence of the troponin complex. Despite its weak binding to actin, des-(254-284)-tropomyosin displayed a regulatory function in the presence of troponin with a marked activation of the actomyosin subfragment-1 ATPase in the presence of Ca2+ and low concentrations of subfragment-1. The data were interpreted in the light of the allosteric models of regulation and suggest the involvement of the sequence coded by exon 9 in the stabilization by tropomyosin of the off state of the thin filament.

Expression of tropomyosin genes during the development of the rat cerebellum

The expression of the tropomyosin genes in the rat nervous system was examined during the postnatal development of the cerebellum, using human-specific alpha-, beta-, gamma-, and delta-tropomyosin cDNA probes and rat-specific alpha-, beta-, and delta-tropomyosin oligonucleotide probes. The beta- and gamma-genes do not seem to be expressed in the rat brain. The delta-tropomyosin gene produces two mRNAs: a major one of 2.4 kb, which is highly concentrated during the first postnatal week and then decreases fourfold in level until the age of 35 days, and a minor one of 2 kb, with the same developmental profile as the 2.4-kb mRNA. A 3-kb mRNA is expressed by the alpha-tropomyosin gene and is characteristic of the mature rat. The expression of the tropomyosin genes during the development of the rat cerebellum does not seem to be regulated through alternative splicing but rather implies the differential expression of two different isogenes. The multiple isoforms of tropomyosin produced during neuronal differentiation may be intimately involved in the regulation of the organization and function of actin microfilaments.

Quantitative analysis of the selective pressure exerted on homologous proteins

Evolution analysis is used to locate the regions of a protein that are important for its function or structure. The rate of evolution is generally constant for a given family of homologous sequences. From the starting point of this observation, an algorithm is proposed to establish quantitatively the sequence zones where selective pressure is maximal. A program that computes this pressure has been written in PASCAL. Analysis of results on some sequences validate this theoretical approach, and this knowledge can be used as a starting-point for carrying out site-directed mutagenesis.

Effect of thyroid deficiency on actin mRNA content in the developing rat cerebellum

The actin mRNA content of the cerebellum was determined in normal and hypothyroid developing rats using RNA dot hybridization with a beta-actin cDNA probe. The decline in actin mRNA content occurring during the second postnatal week in normal development was delayed by about 1 week in hypothyroid rats. Since this effect coincides exactly with the delay in actin filament formation recently reported in thyroid-deficient rats, it strengthens the hypothesis of an inverse relationship in the developing brain between the polymerization state of actin and the production of actin mRNA.

Identification of the calmodulin binding domain of alpha-fodrin and implications for folding

A cDNA clone producing a protein that binds calmodulin has been isolated from a mouse macrophage library. The cDNA was sequenced and identified as coding for fodrin. By deleting part of the sequence, the calmodulin binding domain was located. The site is situated on repeat 11 of fodrin probably on its extra arm. This part of the sequence exhibits great similarity to other calmodulin binding proteins. Analysis of the sequence and spatial structure of calmodulin revealed a domain which is quite complementary to the sequence identified on fodrin. These results provide a new insight into the structure of fodrin and consequently into the structure of proteins of the spectrin family. A model for the general folding of these molecules is proposed, involving a simple three-layer folding. The structure was further corroborated by analysis of charge distribution in the vicinity of the calmodulin binding site. The folding we propose is in good agreement with digestion experiments and explains observations in diseases resulting from mutations of human spectrin.

Purification of synthetic oligonucleotides on a weak ion-exchange column

A weak ion-exchange column (PVDI 4000-5) was used to purify oligonucleotides of relatively large size. The purification of polynucleotides was very rapid, they were separated according to size and retained all their properties relevant to genetic engineering experiments.