Effect of Different Irrigating Solutions on Root Canal Dentin Microhardness-A Systematic Review with Meta-Analysis

The aim of this study was to evaluate the effect of different irrigating solutions as well as their combination and activation modes on root canal dentin microhardness. The protocol was registered in PROSPERO and PRISMA guidelines were followed. The structured question was as follows: "Which type of irrigating solution used in endodontic treatment causes more change in dentin microhardness?" The literature was screened via PubMed, Google Scholar, Scopus, and Science Direct. The last search was carried out in February 2023 with English language restriction. Two reviewers independently performed screening and evaluation of articles. A total of 470 articles were retrieved from all the databases, whereas only 114 articles were selected for full-text analysis. After applying eligibility criteria, 44 studies were evaluated and included in this review. The results showed that with increased contact time with irrigants, dentin microhardness decreases. Increased contact time with sodium hypochlorite (NaOCl) was associated with more reduction in dentin microhardness compared with other irrigants. Other irrigants, with the exception of distilled water, including EDTA, citric acid, herbal irrigants, glycolic acid, phytic acid, etc., in this study significantly decreased dentin microhardness. The maximum reduction in dentin microhardness was seen with 2.5% NaOCl after 15 min of contact time. The use of irrigating solutions alters the chemical composition of dentin, thereby decreasing its microhardness, which affects the clinical performance of endodontically treated teeth.

Effect of exercise based interventions on sleep and circadian rhythm in cancer survivors-a systematic review and meta-analysis

Background

Disrupted circadian rhythm commonly reported in cancer survivors is closely associated with cancer related fatigue, sleep disturbances and compromised quality of life. As more cancer survivors request non-pharmacological treatment strategies for the management of their chronic sleep-related symptoms, there is a need for meta-analyses of various interventions such as exercise on sleep and circadian rhythm disturbances.

Methods

A search for RCT's was conducted in April 2020 and updated in July 2023 using relevant keywords for cancer, sleep, circadian rhythm and exercise interventions on PubMed, Scopus, Web of Science, PEDro and CINAHL.

Results

Thirty-six studies were included for qualitative analysis and 26, for meta-analysis. Thirty-five studies analyzed sleep outcomes, while five analyzed circadian rhythm. RCT's studying the effect of aerobic exercise, resistance exercise, combined aerobic and resistance exercise, physical activity, yoga, or tai chi were included. Meta-analysis results showed significant exercise-related improvements on sleep quality assessed by Pittsburgh Sleep Quality index (PSQI) (SMD = -0.50 [-0.87, -0.13], p = 0.008), wake after sleep onset (WASO) (SMD = -0.29 [-0.53, -0.05], p = 0.02) and circadian rhythm, assessed by salivary cortisol levels (MD = -0.09 (95% CI [-0.13 to -0.06]) mg/dL, p < 0.001). Results of the meta-analysis indicated that exercise had no significant effect on sleep efficiency, sleep onset latency, total sleep time and circadian rhythm assessed by accelerometry values.

Conclusion

While some sleep and circadian rhythm outcomes (PSQI, WASO and salivary cortisol) exhibited significant improvements, it is still somewhat unclear what exercise prescriptions would optimize different sleep and circadian rhythm outcomes across a variety of groups of cancer survivors.

Implication

As exercise does not exacerbate cancer-related circadian rhythm and sleep disturbances, and may actually produce some significant benefits, this meta-analysis provides further evidence for cancer survivors to perform regular exercise.

Impact of COVID-19 on Mental Health Among Healthcare Workers in India: A Mixed-methods Systematic Review

Healthcare workers (HCWs) experienced significant mental health challenges during the COVID-19 pandemic. This review aimed to comprehensively assess the impact of the COVID-19 pandemic on the mental health of HCWs in India. We conducted a mixed-methods systematic review, which adopts a results-based convergent approach that incorporates quantitative and qualitative data. A comprehensive literature search was conducted in relevant databases: PubMed-Medline, CINAHL, Web of Science, and ProQuest. All available full-text studies in the English language that assessed the mental health outcomes (anxiety, stress, and depression) of HCWs during the pandemic and published until 28 February 2022 were included. A total of 31 studies were included in this review (27 quantitative studies, three qualitative studies, and one mixed-method study). The pooled prevalence of depression, anxiety, and stress among HCWs in India was 32.96%, 29.49%, and 33.47%, respectively. Integration of quantitative and qualitative findings using social determinants of health framework resulted in various contributing factors and coping strategies. There is a need for a supportive work environment, mental health support, and mental health policies for HCWs in India.

Quantification of Indoor Respirable Suspended Particulate Matters (RSPM) and Asthma in Rural Children of Delhi-NCR

OBJECTIVES

To assess the exposure of indoor respirable suspended particulate matters (PM10, PM2.5, and PM1) and their association with asthma in children in a rural area of Delhi-NCR.

METHODS

It was a cross-sectional study. Fifty children with asthma from both biomass fuel users in group A and liquefied petroleum gas (LPG) fuel users in group B households were enrolled along with 50 healthy control subjects. The diagnosis of asthma was done as per the Global Initiative for Asthma (GINA), 2014. The 24-h levels of PM from all three groups of households were measured and compared. The level of PM with confounding factors like smoking and room occupancy was also compared between the groups.

RESULTS

The 24-h concentrations of PM10, PM2.5, and PM1 were found significantly higher in the households of group A and group B as opposed to group C (p < 0.001). The number of smokers with a mean pack year and a lack of an exhaust fan was highest in group A and lowest in group C, while diesel and kerosene machines were highest in group B. The PMs were highest in group A even with different confounding factor (p < 0.001). The level of all PM was higher in group B than in group C, despite the presence of both types of fuel in group C households. The level of all PM was highest during the cooking hour.

CONCLUSION

The level of 24-h PM was highest in group-A households. However, the level of PM was higher in group-B households than group C despite the presence of biomass fuel users in group C. This may be due to the higher number of smokers, poor room-occupancy and lack of exhaust fans.

Uncontrolled Diabetes Mellitus Predicts Post-COVID-19 Fibrosis

INTRODUCTION

Post-coronavirus 2019 (COVID-19) complications are now well-recognized and may involve multiple organs. Post-COVID-19 pulmonary fibrosis is one of the serious long-term consequences of COVID-19 infection, and the risk factors for its development largely remain unidentified.

AIMS AND OBJECTIVES

The study aimed to evaluate the clinical and radiological profile of post COVID-19 patients with diagnosed diabetes mellitus (DM).

MATERIALS AND METHODS

All the patients attending the post-COVID-19 respiratory care center over a period of 1 year who were diagnosed with cases of DM were evaluated for residual clinical symptoms and radiological changes and glycosylated hemoglobin (HbA1c) levels were measured from their blood samples.

RESULTS

A total of 50 patients were enrolled in this observational cross-sectional study. Most patients were males in the age group of 45-60 years. Approximately 74% of patients had uncontrolled DM. Patients with uncontrolled DM had a higher probability of having a severe disease with an odds ratio (OR) of 7.30 (0.85, 62.42, and confidence interval (CI) 95%) and were more likely to have fibrotic abnormalities on computed tomography (CT) chest with OR of 3.38 (0.87, 16.86, and CI 95%).

CONCLUSION

Uncontrolled diabetes predisposes to the development of post-COVID-19 fibrosis, so physicians should be more vigilant while managing these patients.

Can Immunoexpression of Cancer Stem Cell Markers Prognosticate Tongue Squamous Cell Carcinoma? A Systematic Review and Meta-Analysis

The objective was to evaluate the association of the immunoexpression of cancer stem cell (CSC) markers with clinicopathological and survival outcomes in tongue squamous cell carcinoma (TSCC) patients. This systematic review and meta-analysis [PROSPERO (CRD42021226791)] included observational studies that compared the association of clinicopathological and survival outcomes with CSC immunoexpression in TSCC patients. Pooled odds ratios (ORs) and hazard ratios (HRs) with 95% confidence intervals (CI) were used as outcome measures. Six studies identified the association with three surface markers (c-MET, STAT3, CD44) and four transcription markers (NANOG, OCT4, BMI, SOX2). The odds of early-stage presentation were 41% (OR = 0.59, 95% CI 0.42-0.83) and 75% (OR = 0.25; 95% CI 0.14-0.45) lower in CSC and SOX2 immuno-positive cases than immuno-negative cases, respectively. The odds of well-differentiated tumors in transcription marker immuno-positive cases were 45% lower compared to immuno-negative cases (OR = 0.55, 95% CI 0.32-0.96). The odds of positive lymph nodes were 2.01 times higher in CSC immuno-positive cases compared to immuno-negative cases (OR = 2.01, 95% CI 1.11-3.65). Mortality in immuno-positive cases was 121% higher than that in immuno-negative cases (HR = 2.21; 95% CI 1.16-4.21). Advanced tumor staging and grading, lymph node metastasis, and mortality were significantly associated with positive immunoexpression of CSC markers.

Knowledge of Medical Imaging Professionals on Healthcare-Associated Infections: A Systematic Review and Meta-Analysis

Healthcare-associated infections (HCAIs) are a significant concern for both healthcare professionals and patients. With recent advances in imaging modalities, there is an increase in patients visiting the radiology department for diagnosis and therapeutic examination. The equipment used for the investigator is contaminated, which may result in HCAIs to the patients and healthcare professionals. Medical imaging professionals (MIPs) should have adequate knowledge to overcome the spread of infection in the radiology department. This systematic review aimed to examine the literature on the knowledge and precaution standard of MIPs on HCIAs. This study was performed with a relative keyword using PRISMA guidelines. The articles were retrieved from 2000 to 2022 using Scopus, PubMed, and ProQuest databases. The NICE public health guidance manual was used to assess the quality of the full-length article. The search yielded 262 articles, of which Scopus published 13 articles, PubMed published 179 articles, and ProQuest published 55 articles. In the present review, out of 262 articles, only 5 fulfilled the criteria that reported MIPs' knowledge of Jordan, Egypt, Sri Lanka, France, and Malawi populations. The present review reported that MIPs have moderate knowledge and precautionary standards regarding HCIAs in the radiology department. However, due to the limited studies published in the literature, the current review limits the application of the outcome in the vast MIPs population. This review recommended further studies to be conducted among the MIPs worldwide to know the actual knowledge and precaution standards regarding HCIAs.

Initial COVID-19 Severity and Long-COVID Manifestations: An Observational Analysis

OBJECTIVE

New-onset or persistent symptoms beyond after 4 weeks from COVID-19 are termed "long-COVID." Whether the initial severity of COVID-19 has a bearing on the clinicoradiological manifestations of long COVID is an area of interest.

MATERIAL AND METHODS

We did an observational analysis of the long-COVID patients after categorizing them based on their course of COVID-19 illness into mild, moderate, and severe groups. The clinical and radiological profile was compared across these groups.

RESULTS

Out of 150 long-COVID patients recruited in the study, about 79% (118), 14% (22), and 7% (10) had a history of mild, moderate, and severe COVID-19, respectively. Fatigue (P = .001), breathlessness (P = .001), tachycardia (P = .002), tachypnea (P < .001), raised blood pressure (P < .001), crepitations (P = .04), hypoxia at rest (P < .001), significant desaturation in 6-minute walk test (P = .27), type 1 respiratory failure (P = .001), and type 2 respiratory failure (P = .001) were found to be significantly higher in the long-COVID patients with a history of severe COVID-19. These patients also had the highest prevalence of abnormal chest X-ray (60%) and honeycombing in computed tomography scan thorax (25%, P = .027).

CONCLUSION

The course of long COVID bears a relationship with initial COVID-19 severity. Patients with severe COVID-19 are prone to develop more serious long-COVID manifestations.

A hybrid particle swarm optimization with multi-objective clustering for dermatologic diseases diagnosis

Effective and personalized treatment relies heavily on skin disease categorization. In the stratification of skin disorders, it is crucial to identify the subtypes of illnesses to provide an efficient therapy. To attain this aim, researchers have focused their attention on cluster algorithms for the stratification of skin disorders in recent decades. But, cluster algorithms have real-world drawbacks, including experimental noises, a large number of dimensions, and a poor ability to comprehend. Cluster algorithms, in particular, determine the quality of clusters using a single internal evaluation operation in the majority of cases. A single internal assessment procedure is difficult to design and robust for all datasets, which is a problem. The multi-objective particle swarm obtained high sensitivity in the existing work, but it is not able to anticipate all kinds of classes. An optimized cluster distance parameter for K-means clustering is determined using a hybrid particle swarm and moth flame optimization. Multi-objective is guided by two cluster value indices, including the K-means clustering misclassification rate and neural network classification rate. Hybrid PSO will solve the multi-objective problem to identify the optimal cluster for clustering. On the dermatological dataset from the UCI repository, MATLAB R2020a will be used to evaluate the proposed method. This will be followed by an evaluation of the proposed method’s performance using the cluster evaluation indices.

Relationship between physical activity, objective sleep parameters, and circadian rhythm in patients with head and neck cancer receiving chemoradiotherapy: A longitudinal study

OBJECTIVES

This study was developed to assess the relationship between physical activity, sleep and circadian rhythm using accelerometer and urine melatonin levels in patients with head and neck cancer (HNC). Also, this study evaluated the changes in physical activity, sleep, and circadian rhythm during the seven-week course of chemoradiotherapy.

METHODS

This longitudinal study recruited 27 participants diagnosed with HNC who were planning to undergo chemoradiotherapy. Accelerometers worn for 3 days during the 1st, 3rd, and 7th weeks of chemoradiotherapy were used to assess physical activity levels (step count and metabolic equivalents [METs]) and sleep quality (total sleep time [TST], sleep onset latency [SOL], and sleep efficiency [SE]). Urine melatonin analysis was conducted using the morning void urine sample on 1st, 3rd, and 7th weeks. The change in variables during the seven weeks and the correlation between them were analyzed.

RESULTS

During the seven weeks, trends of reduction in variables of physical activity, sleep and circadian rhythm were observed with significant decrease in step count, TST and melatonin levels. SE was found to have strong negative correlation with physical activity. TST was found to have moderate correlation with SE and step count. The variables of physical activity also showed moderate correlation among them.

CONCLUSION

This study concludes that higher physical activity is associated with poor SE due to increased night-time activity. There was a significant reduction in physical activity and sleep observed during seven weeks with moderate association between them. The significant circadian rhythm deregulation however showed poor association with the other variables.Level of Evidence: 2b.

Systemic corticosteroids for management of 'long-COVID': an evaluation after 3 months of treatment

Some patients even 4 weeks after Corona Virus Disease 2019 (COVID-19) remain to be symptomatic and are known as "long-COVID". In the present study we performed the follow up evaluation at 3 months of long-COVID patients, after treatment with systemic steroids. During the study duration, out of the 4,542 patients managed in the outpatient department of the particular unit, there were 49 patients of Long-COVID. The patients having abnormal computed tomography (CT) alongwith resting hypoxia or exertional desaturation were treated with systemic steroid (deflazacort) in tapering doses for 8-10 weeks. We retrospectively analysed the clinical and radiological findings of these patients at first presentation and at about 3 months of follow up visit. On follow up, all the 49 long-COVID patients showed improvement. The occurrence of breathlessness decreased from 91.83% to 44.89% (p<0.001) and cough from 77.55% to 8.16% (p<0.001). Twenty-four patients were prescribed systemic steroids. Out of these, nearly 58% patients had MMRC grade 4 breathlessness, which decreased to < 2 MMRC in about 86% of these patients. MMRC grade (median) decreased from 3 to 1 (p<0.001). Majority of patients who were tachypnoeic and hypoxic at rest (n=7) showed improvement (71%), post-treatment with corticosteroids. Occurrence of normal chest X-ray increased from 12% to 71% (p<0.001). All these patients had abnormal CT thorax initially, and post-treatment 25% had normal CT thorax. Hence, we conclude that systemic steroids are helpful in hastening recovery of select subset of long-COVID patients. Simultaneously, we should be cautious of immunosuppressive effects of steroids like tuberculosis reactivation, especially in tuberculosis endemic countries. These findings have therapeutic implications and may serve as guidance for future approach to the management of 'long-COVID' with pulmonary sequalae.

Maximal Respiratory Pressures and Maximum Voluntary Ventilation in Young Arabs: Association with Anthropometrics and Physical Activity

Background

Maximum inspiratory pressure (MIP), maximum expiratory pressure (MEP) and maximum voluntary ventilation (MVV) measurements assist in determining the respiratory muscle strength and endurance. These determinants of respiratory muscles vary significantly by age, gender, height, and ethnic origin. Normative values for maximum respiratory pressures (MRPs) and MVV would aid in evaluating respiratory muscle function in athletes, estimating performance, and assisting in rehabilitation. In addition, the reference values may aid in determining the efficacy of therapeutic interventions in young people with chronic respiratory diseases. The purpose of this study was to see how respiratory muscle strength indices correlated with anthropometric and physical activity characteristics in young Arabs.

Methodology

The study included 80 male volunteers and 85 female volunteers ranging in age from 18 to 30 years. MicroRPM was used to measure MIP and MEP, and pulmonary function test data, including MVV values, were recorded. All subjects completed the Global Physical Activity Questionnaire (GPAQ) and anthropometric measurements. Unpaired t-tests or Mann–Whitney U-tests were used to determine male-female differences. Using the Pearson correlation coefficient and Spearman Rho correlation coefficient tests, MIP and MEP values were correlated with body composition and physical activity. Using stepwise multiple linear regression analysis, the relationships between respiratory function (MVV, MIP, and MEP) and PFT values (FVC, FEV1, and FEV1/FVC), physical activity, and sedentary behavior were investigated.

Results

MIP, MEP, and MVV values were significantly lower in females than in males. MIP, MEP, and MVV values had a moderate correlation with forced vital capacity, forced expiratory volume in 1 second, and height, but not with weight, BMI, or GPAQ. Age, gender, and body mass index were found to be significant predictors of maximal respiratory pressures in a young Arab population.

Conclusion

Maximum respiratory pressures and maximal voluntary ventilation were significantly lower in young Arabs than in other ethnic groups; these values were influenced by gender and height but not by levels of physical activity.

Prevalence of COPD among population above 30 years in India: A systematic review and meta-analysis

Background

By 2030, Sustainable Development Goal 3.4 aims to reduce the premature mortality caused by non-communicable diseases through prevention and treatment. Chronic obstructive pulmonary disease is the second leading cause of mortality and disability-adjusted life years in India. This review was conducted to estimate the prevalence of COPD using systematic review and meta-analysis technique.

Method

Search was conducted using six databases for studies on COPD among population above 30 years in India between years 2000 to 2020. Cross-sectional and cohort studies reporting prevalence of COPD and associated risk factors were included in the present review. Screening and data extraction was done by two authors independently. Studies were appraised for quality using the modified New Castle Ottawa scale and reporting quality was assessed using STROBE guidelines.

Result

Our search returned 8973 records, from which 23 records fulfilled the eligibility criteria. Overall, the prevalence of COPD among population aged 30 years and above in India was 7%. Risk factors like active and passive smoking, biomass fuel exposure, environmental tobacco smoke, occupational exposure to dust, indoor and outdoor pollution, and increasing age were reported to have a significant association with COPD among Indian population.

Conclusion

Our findings suggest the need for a multicentric national-level research study to understand COPD burden and its contributing risk factors. The findings also suggest the need for COPD sensitive health literacy program focused on early screening and primary prevention of risk factors for COPD, which may help early initiation of self-management practices, that are crucial for better quality of life.

Prevalence of musculoskeletal chest pain in the emergency department: a systematic review and meta-analysis

OBJECTIVES

Our objective was to systematically review and meta-analyse relevant studies to determine the prevalence of musculoskeletal chest pain in the emergency department.

METHODS

This review was constructed while confirming to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. PubMed, Cochrane Library, SCOPUS, Science Direct, and OVID were systematically searched from their inception to January 19, 2020, to identify observational studies, where the prevalence of musculoskeletal causes of chest pain was reported in isolation or in combination with other causes or could be calculated from the available data.

RESULTS

A meta-analysis of the nine included studies, having a total of 14,743 participants, showed the global pooled prevalence of musculoskeletal chest pain in the emergency department to be 16% (10-22%) [I ²=99.24%]. The pooled prevalence for the European continent was 17% (9-25%) [I ²=99.51%] and that for the urban areas was 13% (7-19%) [I ²=99.00%].

CONCLUSIONS

This review provides a reliable estimate of the prevalence of musculoskeletal chest pain in the emergency department. More studies providing age and gender-specific data for the prevalence of musculoskeletal chest pain in the emergency department should be carried out. A paucity of such data from rural areas also needs to be addressed in future research work. The prevalence values from this study will be useful in the application of Bayesian reasoning utilised in diagnosing patients, where the process of Bayesian arguing begins by knowing pre-test probabilities of different differential diagnosis, in this case that of musculoskeletal chest pain in the emergency department.

Prevalence of low bone mineral density in inflammatory bowel disease and factors associated with it

BACKGROUND

Patients with inflammatory bowel disease (IBD) have numerous risk factors for low bone mineral density (BMD). We aimed to study the prevalence of low BMD in IBD and the factors associated with it.

METHODS

BMD was measured by radial quantitative ultrasound, and clinical and biochemical characteristics were compared in prospectively enrolled patients and healthy age and gender-matched controls. Chi-square test, t test for independent samples, analysis of variance (ANOVA), Mann-Whitney U test and Kruskal-Wallis H tests were used as appropriate for univariate analysis to compare the characteristics between patients with and without abnormal BMD. Binary logistic regression analysis was done to determine the factors associated with low BMD in IBD patients.

RESULTS

One hundred and six patients (Crohn's disease [CD] = 35, ulcerative colitis [UC] = 71) and 55 controls were included. Low BMD was equally prevalent in CD, UC and controls (42.9%, 36.6%, 36.4% respectively, p = 0.791). Serum calcium and vitamin D were significantly lower in IBD patients compared to controls (p < 0.001 and p = 0.003, respectively) but not between patients with low and normal BMD. Older age (Odds ratio [OR] = 66.12 [9.299-470.243], p < 0.001), late onset of disease (OR = 4.795 [1.067-21.543], p = 0.041) and absence of steroid usage (OR = 0.272 [0.089-0.832], p = 0.022) were significantly associated with low BMD.

CONCLUSIONS

The prevalence of low BMD in patients with IBD was similar to controls and this was associated with increasing age, late onset of disease, and absence of steroid usage. Judicious use of steroids can help preserve bone health in IBD.

RXRα and LXR activate two promoters in placenta- and tumor-specific expression of PLAC1

PLAC1 expression, first characterized as restricted to developing placenta among normal tissues, is also found in a wide range of tumors and transformed cell lines. To understand the basis for its unusual expression profile, we have analyzed the gene structure and its mode of transcription. We find that the gene has a hitherto unique feature, with two promoters, P1 and P2, separated by 105 kb. P2 has been described before. Here we define P1 and show that it and P2 are activated by RXRα in conjunction with LXRα or LXRβ. In placenta, P2 is the preferred promoter, whereas various tumor cell lines tend to express predominantly either one or the other promoter. Furthermore, when each promoter is fused to a luciferase reporter gene and transfected into cancer cell lines, the promoter corresponding to the more active endogenous promoter is preferentially transcribed. Joint expression of activating nuclear receptors can partially account for the restricted expression of PLAC1 in placenta, and may be co-opted for preferential P1 or P2 PLAC1 expression in various tumor cells.

Alteration in hematology of Labeo rohita under stress of pollution from Lakes of Bangalore, Karnataka, India

Blood is an indicator of physiological condition of an animal. Therefore, a field study was conducted to investigate the hematological parameters of wild population of rohu, Labeo rohita (Ham). The following aspects were evaluated in blood: hemoglobin content, red blood cell (RBC) and white blood cell (WBC) count, packed cell volume (PCV), and mean corpuscular volume (MCV) and mean corpuscular hemoglobin concentration (MCHC) values, and in plasma: cholesterol, protein, and glucose levels. For this purpose, rohu fish of varying sizes and weights were sampled from Hebbal (receiving a storm water drain) and Chowkalli lake (received domestic sewage and industrial effluents from various sources and was more polluted than Hebbal lake). It revealed noticeable differences in hemoglobin content, RBC and WBC count, and PCV and MCHC values. Severe anemia can be marked by a significant decrease in RBC count (p < 0.5), hemoglobin content, and PCV and MCHC values, whereas an increase in leukocyte count and MCV values were observed in fish from Chowkalli lake. Fish from lake B had fewer RBC and low concentration of serum protein and cholesterol. Serum concentration of glucose showed initial higher levels and then low concentration (900-1,500 g) in fish from lake B when compared to lake A. The variation in values of different parameters can be attributed to exposure of fish to various types of pollutants present mainly in the Chowkalli lake which receives heavy metals, synthetic detergents, petroleum products, and other acid and alkali substances from the nearby local industries. Other observations of these fish include dark body color and aggressive nature of fish.

X/autosomal translocations in the Xq critical region associated with premature ovarian failure fall within and outside genes

Premature ovarian failure curtails female reproductive life and is often linked to balanced Xq/autosomal translocations in a critical region. We mapped regions around translocations at the edges of this zone (one in Xq13.3, two in Xq26) in large-insert clones and analyzed their sequence. One Xq26 region is extensively transcribed and, in agreement with a recent independent analysis, the breakpoint interrupts a gene that encodes a widely expressed peptidase. In contrast 430 kb around the second Xq26 breakpoint has no putative or detected gene content. In 260 kb around the Xq13 translocation, the breakpoint falls among a cluster of repetitive elements at least 59 kb from the only detected gene (a rarely expressed T-box family transcription factor). We discuss our results in relation to models that ascribe premature ovarian failure to interruption of ovarian genes or to a failure of interactions involving DNA of the critical region during follicle development.

The putative forkhead transcription factor FOXL2 is mutated in blepharophimosis/ptosis/epicanthus inversus syndrome

In type I blepharophimosis/ptosis/epicanthus inversus syndrome (BPES), eyelid abnormalities are associated with ovarian failure. Type II BPES shows only the eyelid defects, but both types map to chromosome 3q23. We have positionally cloned a novel, putative winged helix/forkhead transcription factor gene, FOXL2, that is mutated to produce truncated proteins in type I families and larger proteins in type II. Consistent with an involvement in those tissues, FOXL2 is selectively expressed in the mesenchyme of developing mouse eyelids and in adult ovarian follicles; in adult humans, it appears predominantly in the ovary. FOXL2 represents a candidate gene for the polled/intersex syndrome XX sex-reversal goat.

Recovery and potential utility of YACs as circular YACs/BACs

A method has been established to convert pYAC4-based linear yeast artificial chromosomes (YACs) into circular chromosomes that can also be propagated in Escherichia coli cells as bacterial artificial chromosomes (BACs). The circularization is based on use of a vector that contains a yeast dominant selectable marker (G418R), a BAC cassette and short targeting sequences adjacent to the edges of the insert in the pYAC4 vector. When it is introduced into yeast, the vector recombines with the YAC target sequences to form a circular molecule, retaining the insert but discarding most of the sequences of the YAC telomeric arms. YACs up to 670 kb can be efficiently circularized using this vector. Re-isolation of megabase-size YAC inserts as a set of overlapping circular YAC/BACs, based on the use of an Alu-containing targeting vector, is also described. We have shown that circular DNA molecules up to 250 kb can be efficiently and accurately transferred into E.coli cells by electroporation. Larger circular DNAs cannot be moved into bacterial cells, but can be purified away from linear yeast chromosomes. We propose that the described system for generation of circular YAC derivatives can facilitate sequencing as well as functional analysis of genomic regions.

Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray

cDNA microarray technology has been increasingly used to monitor global gene expression patterns in various tissues and cell types. However, applications to mammalian development have been hampered by the lack of appropriate cDNA collections, particularly for early developmental stages. To overcome this problem, a PCR-based cDNA library construction method was used to derive 52,374 expressed sequence tags from pre- and peri-implantation embryos, embryonic day (E) 12.5 female gonad/mesonephros, and newborn ovary. From these cDNA collections, a microarray representing 15,264 unique genes (78% novel and 22% known) was assembled. In initial applications, the divergence of placental and embryonic gene expression profiles was assessed. At stage E12.5 of development, based on triplicate experiments, 720 genes (6.5%) displayed statistically significant differences in expression between placenta and embryo. Among 289 more highly expressed in placenta, 61 placenta-specific genes encoded, for example, a novel prolactin-like protein. The number of genes highly expressed (and frequently specific) for placenta has thereby been increased 5-fold over the total previously reported, illustrating the potential of the microarrays for tissue-specific gene discovery and analysis of mammalian developmental programs.

Eleven densely clustered genes, six of them novel, in 176 kb of mouse t-complex DNA

Targeted sequencing of the mouse t-complex has started with a 176-kb, gene-rich BAC localized with six PCR-based markers in inversion 2/3 of the highly duplicated region. The sequence contains 11 genes recovered primarily as cDNAs from early embryonic collections, including Igfals (previously placed on chromosome 17), Nubp2 (a fully characterized gene), Jsap1 (a JNK-binding protein), Rsp29 (the mouse homologue of the rat gene), Ndk3 (a nucleoside diphosphate kinase), and six additional putative genes of unknown function. With 50% GC content, 75% of the DNA transcribed, and one gene/16.0 kb (on average), the region may qualify as one of the most gene-dense segments in the mouse genome and provides candidates for dosage-sensitive phenotypes and mouse embryonic lethals mapped to the vicinity.

Large-insert clone/STS contigs in Xq11-q12, spanning deletions in patients with androgen insensitivity and mental retardation

An integrated large-insert clone map of the region Xq11-q12 is presented. A physical map containing markers within a few hundred kilobases of the centromeric locus DXZ1 to DXS1125 spans nearly 5 Mb in two contigs separated by a gap estimated to be approximately 100-250 kb. The contigs combine 75 yeast artificial chromosome clones, 12 bacterial artificial chromosome clones, and 17 P1-derived artificial chromosome clones with 81 STS or EST markers. Overall marker density across this region is approximately 1 STS/60 kb. Mapped within the contigs are 12 ESTs as well as 5 known genes, moesin (MSN), hephaestin (HEPH), androgen receptor (AR), oligophrenin-1 (OPHN1), and Eph ligand-2 (EPLG2). Orientation of the contigs on the X chromosome, as well as marker order within the contigs, was unambiguously determined by reference to a number of X chromosome breakpoints. In addition, the distal contig spans deletions from chromosomes of three patients exhibiting either complete androgen insensitivity (CAI) or a contiguous gene syndrome that includes CAI, impaired vision, and mental retardation.

Characterization of the human glutamate receptor subunit 3 gene (GRIA3), a candidate for bipolar disorder and nonspecific X-linked mental retardation

The X-chromosome breakpoint in a female patient with a balanced translocation t(X;12)(q24;q15), bipolar affective disorder and mental retardation was mapped within the glutamate receptor 3 (GRIA3) gene by fluorescence in situ hybridization. The GRIA3 cDNA of 5894 bp was cloned, and the gene structure and pattern of expression were determined. The most abundant GRIA3 transcript is composed of 17 exons. An additional 5 exons (2a, 2b, 5a, 5b, and 5c) from the 5' end of the GRIA3 open reading frame were identified by EST analysis (ESTs AI379066 and AA947914). Two new polymorphic microsatellite repeats, (TC)(n=12-26) and (AC)(n=15-19), were identified within GRIA3 5' and 3'UTRs. No mutations were detected in families segregating disorders mapping across GRIA3, one with X-linked bipolar affective disorder (BP) and one with a nonspecific X-linked mental retardation (MRX27). To assess the possibility of the involvement of the GRIA3 gene in familial cases of complex BP, a large set of 373 individuals from 40 pedigrees segregating BP were genotyped using closely linked (DXS1001) and intragenic (DXS1212 and GRIA3 3' UTR (AC)(n))) GRIA3 STR markers. No evidence of linkage was found by parametric Lod score analysis (the highest Lod score was 0. 3 at DXS1212, using the dominant transmission model) or by affected sib-pair analysis.

Integrated STS/YAC physical, genetic, and transcript map of human Xq21.3 to q23/q24 (DXS1203-DXS1059)

A map has been assembled that extends from the XY homology region in Xq21.3 to proximal Xq24, approximately 20 Mb, formatted with 200 STSs that include 25 dinucleotide repeat polymorphic markers and more than 80 expressed sequences including 30 genes. New genes HTRP5, CAPN6, STPK, 14-3-3PKR, and CALM1 and previously known genes including BTK, DDP, GLA, PLP, COL4A5, COL4A6, PAK3, and DCX are localized; candidate loci for other disorders for which genes have not yet been identified, including DFN-2, POF, megalocornea, and syndromic and nonsyndromic mental retardation, are also mapped in the region. The telomeric end of the contig overlaps a yeast artificial chromosome (YAC) contig from Xq24-q26 and with other previously published contigs provides complete sequence-tagged site (STS)/YAC-based coverage of the long arm of the X chromosome. The order of published landmark loci in genetic and radiation hybrid maps is in general agreement. Combined with high-density STS landmarks, the multiple YAC clone coverage and integrated genetic, radiation hybrid, and transcript map provide resources to further disease gene searches and sequencing.

Physical map covering a 2 Mb region in human xp11.3 distal to DX6849

A 2Mb contig was constructed of yeast artificial chromosomes (YACs) and P1 artificial chromosomes (PACs), extending from DXS6849 to a new marker EC7034R, 1Mb distal to UBE1, within the p11.3 region of the human X chromosome. This contig, which has on average four-fold cloned coverage, was assembled using 37 markers, including 13 new sequence tagged sites (STSs) developed from YAC and PAC end-fragments, for an average inter-marker distance of 55kb. The inferred marker order predicted from SEGMAP analysis, STS content and cell hybrid data is Xpter-EC7034R-EC8058R-FB20E11-DXS7804-D XS8308-(DXS1264, DXS1055)-DXS1003-UBE1-(UHX), PCTK1)-DXS1364-DXS1266-DXS337-SYN1-DXS6 849-cen. One (TC)n dinucleotide sequence from an end-clone was identified and found to be polymorphic (48% heterozygosity). The contig is merged with published physical maps both in the distal and in the centromeric direction of Xp, and provides reagents to aid in the DNA sequencing and the finding of genes in this region of the human genome.

Integrated YAC/STS physical and genetic map of 22.5 Mb of human Xq24-q26 at 56-kb inter-STS resolution

A yeast artificial chromosome sequence-tagged site-based (YAC/STS) physical map of 22.5 Mb of the Xq24-q26 cytogenetic band region of the human X chromosome has been assembled. DNA coverage includes 857 large-insert clones formatted with 405 STSs to provide ninefold depth of DNA. At five points, no bridging clones have been recovered from 20 X-chromosome equivalents of human DNA in YACs or bacterial clones, but the placement of 25 ("CA")n polymorphic markers permits the ordering of contigs by comparison with the genetic linkage map and radiation hybrid data. The map localizes the X3000 translocation breakpoint and six genes (ANT2, NDUFA1, LAMP2, OCRL, IGSF1, and HDGF) at better than 100-kb resolution. The relatively gene-poor nature of the region is consistent with relatively low uniform 34-42% GC content in STSs across nearly all of the region.

YAC/STS map of 15Mb of Xp21.3-p11.3, at 100kb resolution, with refined comparisons of genetic distances and DMD structure

The 15<HSP SP = "0.25">Mb region between DXS997 and DXS8054 in Xp21.3-p11.3 has been mapped at seven-fold average coverage in yeast artificial chromosomes (YACs) and 100 kb inter-sequence tagged site (STS) distance. YACs from six different collections show self-consistent maps. The STSs include 18 (CA) repeat and one tetranucleotide repeat marker that detect polymorphism, as well as eight well-studied genes, a second site for MXS1 sequences, and three expressed sequence tags (ESTs). One of the ESTs maps to intron 7 of Duchenne muscular dystrophy, and seems to be a processed intronic sequence with a poly(A) tail.

Impact and implications of yeast and human artificial chromosomes

Artificial chromosomes have been developed in the last 10 years to sustain genome mapping and, more recently, to begin initiating functional studies and some approaches to gene therapy. The use of yeast artificial chromosomes (YACs) in mapping the human X chromosome is reported as an example. The requirements which have postponed the development of human artificial chromosomes have now been relatively met, and some prospects are previewed here.

22-Mb integrated physical and genetic map based on YAC/STS content spanning the interval DXS1125-DXS95 in human Xq12-q21.31

A YAC/STS map has been assembled spanning 22 Mb across Xq12-q21.31, between markers DXS1125 and DXS95. In addition to the landmark loci for the X-inactivation center XIST and the ATRX, ATP7A, phosphoglycerate kinase, POU3F4, and choroideremia genes, the candidate disease gene regions for torsion dystonia 3 and two X-linked mental retardation syndromes are included. Also, the human voltage-dependent anion channel gene (HVDAC1) has been placed near DXS986. The current map incorporates 211 YACs from five different libraries, formatted with 185 STSs that comprise 26 genetic linkage markers, 60 newly-developed YAC-end STSs, and eight ESTs. The multiple clone coverage and average resolution of one STS per 120 kb provide resources for disease gene searches and are facilitating complete sequencing of the region.

Linkage analysis of X-linked cone-rod dystrophy: localization to Xp11.4 and definition of a locus distinct from RP2 and RP3

Progressive X-linked cone-rod dystrophy (COD1) is a retinal disease affecting primarily the cone photoreceptors. The COD1 locus originally was localized, by the study of three independent families, to a region between Xp11.3 and Xp21.1, encompassing the retinitis pigmentosa (RP) 3 locus. We have refined the COD1 locus to a limited region of Xp11.4, using two families reported elsewhere and a new extended family. Genotype analysis was performed by use of eight microsatellite markers (tel-M6CA, DXS1068, DXS1058, DXS993, DXS228, DXS1201, DXS1003, and DXS1055-cent), spanning a distance of 20 cM. Nine-point linkage analysis, by use of the VITESSE program for X-linked disorders, established a maximum LOD score (17.5) between markers DXS1058 and DXS993, spanning 4.0 cM. Two additional markers, DXS977 and DXS556, which map between DXS1058 and DXS993, were used to further narrow the critical region. The RP3 gene, RPGR, was excluded on the basis of two obligate recombinants, observed in two independent families. In a third family, linkage analysis did not exclude the RPGR locus. The entire coding region of the RPGR gene from two affected males from family 2 was sequenced and was found to be normal. Haplotype analysis of two family branches, containing three obligate recombinants, two affected and one unaffected, defined the COD1 locus as distal to DXS993 and proximal to DXS556, a distance of approximately 1.0 Mb. This study excludes COD1 as an allelic variant of RP3 and establishes a novel locus that is sufficiently defined for positional cloning.

Escape from X inactivation of two new genes associated with DXS6974E and DXS7020E

Most genes on the X chromosome undergo "inactivation," being transcribed from only one copy in female somatic cells, but several human genes have been shown to be expressed from both the active and the otherwise inactivated homologue. To assess further the fraction and location of genes that escape inactivation, we have analyzed the inactivation status of a set of 73 expressed sequence tags that were derived from the sequencing of cDNA collections and mapped to the X chromosome. Of 33 that were expressed in cultured cells, as assessed by reverse transcription and PCR, 4 (about 12%) were transcribed from both the active and the inactive X chromosome. Two, RPS4 and PCTAIRE1, are already known to escape inactivation; the other 2, of unknown function, include a short cDNA with a full open reading frame and a transcript with no detectable open reading frame. They map, respectively, to Xp11.3-p11.4 and Xp22.2; both regions were previously reported to encode sequences transcribed from the inactive X. Neither transcript has a corresponding sequence on the Y. Thus, they exhibit double dosage in females compared to males, and inactivation status may be inconsequential for these transcribed sequences.

Mapping of 59 EST gene markers in 31 intervals spanning the human X chromosome

The positioning of Expressed Sequence Tags (ESTs) constitutes an important step towards a functional map of the human genome, including candidate genes for human genetic disorders that have been localized by linkage analysis. We localized 59 ESTs on the human X chromosome, including 44 derived from infant brain and 15 from adult muscle cDNA libraries. Localizations by a somatic cell hybrid panel were refined for five cDNAs by mapping them in yeast artificial chromosome (YAC) contigs.

X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content

A YAC/STS map of the X chromosome has reached an inter-STS resolution of 75 kb. The map density is sufficient to provide YACs or other large-insert clones that are cross-validated as sequencing substrates across the chromosome. Marker density also permits estimates of regional gene content and a detailed comparison of genetic and physical map distances. Five regions are detected with relatively high G + C, correlated with gene richness; and a 17-Mb region with very low recombination is revealed between the Xq13.3 [XIST] and Xq21.3 XY homology loci.

4.5-Mb YAC STS contig at 50-kb resolution, spanning Xq25 deletions in two patients with lymphoproliferative syndrome

Sequence-tagged site (STS) content mapping in yeast artificial chromosomes (YACs) was used to cover the region deleted in two patients affected with X-linked lymphoproliferative disorder. The order of markers includes, centromere to telomere, DXS8009-DXS1206-DXS8078-DXS8044-DXS982- DXS6811-DXS8093-AFM240xblO- DXS75-DXS737-DXS100-DXS6-DXS1046-DXS803 8. The order of six major markers is confirmed by fluorescent in situ hybridization, and all the markers assigned by linkage mapping fall within a 1.6-cM interval. The contig comprises 90 clones containing 89 STSs, yielding a resolution of 50 kb; DNA in a gap just telomeric to DXS8044 has not been found in > 20 equivalents of YACs or bacterial clones. The two deletions were found to have centromeric breakpoints that lie close to DXS1206 and may be identical; the telomeric breakpoints are -150 kb apart, one falling between DXS737 and DXS100, the other between DXS100 and DXS1046. Several STSs near the breakpoints show weak amplification from more than one site; one gives products from three groups of YACs, and lie, respectively, within 50 kb of the centromeric and the two telomeric deletion borders. Such partially duplicated segments of DNA are candidates for involvement in the formation of the deletions.

Ordered shotgun sequencing of a 135 kb Xq25 YAC containing ANT2 and four possible genes, including three confirmed by EST matches

Ordered shotgun sequencing (OSS) has been successfully carried out with an Xq25 YAC substrate. yWXD703 DNA was subcloned into lambda phage and sequences of insert ends of the lambda subclones were used to generate a map to select a minimum tiling path of clones to be completely sequenced. The sequence of 135 038 nt contains the entire ANT2 cDNA as well as four other candidates suggested by computer-assisted analyses. One of the putative genes is homologous to a gene implicated in Graves' disease and it, ANT2 and two others are confirmed by EST matches. The results suggest that OSS can be applied to YACs in accord with earlier simulations and further indicate that the sequence of the YAC accurately reflects the sequence of uncloned human DNA.

YAC/STS map of 9 Mb of Xq26 at 100-kb resolution, localizing 6 ESTs, 6 genes, and 32 genetic markers

To facilitate functional analysis of the Xq26 region, the physical map has been extended across 9 Mb with 192 YACs and markers including 90 STSs (sequence-tagged sites) and 50 hybridization probes. Six genes and six ESTs are localized. In addition, 32 markers that detect polymorphism permit an integration of physical with genetic linkage data. The localizations of eight uncloned disease genes are thereby delimited on the physical map. The data also suggest a possible gradient of recombination across the cytogenetic band, with little or no recombination reported in the centromeric 3.5-4 Mb.

Construction of a YAC contig and an STS map spanning 3.6 megabase pairs in Xp22.1

We have constructed a 3.6 Mb sequence tagged sites (STS)-based yeast artificial chromosome (YAC) contig, consisting of 58 individual YAC clones, spanning the region PDHA1 and DXS451 on Xp22.1. In addition to establishing the order of PDHA1, ISPK-1, DXS2504, DXS1528 and the 13 known polymorphic loci as Xpter-PDHA1-DXS443-DXS3424-ISPK-1-DXS12 29-DXS2504-DXS1528-DXS365-DXS7101- DXS1683-DXS1052-DXS274-DXS92-DXS1226-DX S41-DXS989-DXS451-Xcen, we have also developed 35 novel STSs from YAC end clones. These results provide a high density of STS markers (approximately 1 per 70 kb). Furthermore, a detailed long-range restriction map of the contig has been constructed with rare-cutter enzymes and this has refined and verified the physical distances between markers inferred from YAC sizes and their STS content. The integration of the physical mapping data with previous genetic mapping data and the use of STSs and non-chimeric YAC clones reported here should facilitate the construction of a transcript map of this region and the positional cloning of disease genes in this portion of Xp22.1.

Characterization of a YAC contig spanning the pseudoautosomal region

Due to its unique biology of partial sex linkage and high recombination rates, the pseudoautosomal region (PAR1) on both X and Y chromosomes has attracted considerable interest. In addition, an extremely high level of YAC instability has been observed in this region. We have derived 82 YAC clones from six different YAC libraries mapping to this 2.6-Mb region. Of these a subset of 22 YACs was analyzed in detail. YAC contigs were assembled using 67 pseudoautosomal probes, of which 64 were unambiguously ordered. All markers are well distributed over the entire region, including the middle part of the region, which has previously been found difficult to contig. Two gaps of less than 50 kb within the genomic locus of CSF2RA and around XE7 remain, which could not be covered with YACs, cosmids, or phages. This YAC contig anchored on the physical map of PAR1 represents one of the best characterized large regions of the human genome with a map completion greater than 90% at 100-kb resolution and has permitted the accurate localization of all known genes within this region.

Characterization of four human YAC libraries for clone size, chimerism and X chromosome sequence representation

Four collections of human X-specific YACs, derived from human cells containing supernumerary X chromosomes or from somatic cell hybrids containing only X human DNA were characterized. In each collection, 80-85% of YAC strains contained a single X YAC. Five thousand YACs from the various libraries were sized, and cocloning was assessed in subsets by the fraction of YAC insert-ends with non-X sequences. Cocloning was substantial, ranging up to 50% for different collections; and in agreement with previous indications, in all libraries the larger the YACs, the higher the level of cocloning. In libraries made from human-hamster hybrid cells, expected numbers of clones were recovered by STS-based screening; but unexpectedly, the two collections from cells with 4 or 5 X chromosomes yielded numbers of YACs corresponding to an apparent content of only about two X equivalents. Thus it is possible that the DNA of inactive X chromosomes is poorly cloned into YACs, speculatively perhaps because of its specialized chromatin structure.

Protein HU from the cyanobacterium Anabaena

Protein HU was purified from the cyanobacterium Anabaena 7120. Its complete amino acid sequence was determined by automated Edman degradation of the whole protein and of CNBr and chymotryptic peptides. The active DNA-binding protein is a homodimer of 94-amino acid subunits. Approximately half of the residues are identical to those of the two subunits of HU protein from E. coli. The protein binds to both supercoiled and relaxed double-stranded DNA, cooperatively. The contour lengths of circular DNAs were reduced up to six-fold by HU binding at low ratios of HU to DNA. At higher ratios, highly condensed aggregates were observed. Heterocysts are cells specialized for nitrogen fixation that differentiate at regular intervals along the filaments of Anabaena when they are transferred to a medium lacking combined nitrogen. Protein HU, labeled with 35S in cells growing on ammonia, disappears from developing heterocysts, although it is stably maintained in the intervening strings of vegetative cells. Following establishment of the heterocyst pattern, in which the differentiated cells are spaced about ten cells apart, HU is synthesized in the vegetative cells but not in the heterocysts. Several other vegetative cell DNA-binding proteins are also degraded during the differentiation. The major DNA-binding protein in heterocysts is a new one of subunit molecular mass around 12,000, whose relationship to other DNA-binding proteins is unknown. The gene encoding protein HU was cloned from Anabaena DNA and sequenced. The gene sequence is consistent with the amino acid sequence determined previously. Low stringency hybridization to Anabaena DNA digests suggest that there is a single gene for HU, consistent also with the unique amino acid sequence. S1 nuclease protection experiments suggest that the HU gene promoter differs from those of other Anabaena genes determined to date.

Chromosomal bar codes produced by multicolor fluorescence in situ hybridization with multiple YAC clones and whole chromosome painting probes

Colored chromosome staining patterns, termed chromosomal 'bar codes' (CBCs), were obtained on human chromosomes by fluorescence in situ hybridization (FISH) with pools of Alu-PCR products from YAC clones containing human DNA inserts ranging from 100 kbp to 1 Mbp. In contrast to conventional G- or R-bands, the chromosomal position, extent, individual color and relative signal intensity of each 'bar' could be modified depending on probe selection and labeling procedures. Alu-PCR amplification products were generated from 31 YAC clones which mapped to 37 different chromosome bands. For multiple color FISH, Alu-PCR amplification products from various clones were either biotinylated or labeled with digoxigenin. Probes from up to twenty YAC clones were used simultaneously to produce CBCs on selected human chromosomes. Evaluation using a cooled CCD camera and digital image analysis confirmed the high reproducibility of the bars from one metaphase spread to another. Combinatorial FISH with mixtures of whole chromosomes paint probes was applied to paint seven chromosomes simultaneously in different colors along with a set of YAC clones which map to these chromosomes. We discuss the potential to construct analytical chromosomal bar codes adapted to particular needs of cytogenetic investigations and automated image analysis.

Mapping human chromosomes by walking with sequence-tagged sites from end fragments of yeast artificial chromosome inserts

Sequence-tagged sites (STSs) derived from end fragments of chromosome-specific yeast artificial chromosomes (YACs) can facilitate the assembly of an overlapping YAC/STS map. Contigs form rapidly by iteratively screening YAC collections with end-fragment STSs from YACs that have not yet been detected by any previous STS. The map is rendered rapidly useful during its assembly by incorporating supplementary STSs from genes and genetic linkage probes with known locations. Methods for the systematic development and testing of the end-fragments STSs are given here, and a group of 100 STSs is presented for the X chromosome. The mapping strategy is shown to be successful in simulations with portions of the X chromosome already largely mapped into overlapping YACs by other means.

Yeast artificial chromosome-based genome mapping: some lessons from Xq24-q28

Yeast artificial chromosomes (YACs) have recently provided a potential route to long-range coverage of complex genomes in contiguous cloned DNA. In a pilot project for 50 Mb (1.5% of the human genome), a variety of techniques have been applied to assemble Xq24-q28 YAC contigs up to 8 Mb in length and assess their quality. The results indicate the relative strength of several approaches and support the adequacy of YAC-based methods for mapping the human genome.

Isolation of a human DNA sequence which spans the fragile X

To identify the sequences involved in the expression of the fragile X and to characterize the molecular basis of the genetic lesion, we have constructed yeast artificial chromosomes (YACs) containing human DNA and have screened them with cloned DNA probes which map close to the fragile site at Xq27.3. We have isolated and partly characterized a YAC containing approximately 270 kb of human DNA from an X chromosome which expresses the fragile X. This sequence in a yeast artificial ring chromosome, XTY26, hybridizes to the two closest DNA markers, VK16 and Do33, which flank the fragile site. The human DNA sequence in XTY26 also spans the fragile site on chromosome in situ hybridization. When a restriction map of XTY26, derived by using infrequently cutting restriction enzymes, is compared with similar YAC maps derived from non-fragile-X patients, no large-scale differences are observed. This YAC, XTY26, may enable (a) the fragile site to be fully characterized at the molecular level and (b) the pathogenetic basis of the fragile-X syndrome to be determined.

Specificity determinants in the attachment sites of bacteriophages HK022 and lambda

The Int proteins of bacteriophages HK022 and lambda promote recombination between phage and bacterial attachment sites. Although the proteins and attachment sites of the two phages are similar, neither protein promotes efficient recombination between the pair of attachment sites used by the other phage. To analyze this difference in specificity, we constructed and characterized chimeric attachment sites in which segments of one site were replaced with corresponding segments of the other. Most such chimeras recombined with appropriate partner sites in vivo and in vitro, and their differential responses to the Int proteins of the two phages allowed us to locate determinants of the specificity difference in the bacterial attachment sites and a central segment of the phage attachment sites. The location of these determinants encompasses three of the four core-type binding sites for lambda Int: C, B, and most importantly, B'. The regions corresponding to the C' core binding site and the arm-type binding sites of lambda Int play no role in the specificity difference and, indeed, are well conserved in the two phages. We found, unexpectedly, that the effect of replacement of an Int-binding region on the recombinational potency of one chimeric site was reversed by a change of partner. This novel context effect suggests that postsynaptic interactions affect the specificity of recognition of attachment sites by Int.