Fetal gender determination through Y-STR analysis of maternal plasma during the third trimester of pregnancy

Background: The passage of nucleated cells between mother and fetus is well recognized (Lo et al., 1989, 1996). As well as, cell-free fetal DNA in maternal plasma or serum is at present widely investigated as a source of fetal genetic material (Stanghellini et al., 2006) [18]. There has been much recent interest in the use of DNA derived from plasma or serum (Boland, 1996). This DNA can be utilized for molecular diagnosis as well as prenatal sex discernment.Objective: To establish an easy, reliable, and completely safe method for fetal gender determination alternative to conventional exhausting current techniques applied in gynecologic hospitals and clinics, besides its further applications in forensic casework.Methods: EDTA-Blood samples were taken from 30 pregnant women all in the third trimester of pregnancy, then plasma was separated from each sample, from which DNA was isolated using a QIAamp DNA Mini Kit, with special modifications done in the extracting procedure to concentrate and obtain minute quantities of fetal DNA, together with maternal DNA, from maternal plasma. In addition, bloodstain samples were taken from the husbands of women who were pregnant with male fetuses from which DNA was isolated using a QIAamp DNA Micro Kit for comparison. DNA quantification was done using a Real-time PCR utilizing Quantifiler Duo Kit. PCR was done using an AmpFlSTR Y-Filer Kit, then amplified products were typed using a 3130 Genetic Analyzer.Results: Full and partial Y-STR profiles (6–17 STR loci) were obtained from all plasma samples taken from pregnant women with male fetuses, while negative Y-STR profiles (no single STR locus) were obtained from all plasma samples taken from pregnant women with female fetuses.Conclusion: It is recommended to use Y-STR profiling as an alternative technique for fetal gender determination during the third trimester of pregnancy, in addition to its significance in forensic casework.Keywords: Fetal gender; Maternal plasma; Y-STR analysis; Pregnancy; Forensic casewor

Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis

In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesize in the opposite direction. By extending RNA primers, the lagging-strand polymerase restarts at short intervals and produces Okazaki fragments. At least in prokaryotic systems, this directionality problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. Here we use single-molecule techniques to visualize, in real time, the formation and release of replication loops by individual replisomes of bacteriophage T7 supporting coordinated DNA replication. Analysis of the distributions of loop sizes and lag times between loops reveals that initiation of primer synthesis and the completion of an Okazaki fragment each serve as a trigger for loop release. The presence of two triggers may represent a fail-safe mechanism ensuring the timely reset of the replisome after the synthesis of every Okazaki fragment.

Genetic characterization of morphologically variant strains of Paracoccidioides brasiliensis

Molecular characterization of Paracoccidioides brasiliensis variant strains that had been preserved under mineral oil for decades was carried out by random amplified polymorphic DNA analysis (RAPD). On P. brasiliensis variants in the transitional phase and strains with typical morphology, RAPD produced reproducible polymorphic amplification products that differentiated them. A dendrogram based on the generated RAPD patterns placed the 14 P. brasiliensis strains into five groups with similarity coefficients of 72%. A high correlation between the genotypic and phenotypic characteristics of the strains was observed. A 750 bp-RAPD fragment found only in the wild-type phenotype strains was cloned and sequenced. Genetic similarity analysis using BLASTx suggested that this RAPD marker represents a putative domain of a hypothetical flavin-binding monooxygenase (FMO)-like protein of Neurospora crassa.FiocruzBritish Council Progra

Protein–protein HADDocking using exclusively pseudocontact shifts

In order to enhance the structure determination process of macromolecular assemblies by NMR, we have implemented long-range pseudocontact shift (PCS) restraints into the data-driven protein docking package HADDOCK. We demonstrate the efficiency of the method on a synthetic, yet realistic case based on the lanthanide-labeled N-terminal ε domain of the E. coli DNA polymerase III (ε186) in complex with the HOT domain. Docking from the bound form of the two partners is swiftly executed (interface RMSDs < 1 Å) even with addition of very large amount of noise, while the conformational changes of the free form still present some challenges (interface RMSDs in a 3.1–3.9 Å range for the ten lowest energy complexes). Finally, using exclusively PCS as experimental information, we determine the structure of ε186 in complex with the HOT-homologue θ subunit of the E. coli DNA polymerase III

Orthodontic treatment needs in the western region of Saudi Arabia: a research report

BACKGROUND: Evaluation of self perceived and actual need for orthodontic treatment helps in planning orthodontic services and estimating the required resources and man power. In the present study, the perceptive need as evaluated by patients and the actual need to orthodontic treatment, as assessed by orthodontists, were evaluated at two types of dental practices in the city of Jeddah using the Index of Orthodontic Treatment Need (IOTN). METHODS: A consecutive sample of 743 adults seeking orthodontic treatment at two different types of dental practices in Jeddah; King Abdulaziz University, Faculty of Dentistry (KAAU) (Free treatment) and two private dental polyclinics (PDP) (Paid treatment), was examined for orthodontic treatment need using the dental health component (DHC) of the IOTN. The self-perceived need for orthodontic treatment was also determined using the aesthetic component (AC) of the IOTN. The IOTN score and the incidence of each variable were calculated statistically. AC and DHC categories were compared using the Chi-Square and a correlation between them was assessed using Spearman's correlation test. AC and DHC were also compared between the two types of dental practices using the Chi-Square. RESULTS: The results revealed that among the 743 patients studied, 60.6% expressed no or slight need for treatment, 23.3% expressed moderate to borderline need and only16.1% thought they needed orthodontic treatment. Comparing these estimates to professional judgments, only 15.2% conformed to little or no need for treatment, 13.2% were assessed as in borderline need and 71.6% were assessed as in need for treatment (p < 0.001). Spearman's correlation test proved no correlation (r = -.045) between the two components. Comparing the AC and the DHC between the KAAU group and PDP group showed significant differences between the two groups (p < 0.001). CONCLUSION: Patient's perception to orthodontic treatment does not always correlate with professional assessment. The IOTN is a valid screening tool that should be used in orthodontic clinics for better services especially, in health centers that provide free treatment

Utilisation of an operative difficulty grading scale for laparoscopic cholecystectomy

Background A reliable system for grading operative difficulty of laparoscopic cholecystectomy would standardise description of findings and reporting of outcomes. The aim of this study was to validate a difficulty grading system (Nassar scale), testing its applicability and consistency in two large prospective datasets. Methods Patient and disease-related variables and 30-day outcomes were identified in two prospective cholecystectomy databases: the multi-centre prospective cohort of 8820 patients from the recent CholeS Study and the single-surgeon series containing 4089 patients. Operative data and patient outcomes were correlated with Nassar operative difficultly scale, using Kendall’s tau for dichotomous variables, or Jonckheere–Terpstra tests for continuous variables. A ROC curve analysis was performed, to quantify the predictive accuracy of the scale for each outcome, with continuous outcomes dichotomised, prior to analysis. Results A higher operative difficulty grade was consistently associated with worse outcomes for the patients in both the reference and CholeS cohorts. The median length of stay increased from 0 to 4 days, and the 30-day complication rate from 7.6 to 24.4% as the difficulty grade increased from 1 to 4/5 (both p < 0.001). In the CholeS cohort, a higher difficulty grade was found to be most strongly associated with conversion to open and 30-day mortality (AUROC = 0.903, 0.822, respectively). On multivariable analysis, the Nassar operative difficultly scale was found to be a significant independent predictor of operative duration, conversion to open surgery, 30-day complications and 30-day reintervention (all p < 0.001). Conclusion We have shown that an operative difficulty scale can standardise the description of operative findings by multiple grades of surgeons to facilitate audit, training assessment and research. It provides a tool for reporting operative findings, disease severity and technical difficulty and can be utilised in future research to reliably compare outcomes according to case mix and intra-operative difficulty

CD39, NTPDase 1, is attached to the plasma membrane by two transmembrane domains. Why?

Since the identification of CD39 and other members of the e-NTPDase (ecto-nucleoside triphosphate diphosphohydrolase) family as the primary enzymes responsible for cell surface nucleotide hydrolysis, one of their most intriguing features has been their unusual topology. The active site lies in the large extracellular region, but instead of being anchored in the membrane by a single transmembrane domain or lipid link like other ectoenzymes, CD39 has two transmembrane domains, one at each end. In this review we discuss evidence that the structure and dynamics of the transmembrane helices are intricately connected to enzymatic function. Removal of either or both transmembrane domains or disruption of their native state by detergent solubilization reduces activity by 90%, indicating that native function requires both transmembrane domains to be present and in the membrane. Enzymatic and mutational analysis of the native and truncated forms has shown that the active site can exist in distinct functional states characterized by different total activities, substrate specificities, hydrolysis mechanisms, and intermediate ADP release during ATP hydrolysis, depending on the state of the transmembrane domains. Disulfide crosslinking of cysteines introduced within the transmembrane helices revealed that they interact within and between molecules, in particular near the extracellular domain, and that activity depends on their organization. Both helices exhibit a high degree of rotational mobility, and the ability to undergo dynamic motions is required for activity and regulated by substrate binding. Recent reports suggest that membrane composition can regulate NTPDase activity. We propose that mechanical bilayer properties, potentially elasticity, might regulate CD39 by altering the balance between stability and mobility of its transmembrane domains

Search for new physics with same-sign isolated dilepton events with jets and missing transverse energy

A search for new physics is performed in events with two same-sign isolated leptons, hadronic jets, and missing transverse energy in the final state. The analysis is based on a data sample corresponding to an integrated luminosity of 4.98 inverse femtobarns produced in pp collisions at a center-of-mass energy of 7 TeV collected by the CMS experiment at the LHC. This constitutes a factor of 140 increase in integrated luminosity over previously published results. The observed yields agree with the standard model predictions and thus no evidence for new physics is found. The observations are used to set upper limits on possible new physics contributions and to constrain supersymmetric models. To facilitate the interpretation of the data in a broader range of new physics scenarios, information on the event selection, detector response, and efficiencies is provided.Comment: Published in Physical Review Letter