Structure-specific DNA recombination sites: Design, validation, and machine learning-based refinement

Recombination systems are widely used as bioengineering tools, but their sites have to be highly similar to a consensus sequence or to each other. To develop a recombination system free of these constraints, we turned toward attC sites from the bacterial integron system: single-stranded DNA hairpins specifically recombined by the integrase. Here, we present an algorithm that generates synthetic attC sites with conserved structural features and minimal sequence-level constraints. We demonstrate that all generated sites are functional, their recombination efficiency can reach 60%, and they can be embedded into protein coding sequences. To improve recombination of less efficient sites, we applied large-scale mutagenesis and library enrichment coupled to next-generation sequencing and machine learning. Our results validated the efficiency of this approach and allowed us to refine synthetic attC design principles. They can be embedded into virtually any sequence and constitute a unique example of a structure-specific DNA recombination system.

Identification of Plasmodium falciparum nuclear proteins by mass spectrometry and proposed protein annotation

The nuclear proteome of Plasmodium falciparum results from the continual shuttle of proteins between the cell cytoplasm-nucleus and vice versa. Using shotgun proteomics tools, we explored the nuclear proteins of mixed populations of Plasmodium falciparum extracted from infected erythrocytes. We combined GeLC-MS/MS and 2D-LC-MS/MS with a peptide ion exclusion procedure in order to increase the detection of low abundant proteins such as those involved in gene expression. We have identified 446 nuclear proteins covering all expected nuclear protein families involved in gene regulation. All structural ribosomal (40S and 60S) proteins were identified which is consistent with the nuclear localization of ribosomal biogenesis. Proteins involved in the translation machinery were also found suggesting that translational events might occur in the nucleus in P. falciparum as previously hypothesized in eukaryotes. These data were compared to the protein list established by PlasmoDB and submitted to Plasmobase a recently reported Plasmodium annotation website to propose new functional putative annotation of several unknown proteins found in the nuclear extracts.

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

BACKGROUND

Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires the reconstruction of biochemical and regulatory pathways at the community level in a given environment. In order to understand how environmental factors affect the genetic material and the dynamics of the expression from one environment to another, we want to evaluate the quantity of gene protein sequences or transcripts associated to a given pathway by precisely estimating the abundance of protein domains, their weak presence or absence in environmental samples.

RESULTS

MetaCLADE is a novel profile-based domain annotation pipeline based on a multi-source domain annotation strategy. It applies directly to reads and improves identification of the catalog of functions in microbiomes. MetaCLADE is applied to simulated data and to more than ten metagenomic and metatranscriptomic datasets from different environments where it outperforms InterProScan in the number of annotated domains. It is compared to the state-of-the-art non-profile-based and profile-based methods, UProC and HMM-GRASPx, showing complementary predictions to UProC. A combination of MetaCLADE and UProC improves even further the functional annotation of environmental samples.

CONCLUSIONS

Learning about the functional activity of environmental microbial communities is a crucial step to understand microbial interactions and large-scale environmental impact. MetaCLADE has been explicitly designed for metagenomic and metatranscriptomic data and allows for the discovery of patterns in divergent sequences, thanks to its multi-source strategy. MetaCLADE highly improves current domain annotation methods and reaches a fine degree of accuracy in annotation of very different environments such as soil and marine ecosystems, ancient metagenomes and human tissues.

Meet-U: Educating through research immersion

We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, with protein–protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.

Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes

Background

With the availability of complete genome sequences of both human and non-human Plasmodium parasites, it is now possible to use comparative genomics to look for orthology across Plasmodium species and for species specific genes. This comparative analyses could provide important clues for the development of new strategies to prevent and treat malaria in humans, however, the number of functionally annotated proteins is still low for all Plasmodium species. In the context of genomes that are hard to annotate because of sequence divergence, such as Plasmodium, domain co-occurrence becomes particularly important to trust predictions. In particular, domain architecture prediction can be used to improve the performance of existing annotation methods since homologous proteins might share their architectural context.

Results

Plasmobase is a unique database designed for the comparative study of Plasmodium genomes. Domain architecture reconstruction in Plasmobase relies on DAMA, the state-of-the-art method in architecture prediction, while domain annotation is realised with CLADE, a novel annotation tool based on a multi-source strategy. Plasmobase significantly increases the Pfam domain coverage of all Plasmodium genomes, it proposes new domain architectures as well as new domain families that have never been reported before for these genomes. It proposes a visualization of domain architectures and allows for an easy comparison among architectures within Plasmodium species and with other species, described in UniProt.

Conclusions

Plasmobase is a valuable new resource for domain annotation in Plasmodium genomes. Its graphical presentation of protein sequences, based on domain architectures, will hopefully be of interest for comparative genomic studies. It should help to discover species-specific genes, possibly underlying important phenotypic differences between parasites, and orthologous gene families for deciphering the biology of these complex and important Apicomplexan organisms. In conclusion, Plasmobase is a flexible and rich site where any biologist can find something of his/her own interest.

Availability

Plasmobase is accessible at http://genome.lcqb.upmc.fr/plasmobase/.

Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence

Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades. We propose a novel exploitation of the large amount of data available: 1. for each known protein domain, several probabilistic clade-centered models are constructed from a large and differentiated panel of homologous sequences, 2. a decision-making protocol combines outcomes obtained from multiple models, 3. a multi-criteria optimization algorithm finds the most likely protein architecture. The method is evaluated for domain and architecture prediction over several datasets and statistical testing hypotheses. Its performance is compared against HMMScan and HHblits, two widely used search methods based on sequence-profile and profile-profile comparison. Due to their closeness to actual protein sequences, clade-centered models are shown to be more specific and functionally predictive than the broadly used consensus models. Based on them, we improved annotation of Plasmodium falciparum protein sequences on a scale not previously possible. We successfully predict at least one domain for 72% of P. falciparum proteins against 63% achieved previously, corresponding to 30% of improvement over the total number of Pfam domain predictions on the whole genome. The method is applicable to any genome and opens new avenues to tackle evolutionary questions such as the reconstruction of ancient domain duplications, the reconstruction of the history of protein architectures, and the estimation of protein domain age. Website and software: http://www.lcqb.upmc.fr/CLADE.

Current sequence databases contain hundreds of billions of nucleotides coding for genes and a classification of these sequences is a primary problem in genomics. A reasonable way to organize these sequences is through their predicted domains, but the identification of domains in very divergent sequences, spanning the entire phylogenetic tree of species, is a difficult problem. By generating multiple probabilistic models for a domain, describing the spread of evolutionary patterns in different phylogenetic clades, we can effectively explore domains that are likely to be coded in gene sequences. Through a machine learning approach and optimization techniques, coding for expected evolutionary constraints, we filter the many possibilities of domain identification found for a gene and propose the most likely domain architecture associated to it. The application of this novel approach to the full genome of Plasmodium falciparum, to a dataset of sequences from three SCOP datasets highlights the interest of exploring multiple pathways of domain evolution in the aim of extracting biological information from genomic sequences. Our new computational approach was developed with the hope of providing a novel tier of accurate and precise tools that complement existing tools such as HMMer, HHblits and PSI-BLAST, by exploring in a novel way the large amount of sequence data available. The existence of powerful databases for sequences, domains and architectures help make this hope a reality.

Impact of the introduction of fetal central monitoring on hospital expenses with cardiotocographic paper

Digital storage of cardiotocographic (CTG) tracings by fetal central monitoring systems (fCMS) obviates the need for printing, or alternatively, the tracings can be printed in regular paper instead of CTG thermal paper. We aimed at evaluating the impact of the introduction of the Omniview-SisPorto(®) system on CTG paper costs in a large university hospital. After introduction of the fCMS, there was an 87% reduction in median annual expenses with CTG paper in the labour ward (p = 0.011) and a 78% decrease in the prenatal clinic (p = 0.017), despite a more than 40% increase in the median number of observed women. Routine use of fCMS may provide an important reduction in hospital expenses associated with the use of thermal CTG paper, thus reducing the investment made in their acquisition and maintenance.

Access to computerised analysis of intrapartum cardiotocographs improves clinicians' prediction of newborn umbilical artery blood pH

OBJECTIVE

To evaluate the impact of access to computerised cardiotocograph (CTG) analysis on reproducibility and accuracy of clinicians' predictions of umbilical artery blood pH (UAB pH) and 5-minute Apgar score.

DESIGN

Prospective evaluation of pre-recorded cases.

SETTING

A tertiary-care university hospital.

POPULATION

From databases of intrapartum CTGs acquired in singleton term pregnancies, 204 tracings with low signal loss and short time interval to delivery were consecutively selected.

METHODS

Tracings were randomly assigned to computer analysis by the Omniview-SisPorto 3.5 system (study group n = 104) or to no analysis (control group n = 100). Three experienced clinicians evaluated all tracing printouts independently and were asked to predict the newborns' UAB pH and 5-minute Apgar scores from them.

MAIN OUTCOME MEASURES

Interobserver agreement (measured by the intraclass correlation coefficient [ICC]) and accuracy in prediction of neonatal outcomes with 95% CI.

RESULTS

Agreement on prediction of UAB pH was significantly higher in the study group (ICC = 0.70; 95% CI 0.61-0.77) than in the control group (ICC = 0.43; 95% CI 0.21-0.60), and a trend towards better agreement was also seen in estimation of 5-minute Apgar scores (ICC = 0.55; 95% CI 0.38-0.68 versus ICC = 0.43; 95% CI 0.25-0.57). Observers predicted UAB pH values correctly within a 0.10 margin in 70% of cases in the study group (95% CI 0.61-0.79) versus 46% in the control group (95% CI 0.35-0.56). They predicted 5-minute Apgar scores within a margin of one in 81% of cases in the study group (95% CI 0.73-0.88) and in 70% of cases in the control group (95% CI 0.61-0.79).

CONCLUSIONS

Prediction of UAB pH is more reproducible and accurate when clinicians have access to computerised analysis of CTGs.

Impact of labor and delivery simulation classes in undergraduate medical learning

INTRODUCATION: The aim of this study was to evaluate the impact on knowledge and learner satisfaction of adding a labour and delivery simulator-based training module versus a self-study session to the pre-existing theoretical class, in the 5(th) year undergraduate medical curriculum.

METHODS

One hundred and fifty seven students attending the 5-week Obstetrics and Gynecology rotation were enrolled, and 107 completed the study. After a 90-minute "labour and delivery" theoretical interactive class, students were randomized to two groups: the first (n = 56) participated in a 30-minute supervised self-study session, while the second (n = 51) attended a 20-30 minute delivery simulator session. Tests consisting of 10 multiple-choice questions were taken before the theoretical class (pre-test), after the self-study or simulation session (1(st) post-test) and 12-15 days later (2(nd) post-test). A subgroup of 53 students participating in this study (27 from the simulation and 26 from the self-study arm) answered six additional questions on satisfaction with the learning experience, at the time of the 1(st) post-test. Wilcoxon paired rank sum test, Wilcoxon T test, and z-statistic with continuity correction were employed for statistical analysis, setting significance at p < 0.05.

RESULTS

Pre-test scores were similar in both groups (p = 0.9567), but in the first post-test they were significantly higher in the simulation group (p = 0.0017). In the 2(nd) post-test, scores were again similar in both groups (p = 0.2204). Satisfaction was significantly higher in the simulation group (p < 0.0001).

CONCLUSIONS

Adding a simulator-based training session for medical students in management of labour and delivery to the theoretical class led to a higher short-term increase in knowledge and student satisfaction than attending a self-study session. Significant differences in knowledge were no longer demonstrable at 12-15 days.

Mechanical properties of polypropylene mesh used in pelvic floor repair

The aim of this study was the comparison of the stiffness of different meshes under two types of mechanical tests. Five different mesh types were mechanically tested. The methods used consisted on uniaxial tension test (tensile stiffness) and tape ring tests, experimental continuous compression of the mesh loops (flexural stiffness). The most significant difference of tensile stiffness behaviour appears between Aris and TVTO. From the analysis of the experimental data, we divided the flexural stiffness, in two main groups. The first group includes Auto Suture and Aris meshes. The two meshes seem to have a similar flexural behaviour. The second group includes TVTO, Uretex and Avaulta. The difference between these two groups is clearly evident comparing TVTO and Aris. This study shows that there are significant differences on the mechanical properties between urogynecology meshes.

SisPorto 2.0: a program for automated analysis of cardiotocograms

OBJECTIVE

To describe the latest version of SisPorto, a program for automated analysis of cardiotocograms that closely follows the FIGO guidelines, analyses ante- and intrapartum tracings, performs no signal reduction, and has the possibility of simultaneously recording twins.

METHODS

A detailed description of the program's processing algorithms and operation is provided, as well as the main results of the studies performed to-date with this system.

RESULTS

Considering both current and previous versions of the program, SisPorto has been tested in over 6000 pregnancies. The system's FHR baseline was compared with an average of three experts' estimates, and the difference was under 8 bpm in all cases. A fair to good agreement was found with experts' identification of accelerations, decelerations, contractions, and normal/reduced variability (proportions of agreement 0.64-0.89). In a preliminary validity study (n = 85), a sensitivity of 100% and a specificity of 99% were obtained in prediction of poor neonatal outcome. The system is currently undergoing an international multicentre validation study.

CONCLUSIONS

Although still at the research level, a considerable experience has now been gathered with this system. Promising results have been achieved in studies comparing SisPorto with experts' analysis and in those evaluating the validity of the system.

An interactive web site for research on fetal heart rate monitoring

BACKGROUND

Traditional methods of exchange of research information may not be rapid enough, especially for international multicenter studies or when discussing controversial issues such as the value of fetal monitoring. The Internet is a useful tool that provides numerous opportunities for immediate communication within a large and diverse community of researchers.

METHOD

A Web site at http://www.sisporto.med.up.pt was developed for a multicenter research project with interlinked pages on automated fetal heart rate (FHR) monitoring. It includes background knowledge about the subject, detailed information about the project, and a few interactive pages. These pages allow online discussions, simulations of data analysis, and download of data for local FHR analysis.

EXPERIENCE

The Web site has been accessed from all over the world. In particular, participating research centers have had easy and fast access to background project information, and a few other clinicians and researchers participated in our online discussions and used the simulation tools or the data provided for analysis of typical FHR patterns.

CONCLUSION

Web sites can be useful in multicenter research projects and for scientific information exchange.

Fetal heart rate baselines in twins. Interobserver agreement in antepartum estimation

OBJECTIVE

To assess interobserver agreement in antepartum estimation of fetal heart rate (FHR) baselines in twins.

STUDY DESIGN

Two residents and one specialist in obstetrics and gynecology, all with special interest in FHR monitoring, independently estimated baselines in 162 consecutive antepartum FHR tracings recorded in 24 twins. Tracings were obtained with a dual-channel fetal monitor for the simultaneous recording of both twins' heart rates. Baselines were estimated, as single values corresponding to the mean of the lowest stable FHR segment, in the absence of fetal movements and uterine contractions, within physiologic limits (110-150 beats per minute [bpm]). If these criteria were not met, the possibility of persistent bradycardia or tachycardia was considered, and if this was confirmed in a tracing with at least 40 minutes, a baseline < 110 or > 150 bpm was chosen. Interobserver agreement was assessed by the proportions of agreement (PA), kappa statistic (K) and intraclass correlation coefficient (ICCC), with 95% confidence intervals (CIs).

RESULTS

Interobserver agreement was excellent, with a PA of 0.90 (95% CI: 0.89-0.91), K of 0.88 (95% CI: 0.84-0.92) and ICCC of 0.91 (95% CI: 0.88-0.94).

CONCLUSION

Interobserver agreement in antepartum estimation of fetal heart rate baselines in twins was excellent with the baseline concept used in this study.

Inconsistencies in classification by experts of cardiotocograms and subsequent clinical decision

Inter-observer agreement in the interpretation according to the FIGO guidelines of 33 cardiotocographic tracings by experts and subsequent clinical decision was evaluated, using the kappa statistic (K) and the proportions of agreement (Pa). Overall agreement in the classification of tracings was fair (K = 0.48) and was better for normal (Pa = 0.62), than for suspicious (Pa = 0.42) or pathologic tracings (Pa = 0.25). Overall agreement on clinical decision was slightly higher (K = 0.59), but mostly was centred on the decision to take 'no action' (Pa = 0.79). Experts especially disagreed over the decisions to 'monitor closely' (Pa = 0.14) or to 'intervene immediately' (Pa = 0.38). These limitations should be taken into account in clinical audits and in medical jurisprudence.

Objective computerized fetal heart rate analysis

OBJECTIVE

To assess the validity of a computerized methodology for cardiotocogram analysis based on a recently described reproducible visual estimation of the baseline.

METHODS

Forty-two antepartum and 43 intrapartum cardiotocograms (CTGs) acquired by a personal computer were selected. Antepartum tracings were performed in the 48 h that preceded an elective cesarean section, and intrapartum tracings were performed until delivery. FHR baselines were estimated by an expert, according to an objective and reproducible methodology. Using these baselines, automated detection of accelerations and decelerations and estimation of variability was performed by the personal computer. A quantitative adaptation of the FIGO guidelines for fetal monitoring was used to classify tracings. Perinatal outcome was classified according to the Apgar score and umbilical arterial pH. Validity was then assessed by the proportions of agreement (PA), kappa statistic (K), sensitivity and specificity, with 95% confidence intervals (95% CI). Cases showing a disagreement between CTG and perinatal classification were reviewed and an adjustment in baseline definition was tested.

RESULTS

The initial overall PA and kappa between CTG and perinatal classification were, respectively, 0.79 (95% CI: 0.69-0.87) and 0.62 (95% CI: 0.41-0.83). The overall PA and K, after baseline adjustment were, respectively, 0.89 (95% CI: 0.81-0.95) and 0.78 (95% CI: 0.58-0.98). Sensitivities and specificities ranged between 79% (95% CI: 60-92%) and 100% (95% CI: 95-100%).

CONCLUSIONS

Good clinical prediction may be possible with an objective methodology for cardiotocogram analysis based on a recently described reproducible baseline estimation.

Fetal heart-rate monitoring during maternal hypoglycaemic coma: a case report

Contradictory descriptions exist concerning the fetal heart-rate (FHR) patterns that appear during maternal hypoglycaemia. We report a case of maternal hypoglycaemic coma during which a FHR tracing was obtained showing a normal type D accelerative pattern.

Classification of foetal heart rate sequences based on fractal features

Visual inspection of foetal heart rate (FHR) sequences is an important means of foetal well-being evaluation. The application of fractal features for classifying physiologically relevant FHR sequence patterns is reported. The use of fractal features is motivated by the difficulties exhibited by traditional classification schemes to discriminate some classes of FHR sequence and by the recognition that this type of signal exhibits features on different scales of observation, just as fractal signals do. To characterise the signals by fractal features, two approaches are taken. The first modes the FHR sequences as temporal fractals. The second uses techniques from the chaos-theory field and aims to model the attractor based on FHR sequences. The fractal features determined by both approaches are used to design a Bayesian classification scheme. Classification results for three classes are presented; they are quite satisfactory and illustrate the importance of this type of methodology.

Semiautomated ultrasonographic measurement of fetal nuchal translucency using a computer software tool

Nuchal translucency (NT) thickness measurement has been recently proposed as a part of routine ultrasound scanning during the late first trimester of pregnancy, for the early screening of chromosomal abnormalities. Manual determination of NT is currently performed using electronic calipers placed by the operator in the middle of two echogenic lines displayed on the screen. Therefore, intraobserver and interobserver repeatability can be questioned. This paper presents a software tool that has been developed for achieving this goal in a semiautomatic way, improving the reproducibility of the method.

Antepartum fetal cerebral hemorrhage not predicted by current surveillance methods in cholestasis of pregnancy

BACKGROUND

The reason for increased fetal mortality in cholestasis of pregnancy is not completely understood. Intracerebral hemorrhage due to coagulation disorders, similar to those reported in the mother, is a possible explanation.

CASE

Antepartum fetal death occurred at 37 weeks in a primigravida with cholestasis of pregnancy. The woman was taking no medication. Autopsy revealed extensive cerebral hemorrhage. A cardiotocogram and biophysical profile performed 24 hours and 5 days, respectively, before fetal death had been normal.

CONCLUSION

Antepartum fetal death may occur in patients with mild cholestasis who are taking no medication. Intracerebral hemorrhage is a possible cause, and this may be unpredictable with current methods of fetal surveillance. This possibility constitutes an argument in support of delivering these pregnancies as soon as lung maturity is achieved.

Evaluation of interobserver agreement of cardiotocograms

OBJECTIVE

To evaluate interobserver agreement in visual analysis of each cardiotocographic event.

METHODS

Three experts independently divided 16 antepartum and 17 intrapartum cardiotocograms into baseline segments, accelerations and decelerations, according to the FIGO guidelines. Baseline segments were further classified as having normal, reduced or increased variability and decelerations as early, late and variable. Uterine activity was divided into tonus and contractions. Agreement was assessed by the proportions of agreement (pa) with 95% confidence intervals.

RESULTS

Reproducibility in assessment of baseline segments with normal variability, accelerations and uterine activity was acceptable (pa = 0.56-0.71) whereas that of other segments was not (pa = 0.14-0.45).

CONCLUSIONS

Analysis of most cardiotocographic events is poorly reproducible, even when experts use the FIGO guidelines. This may be explained by some still ambiguous guidelines, by eyeball limitations in evaluation of subtle events, and by the incapacity of busy clinicians to assess complex and multiple cardiotocographic events in a systematic and disciplined fashion.

Monitoring of cardiac-extracardiac haemodynamics and automated fetal heart rate preceding intrauterine death

A severely growth-retarded fetus was monitored longitudinally for haemodynamic profiles and automated cardiotocogram analysis in the 30 days preceding death. Initially a pattern of hypoxia and moderately deteriorated cardiac function was detected. Later on, signs of progressive heart failure developed, in conjunction with deteriorating fetal heart rate patterns.