Meta-analysis of 46,000 germline de novo mutations linked to human inherited disease

BACKGROUND

De novo mutations (DNMs) are variants that occur anew in the offspring of noncarrier parents. They are not inherited from either parent but rather result from endogenous mutational processes involving errors of DNA repair/replication. These spontaneous errors play a significant role in the causation of genetic disorders, and their importance in the context of molecular diagnostic medicine has become steadily more apparent as more DNMs have been reported in the literature. In this study, we examined 46,489 disease-associated DNMs annotated by the Human Gene Mutation Database (HGMD) to ascertain their distribution across gene and disease categories.

RESULTS

Most disease-associated DNMs reported to date are found to be associated with developmental and psychiatric disorders, a reflection of the focus of sequencing efforts over the last decade. Of the 13,277 human genes in which DNMs have so far been found, the top-10 genes with the highest proportions of DNM relative to gene size were H3-3 A, DDX3X, CSNK2B, PURA, ZC4H2, STXBP1, SCN1A, SATB2, H3-3B and TUBA1A. The distribution of CADD and REVEL scores for both disease-associated DNMs and those mutations not reported to be de novo revealed a trend towards higher deleteriousness for DNMs, consistent with the likely lower selection pressure impacting them. This contrasts with the non-DNMs, which are presumed to have been subject to continuous negative selection over multiple generations.

CONCLUSION

This meta-analysis provides important information on the occurrence and distribution of disease-associated DNMs in association with heritable disease and should make a significant contribution to our understanding of this major type of mutation.

Validation of the Short Version (TLS-15) of the Triangular Love Scale (TLS-45) across 37 Languages

Love is a phenomenon that occurs across the world and affects many aspects of human life, including the choice of, and process of bonding with, a romantic partner. Thus, developing a reliable and valid measure of love experiences is crucial. One of the most popular tools to quantify love is Sternberg's 45-item Triangular Love Scale (TLS-45), which measures three love components: intimacy, passion, and commitment. However, our literature review reveals that most studies (64%) use a broad variety of shortened versions of the TLS-45. Here, aiming to achieve scientific consensus and improve the reliability, comparability, and generalizability of results across studies, we developed a short version of the scale-the TLS-15-comprised of 15 items with 5-point, rather than 9-point, response scales. In Study 1 (N = 7,332), we re-analyzed secondary data from a large-scale multinational study that validated the original TLS-45 to establish whether the scale could be truncated. In Study 2 (N = 307), we provided evidence for the three-factor structure of the TLS-15 and its reliability. Study 3 (N = 413) confirmed convergent validity and test-retest stability of the TLS-15. Study 4 (N = 60,311) presented a large-scale validation across 37 linguistic versions of the TLS-15 on a cross-cultural sample spanning every continent of the globe. The overall results provide support for the reliability, validity, and cross-cultural invariance of the TLS-15, which can be used as a measure of love components-either separately or jointly as a three-factor measure.

Effects of a Gamified Agent-Based System for Personalized Elderly Care: Pilot Usability Study

BACKGROUND

The global percentage of older people has increased significantly over the last decades. Information and communication technologies have become essential to develop and motivate them to pursue healthier ways of living. This paper examines a personalized coaching health care service designed to maintain living conditions and active aging among older people. Among the technologies the service includes, we highlight the use of both gamification and cognitive assistant technologies designed to support older people and an application combining a cognitive virtual assistant to directly interact with the older person and provide feedback on their current health condition and several gamification techniques to motivate the older person to stay engaged with the application and pursuit of healthier daily habits.

OBJECTIVE

This pilot study aimed to investigate the feasibility and usability of a gamified agent-based system for older people and obtain preliminary results on the effectiveness of the intervention regarding physical activity health outcomes.

METHODS

The study was designed as an intervention study comparing pre- and posttest results. The proposed gamified agent-based system was used by 12 participants over 7 days (1 week), and step count data were collected with access to the Google Fit application programming interface. Step count data after the intervention were compared with average step count data before the intervention (average daily values over a period of 4 weeks before the intervention). A　1-tailed Student t test was used to determine the relationship between the dependent and independent variables. Usability was measured using the System Usability Scale questionnaire, which was answered by 8 of the 12 participants in the study.

RESULTS

The posttest results showed significant pre- to posttest changes (P=.30; 1-tailed Student t test) with a moderate effect size (Cohen d=0.65). The application obtained an average usability score of 78.

CONCLUSIONS

The presented pilot was validated, showing the positive health effects of using gamification techniques and a virtual cognitive assistant. Additionally, usability metrics considered for this study confirmed high adherence and interest from most participants in the pilot.

Group recommender systems for tourism: how does personality predict preferences for attractions, travel motivations, preferences and concerns?

To travel in leisure is an emotional experience, and therefore, the more the information about the tourist is known, the more the personalized recommendations of places and attractions can be made. But if to provide recommendations to a tourist is complex, to provide them to a group is even more. The emergence of personality computing and personality-aware recommender systems (RS) brought a new solution for the cold-start problem inherent to the conventional RS and can be the leverage needed to solve conflicting preferences in heterogenous groups and to make more precise and personalized recommendations to tourists, as it has been evidenced that personality is strongly related to preferences in many domains, including tourism. Although many studies on psychology of tourism can be found, not many predict the tourists' preferences based on the Big Five personality dimensions. This work aims to find how personality relates to the choice of a wide range of tourist attractions, traveling motivations, and travel-related preferences and concerns, hoping to provide a solid base for researchers in the tourism RS area to automatically model tourists in the system without the need for tedious configurations, and solve the cold-start problem and conflicting preferences. By performing Exploratory and Confirmatory Factor Analysis on the data gathered from an online questionnaire, sent to Portuguese individuals from different areas of formation and age groups (n = 1035), we show all five personality dimensions can help predict the choice of tourist attractions and travel-related preferences and concerns, and that only neuroticism and openness predict traveling motivations.

Mapping human pathogens in wastewater using a metatranscriptomic approach

The monitoring of cities' wastewaters for the detection of potentially pathogenic viruses and bacteria has been considered a priority during the COVID-19 pandemic to monitor public health in urban environments. The methodological approaches frequently used for this purpose include deoxyribonucleic acid (DNA)/Ribonucleic acid (RNA) isolation followed by quantitative polymerase chain reaction (qPCR) and reverse transcription (RT)‒qPCR targeting pathogenic genes. More recently, the application of metatranscriptomic has opened opportunities to develop broad pathogenic monitoring workflows covering the entire pathogenic community within the sample. Nevertheless, the high amount of data generated in the process requires an appropriate analysis to detect the pathogenic community from the entire dataset. Here, an implementation of a bioinformatic workflow was developed to produce a map of the detected pathogenic bacteria and viruses in wastewater samples by analysing metatranscriptomic data. The main objectives of this work was the development of a computational methodology that can accurately detect both human pathogenic virus and bacteria in wastewater samples. This workflow can be easily reproducible with open-source software and uses efficient computational resources. The results showed that the used algorithms can predict potential human pathogens presence in the tested samples and that active forms of both bacteria and virus can be identified. By comparing the computational method implemented in this study to other state-of-the-art workflows, the implementation analysis was faster, while providing higher accuracy and sensitivity. Considering these results, the processes and methods to monitor wastewater for potential human pathogens can become faster and more accurate. The proposed workflow is available at https://github.com/waterpt/watermonitor and can be implemented in currently wastewater monitoring programs to ascertain the presence of potential human pathogenic species.

TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa

Bacterial biofilms are a source of infectious human diseases and are heavily linked to antibiotic resistance. Pseudomonas aeruginosa is a multidrug-resistant bacterium widely present and implicated in several hospital-acquired infections. Over the last years, the development of new drugs able to inhibit Pseudomonas aeruginosa by interfering with its ability to form biofilms has become a promising strategy in drug discovery. Identifying molecules able to interfere with biofilm formation is difficult, but further developing these molecules by rationally improving their activity is particularly challenging, as it requires knowledge of the specific protein target that is inhibited. This work describes the development of a machine learning multitechnique consensus workflow to predict the protein targets of molecules with confirmed inhibitory activity against biofilm formation by Pseudomonas aeruginosa. It uses a specialized database containing all the known targets implicated in biofilm formation by Pseudomonas aeruginosa. The experimentally confirmed inhibitors available on ChEMBL, together with chemical descriptors, were used as the input features for a combination of nine different classification models, yielding a consensus method to predict the most likely target of a ligand. The implemented algorithm is freely available at https://github.com/BioSIM-Research-Group/TargIDe under licence GNU General Public Licence (GPL) version 3 and can easily be improved as more data become available.

P-077 Human sperm acrosome becomes alkalinized during capacitation

Study question

Does during the human sperm capacitation the acrosomal pH (pHa) increases naturally and how it change can be modulate?

Summary answer

Sperm acrosome is progressively alkalinized during capacitation in a HCO3- and Ca2+ dependent manner. pHa is regulated by V-ATPase and involving the sAC-PKA signaling pathway.

What is known already

Capacitation involves biochemical and physiological modifications undergone by sperm as they travel through the female reproductive tract. These modifications prepare the sperm to enact the acrosome reaction (AR), an essential step for egg fertilization. Capacitation requires [Ca2+]i and pHi increases. Mouse sperm capacitation is accompanied by acrosomal alkalinization and artificial elevation of the pHa is sufficient to trigger the AR in mouse and human sperm, but it is unknown if the pHa increases physiologically during human sperm capacitation.

Study design, size, duration

In this work we followed pHa changes during human sperm capacitation (6 h) and evaluated the mechanisms of its regulation using pharmacological tools. Sperm were stained with LysoSensor green and the relative fluorescence measurements for pHa kinetics during capacitation were performed at 15 min of incubation (initial time: 0 h) and after 3 and 6 h of incubation. Independent experiments of at least 3 donors were performed per condition.

Participants/materials, setting, methods

We used semen samples from 11 healthy donors fulfilled the requirements defined by the OMS (OMS, 2010). Sperm recovered by swim-up were incubated in a capacitating or non-capacitating HTF medium. LysoSensor green fluorescence dye was used to evaluate pHa dynamic during capacitation using single cell epifluorescence microscopy and image-based flow cytometry. Additionally, pHa was evaluated in the presence of specific inhibitors to assess regulatory mechanisms. A linear model was used to study the pHa kinetics.

Main results and the role of chance

Human sperm pHa is alkalinized progressively at 3 and 6 h of the capacitation (p < 0.05).

V-ATPase activity mainly responsible for the acrosome acidity and can modulate at least in part acrosome alkalinization during capacitation (***p<0.001, *p<0.05). V-ATPase is immunolocalized to the acrosome and equatorial segment of human sperm.

Bicarbonate (HCO3-) was essential for the pHa increase observed during capacitation and its absence inhibits completely the acrosome alkalinization (**p<0.01, *p<0.05). Inhibition of the Cystic Fibrosis Transmembrane Regulator (CFTR) or the Na+/HCO3- Cotransporter (NBC) partially blocked the pHa changes during capacitation.

Extracelular Ca2+ is involved in pHa regulation during capacitation. Under low external Ca2+ the pHa regulation is altered and occurred delay in acrosome alkalinization (*p < 0.05 and **p < 0.001).

Finally, we tested a pharmacological blockade of sAC and PKA during capacitation. sAC inhibition did not prevent acrosome alkalinization, but it significantly reduced the rate of the pHa changes as compared to the capacitation control (***p=0.0009), revealing a certain influence. On the other hand, PKA inhibition induced acrosomal acidification at the start of capacitation and accelerated significantly the alkalinization (*p<0.05). Together these results allow us to assume that a signaling pathway mediated to sAC is participating in the pHa regulation.

Limitations, reasons for caution

Experiments were performed in vitro and due to model limitations is difficult to establish strategies that allow us to know more directly, other molecular mechanisms that regulate the pHa.

Wider implications of the findings

Our findings show that pHa is subject of regulation during human sperm capacitation. The results provide new insights regarding the molecular mechanisms involved in human sperm capacitation and this knowledge results interesting for the study of specific molecules that inhibit capacitation or AR.

Trial registration number

Not applicable

Assessing the effects of PMM2 variants on protein stability

Phosphomannomutase 2 deficiency, PMM2-CDG, is the most frequent disorder of protein N-glycosylation. It is an autosomal recessive disease with a broad clinical and biochemical phenotype. Trying to predict the impact of novel variants is often a challenge due to the high number of variants and the difficulty to establish solid genotype-phenotype correlations. A potential useful strategy is to use computational chemistry calculations as a tool from which relevant information on the structural impact of novel variants may be deduced. Here we present our analyses based on four well-known PMM2 deleterious variants (p.(Leu32Arg), p.(Asp65Tyr), p.(Phe119Leu), p.(Arg141His)) and the polymorphic p.(Glu197Ala) for which we have predicted the effect on protein stability. Our work predicts the effect of different amino acid residues on the conformation and stability of PMM2. These computational simulations are, therefore, an extremely useful methodology which, in combination with routinely used in silico methods of pathogenicity prediction, may help to reveal the structural impact of novel variants at the protein level, potentially leading to a better understanding of target biological molecules.

Compensatory epistasis explored by molecular dynamics simulations

A non-negligible proportion of human pathogenic variants are known to be present as wild type in at least some non-human mammalian species. The standard explanation for this finding is that molecular mechanisms of compensatory epistasis can alleviate the mutations' otherwise pathogenic effects. Examples of compensated variants have been described in the literature but the interacting residue(s) postulated to play a compensatory role have rarely been ascertained. In this study, the examination of five human X-chromosomally encoded proteins (FIX, GLA, HPRT1, NDP and OTC) allowed us to identify several candidate compensated variants. Strong evidence for a compensated/compensatory pair of amino acids in the coagulation FIXa protein (involving residues 270 and 271) was found in a variety of mammalian species. Both amino acid residues are located within the 60-loop, spatially close to the 39-loop that performs a key role in coagulation serine proteases. To understand the nature of the underlying interactions, molecular dynamics simulations were performed. The predicted conformational change in the 39-loop consequent to the Glu270Lys substitution (associated with hemophilia B) appears to impair the protein's interaction with its substrate but, importantly, such steric hindrance is largely mitigated in those proteins that carry the compensatory residue (Pro271) at the neighboring amino acid position.

A microparticle blood analogue suspension matching blood rheology

The handling of blood in vitro is demanding because of ethical, economical and safety issues. Although several Newtonian and non-Newtonian blood analogues are found in the literature, few studies have used particles to mimic red blood cells (RBCs) and built an analogue with similar rheological properties of blood. This work reports the development of a blood analogue suspension composed of polydimethylsiloxane (PDMS) microparticles with an average diameter of ∼7 μm. High throughput production of PDMS particles is possible using a multi-stage membrane emulsification process; up to ∼6 mL of microparticles are manufactured in 3 hours. PDMS particles at a concentration of around 21% (w/w) at 20 °C present steady, oscillatory and extensional rheologies very similar to those of blood under physiological conditions (37 °C and ∼41% hematocrit), making them a good candidate whole blood analogue. Also, flow studies were performed in microchannels with contraction to study the cell-free layer (CFL) formation and particle deformation, achieving good qualitative results. Using the procedure developed, it is possible to obtain blood analogue fluids with a shelf life of at least 6 months.

Effectiveness of treat-and-extend versus pro re nata regimens in the treatment of Neovascular Age Macular Degeneration: A Real World Comparison

PURPOSE

Evaluate and compare the visual and morphological results of Pro re nata (PRN) and treat-and-extend (T&E) treatment regimens at 3 years in real world clinical practice.

METHODS

Retrospective study of patients with neovascular age macular degeneration (AMD) treated with anti-VEGF with 3 years of continuous follow-up and no previous anti-VEGF treatment. Best corrected visual acuity (BCVA), central foveal thickness (CFT) and number of intravitreal injections outcomes were tested for statistical differences between the two groups at baseline and during follow-up.

RESULTS

A total of 240 eyes were included in the study, 170 in the PRN group and 70 in the T&E group. At 12 months, mean BCVA (ETDRS letters) gain from baseline was at its highest point in the T&E group (+6.38±13.32; p=0.25). In the PRN group, BCVA peaked at 3 months and slowly decreased until end of follow-up. With both regimens, from baseline, CFT continued to decrease until the second year (PRN -138.81 [-846.7 to +162.77] and T&E -81 [-604 to +100] μm, p=0.06). After that, T&E group maintained this tendency, reaching the lowest CFT value at 36 months, whereas PRN group showed an increased in CFT values (PRN -104 [-807.7 to +297] μm and T&E -103 [-575 to +244], μm p=0.63). Patients treated with T&E regimen received a significantly higher number of injections (PRN 16.3±7.6 vs T&E 23.9 ±9.4, p<0.01).

CONCLUSION

Our results demonstrated a trend towards for T&E to achieve higher marks in BCVA, peaking at 12 months, and lower CFT thickness at the end of three years. Despite the higher number of injections performed in the T&E group the mean BCVA reverts to baseline values at 3 years.

Geometrical effects in the hemodynamics of stenotic and non-stenotic left coronary arteries-numerical and in vitro approaches

Atherosclerosis is a common cardiovascular disease found in the left coronary artery (LCA), closely linked to local hemodynamic, which, in turn, is highly influenced by the artery geometry. The hemodynamics in the LCA was studied in a patient-specific geometry without any sign of disease using both numerical and in vitro approaches. The influence of non-planarity was evaluated through two models of the patient-specific LCA that deviate from its original geometry in their planarity. Afterwards, in all models, irregular stenoses were created by a procedure in which the stenosis emerges by diffusion from low wall shear stress (WSS) areas. The WSS distribution and flow patterns were evaluated in all the models. The experimental results validate the numerical code developed to study the blood flow assuming a steady state Newtonian behavior. Comparison between the planar and non-planar idealized LCA revealed no significant differences in low WSS regions forming stenotic regions with identical shape. In the patient-specific LCA, the low WSS regions are not consistent with the idealized models leading to a different stenosis shape. The results revealed that the non-planarity has an unquestionable effect in helicity. It was also demonstrated that eccentricity of the vessels cross section and the position of the apex in relation to the axis of the parent branch contribute to the flow patterns observed. Numerical results of pulsatile blood flow assuming a non-Newtonian behavior, in the patient-specific LCA, reinforce the non-planarity effect in local hemodynamics.

Synthesis of ceramic pigments from industrial wastes: Red mud and electroplating sludge

The perception of industrial waste has changed, in the last decades, from an economic and environmental problem to a potential raw material. In this work, the synthesis of a stable pigment was prepared by combining two hazardous and unexplored wastes: red mud (RM, rich in Fe) and electroplating sludge (ES, rich in Ni/Cr). The wastes were mixed in different proportions and calcined at 1200 °C. Black and brown pigments were obtained from the mixture of RM/ES in 1:3 and 1:1 wt proportions, respectively. The color was given by the chrome-iron-nickel spinels, based on Ni^{2+ 3}T_1g(³F) transitions (≈13,000 cm^-1), Cr^{3+ 4}A_2g → ⁴T_1g(⁴F) transitions (≈24,400 cm^-1) and Fe³⁺ (≈15,000-≈22,500 cm^-1). The achieved coloring strength and thermal stability on various ceramic glazes render excellent prospects for the industrial application of such waste-based pigments.

Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard

The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.

The HIV oligonucleotide database (HIVoligoDB)

The human immunodeficiency virus (HIV) is associated with one of the most widespread infectious disease, the acquired immunodeficiency syndrome (AIDS). The development of antiretroviral drugs and methods for virus detection requires a comprehensive analysis of the HIV genomic diversity, particularly in the binding sites of oligonucleotides. Here, we describe a versatile online database (HIVoligoDB) with oligonucleotides selected for the diagnosis of HIV and treatment of AIDS. Currently, the database provides an interface for visualization, analysis and download of 380 HIV-1 and 65 HIV-2 oligonucleotides annotated according to curated reference genomes. The database also allows the selection of the most conserved HIV genomic regions for the development of molecular diagnostic assays and sequence-based candidate therapeutics.

Database URL:http://portugene.com/HIVoligoDB

Event-Based 3D Motion Flow Estimation Using 4D Spatio Temporal Subspaces Properties

State of the art scene flow estimation techniques are based on projections of the 3D motion on image using luminance-sampled at the frame rate of the cameras-as the principal source of information. We introduce in this paper a pure time based approach to estimate the flow from 3D point clouds primarily output by neuromorphic event-based stereo camera rigs, or by any existing 3D depth sensor even if it does not provide nor use luminance. This method formulates the scene flow problem by applying a local piecewise regularization of the scene flow. The formulation provides a unifying framework to estimate scene flow from synchronous and asynchronous 3D point clouds. It relies on the properties of 4D space time using a decomposition into its subspaces. This method naturally exploits the properties of the neuromorphic asynchronous event based vision sensors that allows continuous time 3D point clouds reconstruction. The approach can also handle the motion of deformable object. Experiments using different 3D sensors are presented.

The male and female complete mitochondrial genome sequences of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798) (Bivalvia: Unionidae)

Freshwater mussels of the family Unionidae exhibit a particular form of mitochondria inheritance called double uniparental inheritance (DUI), in which the mitochondria are inherited by both male and female parents. The (M)ale and (F)emale mitogenomes are highly divergent within species. In the present study, we determine and describe the complete M and F mitogenomes of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798). The complete M and F mitogenomes sequences are 16 451 bp and 15 787 bp in length, respectively. Both F and M have the same gene content: 13 protein-coding genes (PCGs), 22 transfer RNA (trn) and 2 ribosomal RNA (rrn) genes. Bayesian analyses based on the concatenated nucleotide sequences of 12 PCGs and 2 rrn genes of both genomes, including mitogenome sequences available from related species, were performed. Male and Female lineages are monophyletic within the family, but reveal distinct phylogenetic relationships.

MitoBreak: the mitochondrial DNA breakpoints database

Mitochondrial DNA (mtDNA) rearrangements are key events in the development of many diseases. Investigations of mtDNA regions affected by rearrangements (i.e. breakpoints) can lead to important discoveries about rearrangement mechanisms and can offer important clues about the causes of mitochondrial diseases. Here, we present the mitochondrial DNA breakpoints database (MitoBreak; http://mitobreak.portugene.com), a free, web-accessible comprehensive list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially duplicated (duplications) and linear mtDNAs. Currently, MitoBreak contains >1400 mtDNA rearrangements from seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta, Drosophila melanogaster, Caenorhabditis elegans and Podospora anserina) and their associated phenotypic information collected from nearly 400 publications. The database allows researchers to perform multiple types of data analyses through user-friendly interfaces with full or partial datasets. It also permits the download of curated data and the submission of new mtDNA rearrangements. For each reported case, MitoBreak also documents the precise breakpoint positions, junction sequences, disease or associated symptoms and links to the related publications, providing a useful resource to study the causes and consequences of mtDNA structural alterations.

Mitochondrial DNA rearrangements in health and disease--a comprehensive study

Mitochondrial DNA (mtDNA) rearrangements cause a wide variety of highly debilitating and often fatal disorders and have been implicated in aging and age-associated disease. Here, we present a meta-analytical study of mtDNA deletions (n = 730) and partial duplications (n = 37) using information from more than 300 studies published over the last 30 years. We show that both classes of mtDNA rearrangements are unequally distributed among disorders and their breakpoints have different genomic locations. We also demonstrate that 100% of cases with sporadic mtDNA deletions and 97.3% with duplications have no breakpoints in the 16,071 breakage hotspot site, in contrast with deletions from healthy and aged tissues. Notably, most deletions removing a section of the D-loop are found in tumors. Deleted mtDNA molecules lacking the origin of L-strand replication (O(L)) represent only 9.5% of all reported cases, whereas extra origins of replication occur in all duplications. As previously shown for deletions, imperfect stretches of homology are common in duplication breakpoints. Finally, we provide a dedicated Website with detailed information on deleted/duplicated mtDNA regions to facilitate the design of efficient methods for identification and screening of rearranged mitochondrial genomes (available at http://www.portugene.com/mtDNArearrangements.html).

The role of recombination in the origin and evolution of Alu subfamilies

Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome.

The evolutionary portrait of metazoan NAD salvage

Nicotinamide Adenine Dinucleotide (NAD) levels are essential for cellular homeostasis and survival. Main sources of intracellular NAD are the salvage pathways from nicotinamide, where Nicotinamide phosphoribosyltransferases (NAMPTs) and Nicotinamidases (PNCs) have a key role. NAMPTs and PNCs are important in aging, infection and disease conditions such as diabetes and cancer. These enzymes have been considered redundant since either one or the other exists in each individual genome. The co-occurrence of NAMPT and PNC was only recently detected in invertebrates though no structural or functional characterization exists for them. Here, using expression and evolutionary analysis combined with homology modeling and protein-ligand docking, we show that both genes are expressed simultaneously in key species of major invertebrate branches and emphasize sequence and structural conservation patterns in metazoan NAMPT and PNC homologues. The results anticipate that NAMPTs and PNCs are simultaneously active, raising the possibility that NAD salvage pathways are not redundant as both are maintained to fulfill the requirement for NAD production in some species.

Event-based 3D reconstruction from neuromorphic retinas

This paper presents a novel N-ocular 3D reconstruction algorithm for event-based vision data from bio-inspired artificial retina sensors. Artificial retinas capture visual information asynchronously and encode it into streams of asynchronous spike-like pulse signals carrying information on, e.g., temporal contrast events in the scene. The precise time of the occurrence of these visual features are implicitly encoded in the spike timings. Due to the high temporal resolution of the asynchronous visual information acquisition, the output of these sensors is ideally suited for dynamic 3D reconstruction. The presented technique takes full benefit of the event-driven operation, i.e. events are processed individually at the moment they arrive. This strategy allows us to preserve the original dynamics of the scene, hence allowing for more robust 3D reconstructions. As opposed to existing techniques, this algorithm is based on geometric and time constraints alone, making it particularly simple to implement and largely linear.

Mitochondrial DNA deletions are associated with non-B DNA conformations

Mitochondrial DNA (mtDNA) deletions are a primary cause of mitochondrial disease and are believed to contribute to the aging process and to various neurodegenerative diseases. Despite strong observational and experimental evidence, the molecular basis of the deletion process remains obscure. In this study, we test the hypothesis that the primary cause of mtDNA vulnerability to breakage resides in the formation of non-B DNA conformations, namely hairpin, cruciform and cloverleaf-like elements. Using the largest database of human mtDNA deletions built thus far (753 different cases), we show that site-specific breakage hotspots exist in the mtDNA. Furthermore, we discover that the most frequent deletion breakpoints occur within or near predicted structures, a result that is supported by data from transgenic mice with mitochondrial disease. There is also a significant association between the folding energy of an mtDNA region and the number of breakpoints that it harbours. In particular, two clusters of hairpins (near the D-loop 3′-terminus and the L-strand origin of replication) are hotspots for mtDNA breakage. Consistent with our hypothesis, the highest number of 5′- and 3′-breakpoints per base is found in the highly structured tRNA genes. Overall, the data presented in this study suggest that non-B DNA conformations are a key element of the mtDNA deletion process.

Refining the genetic portrait of Portuguese Roma through X-chromosomal markers

Due to differences in transmission between X-chromosomal and autosomal DNA, the comparison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portuguese Roma (Gypsies) by analyzing 43 X-chromosomal markers and 53 autosomal markers. Portuguese individuals of non-Gypsy ancestry were also studied. Compared with the host population, reduced levels of diversity on the X chromosome and autosomes were detected in Gypsies; this result was in line with known patterns of genetic diversity typical of Roma groups. As a consequence of the complex demographic past of the Roma, during which admixture and genetic drift played major roles, the amount of linkage disequilibrium (LD) on the X chromosome in Gypsies was considerably higher than that observed in non-Gypsies. When the pattern of differentiation on the X chromosome was compared with that of autosomes, there was evidence for asymmetries in female and male effective population sizes during the admixture between Roma and non-Roma. This result supplements previous data provided by mtDNA and the Y chromosome, underlining the importance of using combined information from the X chromosome and autosomes to dissect patterns of genetic diversity. Following the out-of-India dispersion, the Roma acquired a complex genetic pattern that was influenced by drift and introgression with surrounding populations, with important contributions from both males and females. We provide evidence that a sex-biased admixture with Europeans is probably associated with the founding of the Portuguese Gypsies.

Reactive pulsed-DC sputtered Nb-doped VO2 coatings for smart thermochromic windows with active solar control

Thermochromic VO2 thin films have successfully been grown on SiO2-coated float glass by reactive pulsed-DC magnetron sputtering. Different Nb doping amounts were introduced in the VO2 solid solution during the film growing which resulted in films with distinct semiconducting-metal phase transition temperatures. Pure VO2 showed improved thermochromic behavior as compared with VO2 films prepared by conventional DC sputtering. The transition temperatures were linearly decreased from 59 down to 34 degrees C with the increase in Nb content. However, the luminous transmittance and the infrared modulation efficiency were markedly affected. The surface morphology of the films was examined by scanning electron microscopy (SEM) and showed a tendency for grain sized reduction due to Nb addition. Moreover, the films were found to be very dense with no columnar microstructure. Structural analyses carried out by X-ray diffractometry (XRD) revealed that Nb introduces significant amount of defects in the crystal lattice which clearly degrade the optical properties.

Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds

The phylogeography of wild boars (WB) and domestic pigs (Sus scrofa) has contributed important insights into where and when domestication occurred. The geographic distribution of two core haplotypes (E1a and E1c) of the main European phylogenetic clade suggests that Central Europe was an early domestication centre, although the complexity of the pattern does not exclude the possibility that multiple domestication events occurred in different regions. To investigate the relationships among WB and domestic pig breeds in Iberia, a fragment of the mitochondrial DNA control region from a large sample (n=409) of WB and local pig breeds was co-analysed with published sequences from other European populations. The Iberian sample revealed a high frequency of a sub-cluster (E1c) of the European haplogroup E1 in 77% of total Iberian samples, 96% of WB, 90% of Alentejano (Portugal) and 87% of Iberian breed pigs (Spain; Black Hairy, Black Hairless and Red varieties). Low genetic distance (F'(ST) = 0.105) was observed between Alentejano (Portugal) and Iberian breed pigs (Spain). Alentejano and Iberian breed pigs showed low genetic distances to both Iberian and Central European WB (average F'(ST) =0.345 and 0.215, respectively). This pattern suggests that early pig husbandry in the Iberian Peninsula did not solely rely on imported Central European stock, but also included the recruitment of local WB.

Gains, losses and changes of function after gene duplication: study of the metallothionein family

Metallothioneins (MT) are small proteins involved in heavy metal detoxification and protection against oxidative stress and cancer. The mammalian MT family originated through a series of duplication events which generated four major genes (MT1 to MT4). MT1 and MT2 encode for ubiquitous proteins, while MT3 and MT4 evolved to accomplish specific roles in brain and epithelium, respectively. Herein, phylogenetic, transcriptional and polymorphic analyses are carried out to expose gains, losses and diversification of functions that characterize the evolutionary history of the MT family. The phylogenetic analyses show that all four major genes originated through a single duplication event prior to the radiation of mammals. Further expansion of the MT1 gene has occurred in the primate lineage reaching in humans a total of 13 paralogs, five of which are pseudogenes. In humans, the reading frame of all five MT1 pseudogenes is reconstructed by sequence homology with a functional duplicate revealing that loss of invariant cysteines is the most frequent event accounting for pseudogeneisation. Expression analyses based on EST counts and RT-PCR experiments show that, as for MT1 and MT2, human MT3 is also ubiquitously expressed while MT4 transcripts are present in brain, testes, esophagus and mainly in thymus. Polymorphic variation reveals two deleterious mutations (Cys30Tyr and Arg31Trp) in MT4 with frequencies reaching about 30% in African and Asian populations suggesting the gene is inactive in some individuals and physiological compensation for its loss must arise from a functional equivalent. Altogether our findings provide novel data on the evolution and diversification of MT gene duplicates, a valuable resource for understanding the vast set of biological processes in which these proteins are involved.

Identification of species by multiplex analysis of variable-length sequences

The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups. We also demonstrate that the identification of prokaryotic and viral species with numeric profiles of fragment lengths is generally straightforward. A computational platform is presented to facilitate the planning of projects and includes a large data set with nearly 1800 numeric profiles for species in all domains of life (1556 for eukaryotes, 105 for prokaryotes and 130 for viruses). Finally, a SPInDel profiling kit for discrimination of 10 mammalian species was successfully validated on highly processed food products with species mixtures and proved to be easily adaptable to multiple screening procedures routinely used in molecular biology laboratories. These results suggest that SPInDel is a reliable and cost-effective method for broad-spectrum species identification that is appropriate for use in suboptimal samples and is amenable to different high-throughput genotyping platforms without the need for DNA sequencing.

Nanocomposite metal amorphous-carbon thin films deposited by hybrid PVD and PECVD technique

Carbon based films can combine the properties of solid lubricating graphite structure and hard diamond crystal structure, i.e., high hardness, chemical inertness, high thermal conductivity and optical transparency without the crystalline structure of diamond. Issues of fundamental importance associated with nanocarbon coatings are reducing stress, improving adhesion and compatibility with substrates. In this work new nanocomposite coatings with improved toughness based in nanocrystalline phases of metals and ceramics embedded in amorphous carbon matrix are being developed within the frame of a research project: nc-MeNxCy/a-C(Me) with Me = Mo, Si, Al, Ti, etc. Carbide forming metal/carbon (Me/C) composite films with Me = Mo, W or Ti possess appropriate properties to overcome the limitation of pure DLC films. These novel coating architectures will be adopted with the objective to decrease residual stress, improve adherence and fracture toughness, obtain low friction coefficient and high wear-resistance. Nanocomposite DLC's films were deposited by hybrid technique using a PVD-Physically Vapor Deposition (magnetron sputtering) and Plasma Enhanced Chemical Vapor Deposition (PECVD), by the use of CH4 gas. The parameters varied were: deposition time, substrate temperature (180 degrees C) and dopant (Si + Mo) of the amorphous carbon matrix. All the depositions were made on silicon wafers and steel substrates precoated with a silicon inter-layer. The characterisation of the film's physico-mechanical properties will be presented in order to understand the influence of the deposition parameters and metal content used within the a-C matrix in the thin film properties. Film microstructure and film hybridization state was characterized by Raman Spectroscopy. In order to characterize morphology SEM and AFM will be used. Film composition was measured by Energy-Dispersive X-ray analysis (EDS) and by X-ray photoelectron spectroscopy (XPS). The contact angle for the produced DLC's on silicon substrates were also measured. Thin film adherence was studied by micro-scratch test. Residual stresses in the produced coatings will be analysed by bending technique.

DC sputtered W-doped VO2 thermochromic thin films for smart windows with active solar control

Doped VO2 thin films, with different W at.% and consequent dissimilar transition temperatures, were successfully deposited onto SiO2-coated float-glass substrates by reactive direct current (DC) magnetron sputtering. Structural analyses have shown, for undoped films, single phase VO2(M) films with c-axis (002) direction as the preferred crystal orientation. The addition of tungsten into the VO2 solid solution favored the crystallization in the (011) direction which became dominant above a critical level of dopant concentration. The surface morphology of pure VO2 films revealed elongated grains oriented within the film plane. The doped films evidenced an increased tendency to be oriented out of the film plane which has resulted in increased roughness levels. The doping methodology associated with optimized processing conditions allowed the production of W-doped VO2 films with reduced transition temperatures, from 63 down to 28 degrees C, and maximum transmittances at the visible region ranging 40%. The relationship between tungsten content in the film and consequent transition temperature expressed a linear behavior.

Epistatic interactions modulate the evolution of mammalian mitochondrial respiratory complex components

BACKGROUND

The deleterious effect of a mutation can be reverted by a second-site interacting residue. This is an epistatic compensatory process explaining why mutations that are deleterious in some species are tolerated in phylogenetically related lineages, rendering evident that those mutations are, by all means, only deleterious in the species-specific context. Although an extensive and refined theoretical framework on compensatory evolution does exist, the supporting evidence remains limited, especially for protein models. In this current study, we focused on the molecular mechanism underlying the epistatic compensatory process in mammalian mitochondrial OXPHOS proteins using a combination of in-depth structural and sequence analyses.

RESULTS

Modeled human structures were used in this study to predict the structural impairment and recovery of deleterious mutations alone and combined with an interacting compensatory partner, respectively. In two cases, COI and COIII, intramolecular interactions between spatially linked residues restore the folding pattern impaired by the deleterious mutation. In a third case, intermolecular contact between mitochondrial CYB and nuclear CYT1 encoded components of the cytochrome bc1 complex are likely to restore protein binding. Moreover, we observed different modes of compensatory evolution that have resulted in either a quasi-simultaneous occurrence of a mutation and corresponding compensatory partner, or in independent occurrences of mutations in distinct lineages that were always preceded by the compensatory site.

CONCLUSION

Epistatic interactions between individual replacements involving deleterious mutations seems to follow a parsimonious model of evolution in which genomes hold pre-compensating states that subsequently tolerate deleterious mutations. This phenomenon is likely to have been constraining the variability at coevolving sites and shaping the interaction between the mitochondrial and the nuclear genome.

Identification of species with DNA-based technology: current progress and challenges

One of the grand challenges of modern biology is to develop accurate and reliable technologies for a rapid screening of DNA sequence variation. This topic of research is of prime importance for the detection and identification of species in numerous fields of investigation, such as taxonomy, epidemiology, forensics, archaeology or ecology. Molecular identification is also central for the diagnosis, treatment and control of infections caused by different pathogens. In recent years, a variety of DNA-based approaches have been developed for the identification of individuals in a myriad of taxonomic groups. Here, we provide an overview of most commonly used assays, with emphasis on those based on DNA hybridizations, restriction enzymes, random PCR amplifications, species-specific PCR primers and DNA sequencing. A critical evaluation of all methods is presented focusing on their discriminatory power, reproducibility and user-friendliness. Having in mind that the current trend is to develop small-scale devices with a high-throughput capacity, we briefly review recent technological achievements for DNA analysis that offer great potentials for the identification of species.