ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing

Massive gene expression analyses are widely used to find differentially expressed genes under specific conditions. The results of these experiments are often available in public databases that are undergoing a growth similar to that of molecular sequence databases in the past. This now allows novel secondary computational tools to emerge that use such information to gain new knowledge. If several genes have a similar expression profile across heterogeneous transcriptomics experiments, they could be functionally related. These associations are usually useful for the annotation of uncharacterized genes. In addition, the search for genes with opposite expression profiles is useful for finding negative regulators and proposing inhibitory compounds in drug repurposing projects. Here we present a new web application, Automatic and Serial Analysis of CO-expression (ASACO), which has the potential to discover positive and negative correlator genes to a given query gene, based on thousands of public transcriptomics experiments. In addition, examples of use are presented, comparing with previous contrasted knowledge. The results obtained propose ASACO as a useful tool to improve knowledge about genes associated with human diseases and noncoding genes. ASACO is available at http://www.bioinfocabd.upo.es/asaco/.

The most exposed regions of SARS-CoV-2 structural proteins are subject to strong positive selection and gene overlap may locally modify this behavior

The SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic that emerged in 2019 has been an unprecedented event in international science, as it has been possible to sequence millions of genomes, tracking their evolution very closely. This has enabled various types of secondary analyses of these genomes, including the measurement of their sequence selection pressure. In this work, we have been able to measure the selective pressure of all the described SARS-CoV-2 genes, even analyzed by sequence regions, and we show how this type of analysis allows us to separate the genes between those subject to positive selection (usually those that code for surface proteins or those exposed to the host immune system) and those subject to negative selection because they require greater conservation of their structure and function. We have also seen that when another gene with an overlapping reading frame appears within a gene sequence, the overlapping sequence between the two genes evolves under a stronger purifying selection than the average of the non-overlapping regions of the main gene. We propose this type of analysis as a useful tool for locating and analyzing all the genes of a viral genome when an adequate number of sequences are available.IMPORTANCEWe have analyzed the selection pressure of all severe acute respiratory syndrome coronavirus 2 genes by means of the nonsynonymous (Ka) to synonymous (Ks) substitution rate. We found that protein-coding genes are exposed to strong positive selection, especially in the regions of interaction with other molecules (host receptor and genome of the virus itself). However, overlapping coding regions are more protected and show negative selection. This suggests that this measure could be used to study viral gene function as well as overlapping genes.

Ultrafast electron localization and screening in a transition metal dichalcogenide

The coupling of light to electrical charge carriers in semiconductors is the foundation of many technological applications. Attosecond transient absorption spectroscopy measures simultaneously how excited electrons and the vacancies they leave behind dynamically react to the applied optical fields. In compound semiconductors, these dynamics can be probed via any of their atomic constituents with core-level transitions into valence and conduction band. Typically, the atomic species forming the compound contribute comparably to the relevant electronic properties of the material. One therefore expects to observe similar dynamics, irrespective of the choice of atomic species via which it is probed. Here, we show in the two-dimensional transition metal dichalcogenide semiconductor MoSe₂, that through a selenium-based core-level transition we observe charge carriers acting independently from each other, while when probed through molybdenum, the collective, many-body motion of the carriers dominates. Such unexpectedly contrasting behavior can be explained by a strong localization of electrons around molybdenum atoms following absorption of light, which modifies the local fields acting on the carriers. We show that similar behavior in elemental titanium metal [M. Volkov et al., Nat. Phys. 15, 1145-1149 (2019)] carries over to transition metal-containing compounds and is expected to play an essential role for a wide range of such materials. Knowledge of independent particle and collective response is essential for fully understanding these materials.

Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems

CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter. By analyzing the spacers of tens of thousands of genomes from six bacterial species, we have been able to reduce the CRISPR dark matter from 80% to as low as 15% in some of the species. In addition, we have observed that, when a genome presents CRISPR-Cas systems, this is accompanied by particular sets of membrane proteins. Our results suggest that when bacteria present membrane proteins that make it compete better in its environment and these proteins are, in turn, receptors for specific phages, they would be forced to acquire CRISPR-Cas.

Negative refraction in hyperbolic hetero-bicrystals

We visualized negative refraction of phonon polaritons, which occurs at the interface between two natural crystals. The polaritons-hybrids of infrared photons and lattice vibrations-form collimated rays that display negative refraction when passing through a planar interface between the two hyperbolic van der Waals materials: molybdenum oxide (MoO₃) and isotopically pure hexagonal boron nitride (h¹¹BN). At a special frequency ω₀, these rays can circulate along closed diamond-shaped trajectories. We have shown that polariton eigenmodes display regions of both positive and negative dispersion interrupted by multiple gaps that result from polaritonic-level repulsion and strong coupling.

A particulate blood analogue based on artificial viscoelastic blood plasma and RBC-like microparticles at a concentration matching the human haematocrit

There has been enormous interest in the production of fluids with rheological properties similar to those of real blood over the last few years. Application fields range from biomicrofluidics (microscale) to forensic science (macroscale). The inclusion of flexible microparticles in blood analogue fluids has been demonstrated to be essential in order to reproduce the behaviour of blood flow in these fields. Here, we describe a protocol to produce a whole human blood analogue composed of a proposed plasma analogue and flexible spherical microparticles that mimic the key structural attributes of RBCs (size and mechanical properties), at a concentration matching the human haematocrit (∼42% by volume). Polydimethylsiloxane (PDMS) flexible microparticles were used to mimic RBCs, whose capability to deform is tunable by means of the mixing ratio of the PDMS precursor. Their flow through glass micronozzles allowed us to find the appropriate mixing ratio of PDMS to have approximately the same Young's modulus (E) as that exhibited by real RBCs. Shear and extensional rheology and microrheology techniques were used to match the properties exhibited by human plasma and whole blood at body temperature (37 °C). Finally, we study the flow of our proposed fluid through a microfluidic channel, showing the in vitro reproduction of the multiphase flow effects taking place in the human microcirculatory system, such as the cell-free layer (CFL) and the Fåhræus-Lindqvist effect. A macroscale application in the field of forensic science is also presented, concerning the impact of our blood analogue droplets on a solid surface for bloodstain pattern analysis.

Fire-Shaped Nozzles to Produce a Stress Peak for Deformability Studies

Fire-shaped nozzles can be used to study the deformability of microcapsules, particles, or cells traveling in a flow. Though their geometry depends on the dimensions of the original glass capillary and the heating conditions, they all produce a strain rate peak approximately at the section where the diameter is 1.5 times the minimum. The intensity of this peak and the time from its position to the neck can be easily estimated from the flow rate and three geometrical parameters, without the need for any simulation. In the convergent region of these nozzles, it is possible to observe the evolution of the deformation. It is necessary to use a sufficiently long nozzle to produce the maximum deformation before the neck.

Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes

The requirement for Cas nucleases to recognize a specific PAM is a major restriction for genome editing. SpCas9 variants SpG and SpRY, recognizing NGN and NRN PAMs, respectively, have contributed to increase the number of editable genomic sites in cell cultures and plants. However, their use has not been demonstrated in animals. Here we study the nuclease activity of SpG and SpRY by targeting 40 sites in zebrafish and C. elegans. Delivered as mRNA-gRNA or ribonucleoprotein (RNP) complexes, SpG and SpRY were able to induce mutations in vivo, albeit at a lower rate than SpCas9 in equivalent formulations. This lower activity was overcome by optimizing mRNA-gRNA or RNP concentration, leading to mutagenesis at regions inaccessible to SpCas9. We also found that the CRISPRscan algorithm could help to predict SpG and SpRY targets with high activity in vivo. Finally, we applied SpG and SpRY to generate knock-ins by homology-directed repair. Altogether, our results expand the CRISPR-Cas targeting genomic landscape in animals.

E-learning strategies from a bioinformatics postgraduate programme to improve student engagement and completion rate

Motivation

E-learning is the standard solution adopted in transnational study programmes for which multiple face-to-face learning places are not an option. Bioinformatics is compatible with e-learning because its resource requirements are low. Online learning, however, is usually associated with high dropout rates because students start from a very low computational level and/or they need support to conduct practical analyses on their own.

Results

In this article, we analyse the academic results of an online bioinformatics educational programme based on learning communities. The programme has been offered by the Spanish Pablo de Olavide University for more than 5 years with a completion rate of close to 90%. Learning bioinformatics requires technical and operational competencies that can only be acquired through a practical methodology. We have thus developed a student-centred and problem-based constructivist learning model; the model uses faculty and peer mentoring to drive individual work and retain students. Regarding our innovative learning model, the recruitment level (i.e. the number of applicants per available places and international origin), the results obtained (i.e. the retention index and learning outcomes) as well as the satisfaction index expressed by students and faculty lead us to regard this programme as a successful strategy for online graduate learning in bioinformatics.

Availability and implementation

All data and results for this article are available in the figures and supplementary files. The current syllabus (Supplementary File S7) and other details of the course are available at: https://www.upo.es/postgrado/Diploma-de-Especializacion-Analisis-Bioinformatico and https://www.upo.es/postgrado/Master-Analisis-Bioinformatico-Avanzado.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Assessment of selection pressure exerted on genes from complete pangenomes helps to improve the accuracy in the prediction of new genes

Bacterial genomes are massively sequenced, and they provide valuable data to better know the complete set of genes of a species. The analysis of thousands of bacterial strains can identify both shared genes and those appearing only in the pathogenic ones. Current computational gene finders facilitate this task but often miss some existing genes. However, the present availability of different genomes from the same species is useful to estimate the selective pressure applied on genes of complete pangenomes. It may assist in evaluating gene predictions either by checking the certainty of a new gene or annotating it as a gene under positive selection. Here, we estimated the selective pressure of 19 271 genes that are part of the pangenome of the human opportunistic pathogen Acinetobacter baumannii and found that most genes in this bacterium are subject to negative selection. However, 23% of them showed values compatible with positive selection. These latter were mainly uncharacterized proteins or genes required to evade the host defence system including genes related to resistance and virulence whose changes may be favoured to acquire new functions. Finally, we evaluated the utility of measuring selection pressure in the detection of sequencing errors and the validation of gene prediction.

L-Arginine Ameliorates Defective Autophagy in GM2 Gangliosidoses by mTOR Modulation

Aims: Tay–Sachs and Sandhoff diseases (GM2 gangliosidosis) are autosomal recessive disorders of lysosomal function that cause progressive neurodegeneration in infants and young children. Impaired hydrolysis catalysed by β-hexosaminidase A (HexA) leads to the accumulation of GM2 ganglioside in neuronal lysosomes. Despite the storage phenotype, the role of autophagy and its regulation by mTOR has yet to be explored in the neuropathogenesis. Accordingly, we investigated the effects on autophagy and lysosomal integrity using skin fibroblasts obtained from patients with Tay–Sachs and Sandhoff diseases. Results: Pathological autophagosomes with impaired autophagic flux, an abnormality confirmed by electron microscopy and biochemical studies revealing the accelerated release of mature cathepsins and HexA into the cytosol, indicating increased lysosomal permeability. GM2 fibroblasts showed diminished mTOR signalling with reduced basal mTOR activity. Accordingly, provision of a positive nutrient signal by L-arginine supplementation partially restored mTOR activity and ameliorated the cytopathological abnormalities. Innovation: Our data provide a novel molecular mechanism underlying GM2 gangliosidosis. Impaired autophagy caused by insufficient lysosomal function might represent a new therapeutic target for these diseases. Conclusions: We contend that the expression of autophagy/lysosome/mTOR-associated molecules may prove useful peripheral biomarkers for facile monitoring of treatment of GM2 gangliosidosis and neurodegenerative disorders that affect the lysosomal function and disrupt autophagy.

The 2021 ultrafast spectroscopic probes of condensed matter roadmap

In the 60 years since the invention of the laser, the scientific community has developed numerous fields of research based on these bright, coherent light sources, including the areas of imaging, spectroscopy, materials processing and communications. Ultrafast spectroscopy and imaging techniques are at the forefront of research into the light-matter interaction at the shortest times accessible to experiments, ranging from a few attoseconds to nanoseconds. Light pulses provide a crucial probe of the dynamical motion of charges, spins, and atoms on picosecond, femtosecond, and down to attosecond timescales, none of which are accessible even with the fastest electronic devices. Furthermore, strong light pulses can drive materials into unusual phases, with exotic properties. In this roadmap we describe the current state-of-the-art in experimental and theoretical studies of condensed matter using ultrafast probes. In each contribution, the authors also use their extensive knowledge to highlight challenges and predict future trends.

Protein-Coding Genes of Helicobacter pylori Predominantly Present Purifying Selection though Many Membrane Proteins Suffer from Selection Pressure: A Proposal to Analyze Bacterial Pangenomes

The current availability of complete genome sequences has allowed knowing that bacterial genomes can bear genes not present in the genome of all the strains from a specific species. So, the genes shared by all the strains comprise the core of the species, but the pangenome can be much greater and usually includes genes appearing in one only strain. Once the pangenome of a species is estimated, other studies can be undertaken to generate new knowledge, such as the study of the evolutionary selection for protein-coding genes. Most of the genes of a pangenome are expected to be subject to purifying selection that assures the conservation of function, especially those in the core group. However, some genes can be subject to selection pressure, such as genes involved in virulence that need to escape to the host immune system, which is more common in the accessory group of the pangenome. We analyzed 180 strains of Helicobacter pylori, a bacterium that colonizes the gastric mucosa of half the world population and presents a low number of genes (around 1500 in a strain and 3000 in the pangenome). After the estimation of the pangenome, the evolutionary selection for each gene has been calculated, and we found that 85% of them are subject to purifying selection and the remaining genes present some grade of selection pressure. As expected, the latter group is enriched with genes encoding for membrane proteins putatively involved in interaction to host tissues. In addition, this group also presents a high number of uncharacterized genes and genes encoding for putative spurious proteins. It suggests that they could be false positives from the gene finders used for identifying them. All these results propose that this kind of analyses can be useful to validate gene predictions and functionally characterize proteins in complete genomes.

Programmable hyperbolic polaritons in van der Waals semiconductors

Collective electronic modes or lattice vibrations usually prohibit propagation of electromagnetic radiation through the bulk of common materials over a frequency range associated with these oscillations. However, this textbook tenet does not necessarily apply to layered crystals. Highly anisotropic materials often display nonintuitive optical properties and can permit propagation of subdiffractional waveguide modes, with hyperbolic dispersion, throughout their bulk. Here, we report on the observation of optically induced electronic hyperbolicity in the layered transition metal dichalcogenide tungsten diselenide (WSe₂). We used photoexcitation to inject electron-hole pairs in WSe₂ and then visualized, by transient nanoimaging, the hyperbolic rays that traveled along conical trajectories inside of the crystal. We establish here the signatures of programmable hyperbolic electrodynamics and assess the role of quantum transitions of excitons within the Rydberg series in the observed polaritonic response.

Measuring farmers' attitude towards breeding tools: the Livestock Breeding Attitude Scale

Under-use of genetic improvement tools and low participation in breeding programmes are key drivers of breeding programmes under-performance. Both aspects are heavily influenced by farmers attitudes which, to date, have not been analysed in an objective and systematic manner. A key factor constraining the implementation of attitudinal studies towards livestock breeding tools is the lack of a reference scale for measuring attitudes. In this research, we provide the livestock breeding sector with such a reference measure. We developed the scale following the standardized psychometric methodologies and statistical tools. Then, as a case study, we used the scale to explore the attitudes of beef and dairy sheep farmers in Australia, New Zealand and Spain and analysed farmer and farming system factors related to those attitudes. Fourteen sheep and beef breed associations facilitated the implementation of a survey of 547 farmers, generating data that was used for the scale evaluation. The relationship between attitudinal factors and farmer and farming system factors was analysed using generalized linear models across and within breeds. The results suggest that the 8-item definitive scale we have developed is appropriate to measure farmer attitudes. We found that attitudes towards genetic improvement tools have two components; i) traditional selection and ii) genetic and genomic selection combined. This means that positive attitudes towards traditional phenotypic selection do not necessarily imply a negative attitude towards genetic and genomic selection tools. Farmer attitudes varied greatly not only across the studied breeds, species and countries, but also within them. High-educated farmers of business-oriented farms tend to have the most negative attitude towards traditional selection. However, attitudes towards genetic and genomic selection tools could not be linked to these factors. Finally, we found that the breed raised had a large effect on farmer attitude. These findings may help in the evolution of breeding programmes by identifying both the farmers most inclined to uptake breeding innovations in the early stages of its establishment and the farmers who would be more reluctant to participate in such programmes, thus informing where to focus extension efforts.

Light-Induced Renormalization of the Dirac Quasiparticles in the Nodal-Line Semimetal ZrSiSe

In nodal-line semimetals, linearly dispersing states form Dirac loops in the reciprocal space with a high degree of electron-hole symmetry and a reduced density of states near the Fermi level. The result is reduced electronic screening and enhanced correlations between Dirac quasiparticles. Here we investigate the electronic structure of ZrSiSe, by combining time- and angle-resolved photoelectron spectroscopy with ab initio density functional theory (DFT) complemented by an extended Hubbard model (DFT+U+V) and by time-dependent DFT+U+V. We show that electronic correlations are reduced on an ultrashort timescale by optical excitation of high-energy electrons-hole pairs, which transiently screen the Coulomb interaction. Our findings demonstrate an all-optical method for engineering the band structure of a quantum material.

Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation

Acinetobacter baumannii is an opportunistic bacterium that causes hospital-acquired infections with a high mortality and morbidity, since there are strains resistant to virtually any kind of antibiotic. The chase to find novel strategies to fight against this microbe can be favoured by knowledge of the complete catalogue of genes of the species, and their relationship with the specific characteristics of different isolates. In this work, we performed a genomics analysis of almost 2500 strains. Two different groups of genomes were found based on the number of shared genes. One of these groups rarely has plasmids, and bears clustered regularly interspaced short palindromic repeat (CRISPR) sequences, in addition to CRISPR-associated genes (cas genes) or restriction-modification system genes. This fact strongly supports the lack of plasmids. Furthermore, the scarce plasmids in this group also bear CRISPR sequences, and specifically contain genes involved in prokaryotic toxin–antitoxin systems that could either act as the still little known CRISPR type IV system or be the precursors of other novel CRISPR/Cas systems. In addition, a limited set of strains present a new cas9-like gene, which may complement the other cas genes in inhibiting the entrance of new plasmids into the bacteria. Finally, this group has exclusive genes involved in biofilm formation, which would connect CRISPR systems to the biogenesis of these bacterial resistance structures.

Attosecond timing of the dynamical Franz–Keldysh effect

To what extent do intra- or inter-band transitions dominate the optical response of dielectrics when pumped by a few-cycle near-infrared transient electric field? In order to find an answer to this question we investigate the dynamical Franz–Keldysh effect in polycrystalline diamond and discuss in detail the attosecond delay of the induced electron dynamics with regard to the driving transient electric field while the peak intensity is varied between 1 × 1012 and 10 × 1012 W cm−2. We found that the main oscillating feature in transient absorption at 43 eV is in phase with the electric field of the pump, to within 49 ± 78 as. However, the phase delay shows a slightly asymmetric V-shaped linear energy dispersion with a rate of about 200 as eV–1. Theoretical calculations within the dipole approximation reproduce the data and allow us to conclude that intra-band motion dominates under our experimental conditions.

Ancient evolutionary signals of protein-coding sequences allow the discovery of new genes in the Drosophila melanogaster genome

Background

The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive. The number of this kind of genes continuously increases due to new experimental data and development of improved bioinformatics algorithms.

Results

In this context, AnABlast represents a novel in silico strategy, based on the accumulation of short evolutionary signals identified by protein sequence alignments of low score. This strategy potentially highlights protein-coding regions in genomic sequences regardless of traditional homology or translation signatures. Here, we analyze the evolutionary information that the accumulation of these short signals encloses. Using the Drosophila melanogaster genome, we stablish optimal parameters for the accurate gene prediction with AnABlast and show that this new strategy significantly contributes to add genes, exons and pseudogenes regions, yet to be discovered in both already annotated and new genomes.

Conclusions

AnABlast can be freely used to analyze genomic regions of whole genomes where it contributes to complete the previous annotation.

A rural-urban latitudinal study of the distributions of Culex quinquefasciatus and Culex pipiens bioforms in their southernmost sympatric fringe

Mosquitoes grouped in the complex Culex pipiens L. (Diptera: Culicidae) are important vectors of medical and veterinary diseases. In the South American sympatric region, Cx. pipiens and Culex quinquefasciatus Say coexist and potentially hybridize. To identify key drivers of their geographical distribution, mosquito immatures were collected from flower vases of eight urban/rural cemetery pairs within a 5° latitudinal transect along Buenos Aires Province, Argentina. The specimens were identified by molecular methods and their relative proportion modelled as a function of environmental variables. At the beginning of the warm season, northern and southern cemeteries presented exclusively Cx. quinquefasciatus and Cx. pipiens, respectively, with different proportions of both at mid latitudes. By the end of the summer, Cx. quinquefasciatus was present throughout the study area, exclusively in 11 of the 16 cemeteries both rural and urban, whereas Cx. pipiens was predominant only in the southernmost pair. Mean annual temperature, photoperiod variability and time of the season were key drivers of their distributions. All specimens of Cx. pipiens were identified as form molestus and no hybrids were recognized. The reported distribution patterns and the potential absence of Cx. pipiens f. pipiens and hybrids are discussed, along with their implications in disease transmission.

One-dimensional flat bands in twisted bilayer germanium selenide

Experimental advances in the fabrication and characterization of few-layer materials stacked at a relative twist of small angle have recently shown the emergence of flat energy bands. As a consequence electron interactions become relevant, providing inroads into the physics of strongly correlated two-dimensional systems. Here, we demonstrate by combining large scale ab initio simulations with numerically exact strong correlation approaches that an effective one-dimensional system emerges upon stacking two twisted sheets of GeSe, in marked contrast to all moiré systems studied so far. This not only allows to study the necessarily collective nature of excitations in one dimension, but can also serve as a promising platform to scrutinize the crossover from two to one dimension in a controlled setup by varying the twist angle, which provides an intriguing benchmark with respect to theory. We thus establish twisted bilayer GeSe as an intriguing inroad into the strongly correlated physics of lowdimensional systems.

Time-Dependent Magnons from First Principles

We propose an efficient and non-perturbative scheme to compute magnetic excitations for extended systems employing the framework of time-dependent density functional theory. Within our approach, we drive the system out of equilibrium using an ultrashort magnetic kick perpendicular to the ground-state magnetization of the material. The dynamical properties of the system are obtained by propagating the time-dependent Kohn–Sham equations in real time, and the analysis of the time-dependent magnetization reveals the transverse magnetic excitation spectrum of the magnet. We illustrate the performance of the method by computing the magnetization dynamics, obtained from a real-time propagation, for iron, cobalt, and nickel and compare them to known results obtained using the linear-response formulation of time-dependent density functional theory. Moreover, we point out that our time-dependent approach is not limited to the linear-response regime, and we present the first results for nonlinear magnetic excitations from first principles in iron.

CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats

The genomics era is resulting in the generation of a plethora of biological sequences that are usually stored in public databases. There are many computational tools that facilitate the annotation of these sequences, but sometimes they produce mistakes that enter the databases and can be propagated when erroneous data are used for secondary analyses, such as gene prediction or homology searching. While developing a computational gene finder based on protein-coding sequences, we discovered that the reference UniProtKB protein database is contaminated with some spurious sequences translated from DNA containing clustered regularly interspaced short palindromic repeats. We therefore encourage developers of prokaryotic computational gene finders and protein database curators to consider this source of error.

Splenic infarction associated with transient anti-prothrombin antibodies is a rare manifestation of acute Mycoplasma pneumoniae infection

We report the first paediatric case of splenic infarction following acute Mycoplasma pneumoniae infection with induction of anti-prothrombin (aPT) antibodies. A 12-year-old boy was admitted to the paediatric emergency department for a left pleuropneumonia and a splenic infarction. aPT antibodies were transitorily detected. The patient recovered fully after antibiotic therapy and a 3-month course of anticoagulation treatment. Antiphospholipid (aPL) antibodies induced by acute infections have already been reported but cases of clinically relevant thrombosis remain rare. The pathogenicity of aPT antibodies is discussed here. We hypothesize that these antibodies were involved in this symptomatic hypercoagulable state.

AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions

AnABlast is a computational tool that highlights protein-coding regions within intergenic and intronic DNA sequences which escape detection by standard gene prediction algorithms. DNA sequences with small protein-coding genes or exons, complex intron-containing genes, or degenerated DNA fragments are efficiently targeted by AnABlast. Furthermore, this algorithm is particularly useful in detecting protein-coding sequences with nonsignificant homologs to sequences in databases. AnABlast can be executed online at http://www.bioinfocabd.upo.es/anablast/ .

Polarization-state-resolved high-harmonic spectroscopy of solids

Attosecond metrology sensitive to sub-optical-cycle electronic and structural dynamics is opening up new avenues for ultrafast spectroscopy of condensed matter. Using intense lightwaves to precisely control the fast carrier dynamics in crystals holds great promise for next-generation petahertz electronics and devices. The carrier dynamics can produce high-order harmonics of the driving field extending up into the extreme-ultraviolet region. Here, we introduce polarization-state-resolved high-harmonic spectroscopy of solids, which provides deeper insights into both electronic and structural sub-cycle dynamics. Performing high-harmonic generation measurements from silicon and quartz, we demonstrate that the polarization states of the harmonics are not only determined by crystal symmetries, but can be dynamically controlled, as a consequence of the intertwined interband and intraband electronic dynamics. We exploit this symmetry-dynamics duality to efficiently generate coherent circularly polarized harmonics from elliptically polarized pulses. Our experimental results are supported by ab-initio simulations, providing evidence for the microscopic origin of the phenomenon.

High-harmonic generation in solids is related to the carrier dynamics and can be used to probe dynamic processes. Here, Klemke et al. show that the polarization states of high harmonics generated from silicon and quartz are determined by the crystal symmetries but can also be dynamically controlled.

Local adsorption structure and bonding of porphine on Cu(111) before and after self-metalation

We have experimentally determined the lateral registry and geometric structure of free-base porphine (2H-P) and copper-metalated porphine (Cu-P) adsorbed on Cu(111), by means of energy-scanned photoelectron diffraction (PhD), and compared the experimental results to density functional theory (DFT) calculations that included van der Waals corrections within the Tkatchenko-Scheffler approach. Both 2H-P and Cu-P adsorb with their center above a surface bridge site. Consistency is obtained between the experimental and DFT-predicted structural models, with a characteristic change in the corrugation of the four N atoms of the molecule's macrocycle following metalation. Interestingly, comparison with previously published data for cobalt porphine adsorbed on the same surface evidences a distinct increase in the average height of the N atoms above the surface through the series 2H-P, Cu-P, and cobalt porphine. Such an increase strikingly anti-correlates the DFT-predicted adsorption strength, with 2H-P having the smallest adsorption height despite the weakest calculated adsorption energy. In addition, our findings suggest that for these macrocyclic compounds, substrate-to-molecule charge transfer and adsorption strength may not be univocally correlated.

Cavity quantum-electrodynamical polaritonically enhanced electron-phonon coupling and its influence on superconductivity

So far, laser control of solids has been mainly discussed in the context of strong classical nonlinear light-matter coupling in a pump-probe framework. Here, we propose a quantum-electrodynamical setting to address the coupling of a low-dimensional quantum material to quantized electromagnetic fields in quantum cavities. Using a protoypical model system describing FeSe/SrTiO3 with electron-phonon long-range forward scattering, we study how the formation of phonon polaritons at the two-dimensional interface of the material modifies effective couplings and superconducting properties in a Migdal-Eliashberg simulation. We find that through highly polarizable dipolar phonons, large cavity-enhanced electron-phonon couplings are possible, but superconductivity is not enhanced for the forward-scattering pairing mechanism due to the interplay between coupling enhancement and mode softening. Our results demonstrate that quantum cavities enable the engineering of fundamental couplings in solids, paving the way for unprecedented control of material properties.

Transient Charge and Energy Flow in the Wide-Band Limit

The wide-band limit is a commonly used approximation to analyze transport through nanoscale devices. In this work we investigate its applicability to the study of charge and heat transport through molecular break junctions exposed to voltage biases and temperature gradients. We find by comparative simulations that while the wide-band-limit approximation faithfully describes the long-time charge and heat transport, it fails to characterize the short-time behavior of the junction. In particular, we show that the charge current flowing through the device shows a discontinuity when a temperature gradient is applied, while the energy flow is discontinuous when a voltage bias is switched on and even diverges when the junction is exposed to both a temperature gradient and a voltage bias. We provide an explanation for this pathological behavior and propose two possible solutions to this problem.

Heterogeneous distribution of Culex pipiens, Culex quinquefasciatus and their hybrids along the urbanisation gradient

The mosquitoes of the Culex pipiens complex, hereafter referred to as the Pipiens Assemblage, are vectors of arbovirus of worldwide concern including West Nile and St. Louis encephalitis. Given their distinct eco-physiology and vectorial capacity, accurate specimen identification and insight in the environmental drivers of their distribution are essential for the understanding of disease transmission patterns. Using a PCR-based identification protocol, we characterized the spatial distribution of Cx. pipiens, Cx. quinquefasciatus and their hybrids developing in used tyres located within the overlapping region in South America as a function of different estimators of the urbanisation gradient. Out of 84 samples collected from tyre piles of 20 sites, we identified 369 larvae which corresponded predominantly to Cx. quinquefasciatus (76.4% of immatures) all along the gradient but more frequent at the urban end. Cx. pipiens (21.4%) was more conspicuous at the low urbanised end but was also present in highly urbanised sites, whereas hybrids were collected in very low numbers (2.2%). The urbanisation estimator best associated with the heterogeneous occurrence of the Pipiens Assemblage members was the proportion of impervious surface 1km around each tyre pile, which explained 41.7% of the variability in the data, followed closely by the distance to the Capital City (38.3%). Cumulative annual precipitation, population number in a 1km radius around each pile and distance to the de la Plata River were significantly associated with the distribution of the Pipiens Assemblage at lower explanation percentages (20-23%). A thorough understanding of the ecological basis and environmental associations of the distribution of Pipiens Assemblage members will enable forecasting population trends in changing environments to develop effective control measures for mosquitoes and the diseases they transmit.

Momentum-Resolved View of Electron-Phonon Coupling in Multilayer WSe_{2}

We investigate the interactions of photoexcited carriers with lattice vibrations in thin films of the layered transition metal dichalcogenide (TMDC) WSe_{2}. Employing femtosecond electron diffraction with monocrystalline samples and first-principles density functional theory calculations, we obtain a momentum-resolved picture of the energy transfer from excited electrons to phonons. The measured momentum-dependent phonon population dynamics are compared to first-principles calculations of the phonon linewidth and can be rationalized in terms of electronic phase-space arguments. The relaxation of excited states in the conduction band is dominated by intervalley scattering between Σ valleys and the emission of zone boundary phonons. Transiently, the momentum-dependent electron-phonon coupling leads to a nonthermal phonon distribution, which, on longer time scales, relaxes to a thermal distribution via electron-phonon and phonon-phonon collisions. Our results constitute a basis for monitoring and predicting out of equilibrium electrical and thermal transport properties for nanoscale applications of TMDCs.

[Nasogastric rehydration for treating children with gastroenteritis]

INTRODUCTION

When oral rehydration is not feasible, enteral rehydration via the nasogastric route has been the ESPGHAN recommended method of rehydration since 2008, rather than intravenous rehydration (IVR), for children with acute gastroenteritis. However, these recommendations are rarely followed in France. Since 2011, in case of failure of oral rehydration, enteral rehydration has been used as a first-line therapy in the Children's Emergency Department at the Grenoble-Alpes University Hospital.

PURPOSE

The aims of the study were to compare the length of the hospital stay, the duration of initial rehydration, and the incidence of complications and failure with the use of enteral nasogastric versus intravenous rehydration.

METHODS

This study compared two cohorts of children (<3 years of age) with mild-to-moderate dehydration caused by acute gastroenteritis and failure of rehydration via the oral route. The first group (winter 2010-2011) was managed according to the previous protocol (intravenous rehydration). The second group (winter 2011-2012) was managed according the new protocol (nasogastric tube rehydration [NGR]). The rest of the gastroenteritis management was identical in both groups.

RESULTS

A total of 132 children were included, 65 were treated with nasogastric tube rehydration (NGR) and 67 with intravenous rehydration. There was a significant reduction in the duration of hospitalization in the post-emergency unit in the NGR group: 23.6h vs 40.1h (P<0.05). The duration of initial rehydration was also significantly reduced (10.5h vs 22.0h). There was no significant difference regarding serious adverse events. However, the NGR group presented more mild adverse events (22 vs 7, P<0.05) and more treatment failures (15.3% vs 3%, P=0.013).

CONCLUSION

Nasogastric rehydration reduces the duration of rehydration and the length of the hospital stay without increasing the incidence of serious adverse events for dehydrated children hospitalized for acute gastroenteritis.

Prevalence and Phylogenetic Analysis of Bartonella Species of Wild Carnivores and Their Fleas in Northwestern Mexico

The host-parasite-vector relationship of Bartonella spp. system in wild carnivores and their fleas from northwestern Mexico was investigated. Sixty-six carnivores belonging to eight species were sampled, and 285 fleas belonging to three species were collected during spring (April-May) and fall (October-November) seasons. We detected Bartonella species in 7 carnivores (10.6%) and 27 fleas (9.5%) through either blood culture or PCR. Of the 27 Bartonella-positive fleas, twenty-two were Pulex simulans, three were Pulex irritans and one was Echidnophaga gallinacea. The gltA gene and ITS region sequences alignment revealed six and eight genetic variants of Bartonella spp., respectively. These variants were clustered into Bartonella rochalimae, Bartonella vinsonii subsp. berkhoffii and another genotype, which likely represents a novel species of Bartonella spp. Although experimental infection studies are required to prove the vector role of P. simulans, our results suggest that this flea may play an important role in the Bartonella transmission. The results indicated possible host-specific relationships between Bartonella genotypes and the families of the carnivores, but further studies are needed to verify this finding. The presence of zoonotic species of Bartonella spp. in wild carnivores raises the issue of their potential risk for humans in fragmented ecosystems.

FOTROCAN Delphi consensus statement regarding the prevention and treatment of cancer-associated thrombosis in areas of uncertainty and low quality of evidence

INTRODUCTION

Decision-making in cancer-related venous thromboembolism (VTE) is often founded on scant lines of evidence and weak recommendations. The aim of this work is to evaluate the percentage of agreement surrounding a series of statements about complex, clinically relevant, and highly uncertain aspects to formulate explicit action guidelines.

MATERIALS AND METHODS

Opinions were based on a structured questionnaire with appropriate scores and were agreed upon using a Delphi method. Questions were selected based on a list of recommendations with low evidence from the Spanish Society of Oncology Clinical Guideline for Thrombosis. The questionnaire was completed in two iterations by a multidisciplinary panel of experts in thrombosis.

RESULTS

Of the 123 statements analyzed, the panel concurred on 22 (17%) and another 81 (65%) were agreed on by qualified majority, including important aspects of long-term and prolonged anticoagulation, major bleeding and rethrombosis management, treatment in special situations, catheter-related thrombosis and thromboprophylaxis. Among them, the panelists agreed the incidental events should be equated to symptomatic ones, long-term and extended use of full-dose low-molecular weight heparin, and concluded that the Khorana score is not sensitive enough to uphold an effective thromboprophylaxis strategy.

CONCLUSION

Though the level of consensus varied depending on the scenario presented, overall, the iterative process achieved broad agreement as to the general treatment principles of cancer-associated VTE. Clinical validation of these statements in genuine practice conditions would be useful.

Generation and Evolution of Spin-, Valley-, and Layer-Polarized Excited Carriers in Inversion-Symmetric WSe_{2}

We report the spin-selective optical excitation of carriers in inversion-symmetric bulk samples of the transition metal dichalcogenide (TMDC) WSe_{2}. Employing time- and angle-resolved photoelectron spectroscopy (trARPES) and complementary time-dependent density functional theory (TDDFT), we observe spin-, valley-, and layer-polarized excited state populations upon excitation with circularly polarized pump pulses, followed by ultrafast (<100  fs) scattering of carriers towards the global minimum of the conduction band. TDDFT reveals the character of the conduction band, into which electrons are initially excited, to be two-dimensional and localized within individual layers, whereas at the minimum of the conduction band, states have a three-dimensional character, facilitating interlayer charge transfer. These results establish the optical control of coupled spin-, valley-, and layer-polarized states in centrosymmetric materials with locally broken symmetries and suggest the suitability of TMDC multilayer and heterostructure materials for valleytronic and spintronic device concepts.

Engineered LINE-1 retrotransposition in nondividing human neurons

Half the human genome is made of transposable elements (TEs), whose ongoing activity continues to impact our genome. LINE-1 (or L1) is an autonomous non-LTR retrotransposon in the human genome, comprising 17% of its genomic mass and containing an average of 80-100 active L1s per average genome that provide a source of inter-individual variation. New LINE-1 insertions are thought to accumulate mostly during human embryogenesis. Surprisingly, the activity of L1s can further impact the somatic human brain genome. However, it is currently unknown whether L1 can retrotranspose in other somatic healthy tissues or if L1 mobilization is restricted to neuronal precursor cells (NPCs) in the human brain. Here, we took advantage of an engineered L1 retrotransposition assay to analyze L1 mobilization rates in human mesenchymal (MSCs) and hematopoietic (HSCs) somatic stem cells. Notably, we have observed that L1 expression and engineered retrotransposition is much lower in both MSCs and HSCs when compared to NPCs. Remarkably, we have further demonstrated for the first time that engineered L1s can retrotranspose efficiently in mature nondividing neuronal cells. Thus, these findings suggest that the degree of somatic mosaicism and the impact of L1 retrotransposition in the human brain is likely much higher than previously thought.

Brain responses to uncertainty about upcoming rectal discomfort in quiescent Crohn's disease - a fMRI study

BACKGROUND

Patients with Crohn's disease (CD) in remission are exposed to chronic psychological distress, due to the constant risk of relapse. This permanent situation of anticipation and uncertainty can lead to anxiety, which may, in turn, trigger relapse. We aimed to investigate the effects of uncertainty on behavioral and brain responses to anticipation of visceral discomfort in quiescent CD patients.

METHODS

Barostat-controlled rectal distensions were preceded by cued uncertain or certain anticipation in nine CD patients and nine matched healthy volunteers. Brain responses obtained before distension across the different anticipation conditions in regions of interest (ROI) involved in (anticipation of) pain were measured using functional magnetic resonance imaging and compared between CD and controls. The association between anxiety-related psychological variables and cerebral anticipatory activity was tested.

KEY RESULTS

During uncertainty, CD patients had significantly stronger activations than controls in the cingulate cortex, insula, amygdala, and thalamus with trends in the hippocampus, prefrontal, and secondary somatosensory cortex. In patients, brain responses to uncertainty in the majority of ROI correlated positively with gastrointestinal symptom-specific anxiety, trait-anxiety, and intolerance of uncertainty.

CONCLUSIONS & INFERENCES

In a context of uncertainty regarding occurrence of uncomfortable visceral sensations, CD is associated with excessive reactivity in brain regions known to be involved in sensory, cognitive and emotional aspects of pain processing and modulation, and threat appraisal. Our findings contribute to a better understanding of the role of emotional and cognitive processes in CD. This may, in turn, lead to the development of new (psycho)therapeutic approaches for management of symptoms and related anxiety.

[Collagenous gastritis and colitis in a 10-year-old girl]

There are few data in the literature on microscopic gastritis and colitis in the pediatric population. The diagnosis is often made after the occurrence of complications. We report the case of a 10.5 year-old girl for whom the diagnosis was made several years after the initial symptoms. Test for infections, inflammation, and auto-immunity yielded normal results. Upper endoscopy and colonoscopy revealed an abnormal mucosa. However, histology showed microscopic inflammation and fibrotic lesions in the lamina propria, and a thick subepithelial collagenous band. This led to the diagnosis of collagenous gastritis and colitis. Budesonide treatment resulted in the cessation of diarrhea and significant weight gain. Treatment by oral budesonide indeed seems to be highly effective but relapses are frequent when the treatment is stopped. This case shows the importance of being vigilant regarding transit disorders with impact on growth kinetics. Upper endoscopy and colonoscopy need to be carried out when children have organic diarrhea with normal blood tests.

Characterization and isolation of immature neurons of the adult mouse piriform cortex

Physiological studies indicate that the piriform or primary olfactory cortex of adult mammals exhibits a high degree of synaptic plasticity. Interestingly, a subpopulation of cells in the layer II of the adult piriform cortex expresses neurodevelopmental markers, such as the polysialylated form of neural cell adhesion molecule (PSA-NCAM) or doublecortin (DCX). This study analyzes the nature, origin, and potential function of these poorly understood cells in mice. As previously described in rats, most of the PSA-NCAM expressing cells in layer II could be morphologically classified as tangled cells and only a small proportion of larger cells could be considered semilunar-pyramidal transitional neurons. Most were also immunoreactive for DCX, confirming their immature nature. In agreement with this, detection of PSA-NCAM combined with that of different cell lineage-specific antigens revealed that most PSA-NCAM positive cells did not co-express markers of glial cells or mature neurons. Their time of origin was evaluated by birthdating experiments with halogenated nucleosides performed at different developmental stages and in adulthood. We found that virtually all cells in this paleocortical region, including PSA-NCAM-positive cells, are born during fetal development. In addition, proliferation analyses in adult mice revealed that very few cells were cycling in layer II of the piriform cortex and that none of them was PSA-NCAM-positive. Moreover, we have established conditions to isolate and culture these immature neurons in the adult piriform cortex layer II. We find that although they can survive under certain conditions, they do not proliferate in vitro either. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 748-763, 2016.