Descriptive study of perineuronal net in enteric nervous system of humans and mice.

Perineuronal nets (PNN) are highly specialized structures of the extracellular matrix around specific groups of neurons in the central nervous system (CNS). They play functions related to optimizing physiological processes and protection neurons against harmful stimuli. Traditionally, their existence was only described in the CNS. However, there was no description of the presence and composition of PNN in the enteric nervous system (ENS) until now. Thus, our aim was to demonstrate the presence and characterize the components of the PNN in the enteric nervous system. Samples of intestinal tissue from mice and humans were analyzed by RT-PCR and immunofluorescence assays. We used a marker (Wisteria floribunda agglutinin) considered as standard for detecting the presence of PNN in the CNS and antibodies for labeling members of the four main PNN-related protein families in the CNS. Our results demonstrated the presence of components of PNN in the ENS of both species; however its molecular composition is species-specific.

The Gemstone Cyborg: How Diamond Films Are Creating New Platforms for Cell Regeneration and Biointerfacing.

Diamond is a promising material for the biomedical field, mainly due to its set of characteristics such as biocompatibility, strength, and electrical conductivity. Diamond can be synthesised in the laboratory by different methods, is available in the form of plates or films deposited on foreign substrates, and its morphology varies from microcrystalline diamond to ultrananocrystalline diamond. In this review, we summarise some of the most relevant studies regarding the adhesion of cells onto diamond surfaces, the consequent cell growth, and, in some very interesting cases, the differentiation of cells into neurons and oligodendrocytes. We discuss how different morphologies can affect cell adhesion and how surface termination can influence the surface hydrophilicity and consequent attachment of adherent proteins. At the end of the review, we present a brief perspective on how the results from cell adhesion and biocompatibility can make way for the use of diamond as biointerface.

Microbial gut evaluation in an angolan paediatric population with sickle cell disease.

Sickle cell disease (SCD) is one of the most common genetic conditions worldwide. It can contribute up to 90% of under-5 mortality in sub-Saharan Africa. Clinical manifestations are very heterogeneous, and the intestinal microbiome appears to be crucial in the modulation of inflammation, cell adhesion and induction of aged neutrophils, the main interveners of recurrent vaso-occlusive crisis. Enterocyte injury, increased permeability, altered microbial composition and bacterial overgrowth have all been documented as microbial and pathophysiologic changes in the gut microbiome of SCD patients in recent studies. Our aim was to sequence the bacterial 16S rRNA gene in order to characterize the gut microbiome of Angolan children with SCA and healthy siblings as a control. A total of 72 stool samples were obtained from children between 3 and 14 years old. Our data showed that the two groups exhibit some notable differences in microbiota relative abundance at different classification levels. Children with SCA have a higher number of the phylum Actinobacteria. As for the genus level, Clostridium cluster XI bacteria was more prevalent in the SCA children, whereas the siblings had a higher abundance of Blautia, Aestuariispira, Campylobacter, Helicobacter, Polaribacter and Anaerorhabdus. In this study, we have presented the first microbiota analysis in an Angolan paediatric population with SCD and provided a detailed view of the microbial differences between patients and healthy controls. There is still much to learn before fully relying on the therapeutic approaches for gut modulation, which is why more research in this field is crucial to making this a reality.

Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins.

Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have identified a set of ORIs of Arabidopsis thaliana and their chromatin landscape at two stages of post-embryonic development. ORIs associate with multiple chromatin signatures including transcription start sites (TSS) but also proximal and distal regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin, but at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the set of ORIs active in an organism at the post-embryo stage that should allow us to study ORI biology in response to development, environment, and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.

Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models.

Podarcis wall lizards are endemic to the Mediterranean Basin where they represent the predominant reptile group. Despite being extensively used as model organisms in evolutionary and ecological studies their phylogeny and historical biogeography are still incompletely resolved. Moreover, molecular clock calibrations used in wall lizard phylogeography are based on the assumption of vicariant speciation triggered by the abrupt Mediterranean Sea level rise at the end of the Messinian salinity crisis (MSC). However, the validity of this biogeographic calibration remains untested. In this study we inferred a robust time tree based on multilocus data and fossil calibrations using both gene concatenation and species-tree approaches and including models with gene-flow. We found five deeply divergent, geographically coherent, and well-supported clades comprising species from i) Iberian Peninsula and North Africa; ii) Western Mediterranean islands, iii) Sicilian and Maltese islands; and iv-v) Balkan region and Aegean islands. The mitochondrial tree shows some inconsistencies with the species tree that warrant future investigation. Diversification of main clades is estimated in a short time frame during the Middle Miocene and might have been associated with a period of global climate cooling with the establishment of a marked climatic zonation in Europe. Cladogenetic events within the main clades are scattered throughout the time tree, from the Late Miocene to the Early Pleistocene, suggesting that speciation events in wall lizards reflect a complex interplay between regional topography, climate and geological history rather than a shared major climatic or paleogeographic event. Our absolute time estimates, as well as a relative dating approach, demonstrate that the assumption of a causal link between sea-level rise at the end of the MSC and the diversification of many island endemics is not justified. This study reinforces the notion that multiple dispersal and vicariant events, at different time frames, are required to explain current allopatric distributions and to account for the historical assembly of Mediterranean biota, and cautions against the use of biogeographic calibrations based on the assumption of vicariance.

Handgrip Strength and Its Association With Hydration Status and Urinary Sodium-to-Potassium Ratio in Older Adults.

Objective: Older adults present higher risk of functional disability detected by handgrip strength and an increased risk of poor health conditions, such as dehydration and low values of the sodium-to-potassium (Na/K) ratio. This study aimed to quantify the association of hydration status and Na/K ratio with handgrip strength, based on the urinary excretion of older adults.Methods: A cross-sectional study was conducted in 735 older adults ≥ 65 years old. Handgrip strength was measured with a Jamar Dynamometer and low values were defined according to body mass index and to sex-specific cutoff points. The hydration status was evaluated based on free water reserve. Sodium and potassium intake were evaluated after converting 24-hour urinary sodium and potassium excretion, respectively. A logistic regression model was used to estimate the probability of presenting low handgrip strength, according to risk of hypohydration and to quartiles of Na/K, stratified by sex and adjusted for potential confounders.Results: The adjusted odds ratio (OR) for presenting low handgrip strength was higher in women at risk of hypohydration, but this association was not found in men. Both women and men with the highest values of Na/K ratio presented higher adjusted OR for low handgrip strength (OR in women was 2.03; 95% confidence interval [CI]: 1.12-3.68, and in men was 2.19; 95% CI: 1.11-4.29).Conclusions: The risk of hypohydration was directly associated with low handgrip strength in older women. In older adults, higher values of urinary Na/K ratio were also directly associated with low handgrip strength.

Estimation of maximum temperature and thermal crosstalk between two active elements in a PIC: development of a thermal equivalent circuit.

The operating temperature plays a key role in the performance and lifetime of photonic integrated circuits (PICs). Miniaturization and increasing heat dissipation promote thermal crosstalk effects and pose additional challenges to the PIC designer. The European Photonics Industry Consortium recommends thermal modeling during design phase. However, a fully numerical optimization of a particular layout requires an unrealistically large number of simulations. Here, we propose a compromise approach: a set of carefully chosen simulations are performed with a multi-physics software. The obtained results are used to derive a linearized equivalent thermal circuit that can be used to maximize the power levels and to minimize the distance between the chosen components while guaranteeing the absence of a thermal crosstalk. For simplification, this model is derived considering a PIC with only two active components. Other parameters are varied, such as the material of the holder (silicon or diamond) and the layer of epoxy that is used to attach the PIC to the holder. The obtained circuit is used to determine the maximum dissipated power or the minimum distance between the components while keeping some predetermined specifications. The model can be extended to contain more elements or to include transient analysis of the temperature distribution.

Thermal management of photonic integrated circuits: impact of holder material and epoxies.

The thermal management of photonic integrated circuits (PICs) poses a few challenges at the packaging level. The integration of a PIC with a proper holder provides mechanical support and electrical interconnection, as well as spreading of the heat generated during PIC operation. This study proposes and evaluates the thermal behavior of silicon and diamond holders and estimates the impact of integrating them with PICs as a packaged system; to this end, the thermal profile of a PIC with distributed feedback lasers mounted on silicon or diamond holders was simulated for different power levels using ANSYS Mechanical software. The impact of the epoxy resin used to mount the PIC on the holder and the thermal crosstalk between the active components were also evaluated. Based on steady-state thermal analysis, when the PIC is assembled via wire bonding, the replacement of the silicon holder with a diamond holder brings only a marginal advantage. The choice of epoxy has a larger impact on the maximum PIC temperature and the thermal crosstalk between active components. Choosing a large-thermal-conductivity-value epoxy is thus a mandatory requirement in order to guarantee the proper thermal management of PICs and their corresponding holders.

Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin.

Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. The DNA and chromatin features determining ORI specification are not presently known. We have generated a high-resolution genome-wide map of 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused on defining the features associated with ORIs in heterochromatin. In pericentromeric gene-poor domains ORIs associate almost exclusively with the retrotransposon class of transposable elements (TEs), in particular of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with retrotransposons is determined by their transposition mechanism based on transcription, and a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin and of the entire genome.

Quality predictors of parental satisfaction after birth of infants with life-limiting conditions.

AIM: This study examines parental satisfaction with care received in the context of a life-limiting foetal diagnosis and subsequent birth. METHODS: Survey methods were utilised to embed the Quality Indicators (QI) and Parental Satisfaction of Perinatal Palliative Care Instrument in a survey: 'The Voice of Parents'. RESULTS: The web-based survey had a final sample of N = 405 parent responders. Overall, parents reported satisfaction with care (80.2%; n = 393). Parents satisfied with care reported higher agreement with quality indicator items for all subscales. In total, 17 items from the 41-item instrument revealed the ability to predict higher parental satisfaction when particular QI are reported. CONCLUSION: This study has led to credible insights into parental satisfaction with care given after the birth of an infant with a life-limiting condition. The findings contribute to development of a model with a good fit in ascertaining the importance of compassion, unhurried provider-patient communication and bereavement interventions.

Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus.

The genetic information is stored in the eukaryotic nucleus in the form of chromatin. This is a macromolecular entity that includes genomic DNA and histone proteins that form nucleosomes, plus a large variety of chromatin-associated non-histone proteins. Chromatin is structurally and functionally organised at various levels. One reveals the linear topography of DNA, histones and their post-translational modifications and non-histone proteins along each chromosome. This level provides regulatory information about the association of genomic elements with particular signatures that have been used to define chromatin states. Importantly, these chromatin states correlate with structural and functional genomic features. Another regulatory layer is established at the level of the 3D organisation of chromatin within the nucleus, which has been revealed clearly as non-random. Instead, a variety of intra- and inter-chromosomal genomic domains with specific epigenetic and functional properties has been identified. In this review, we discuss how the recent advances in genomic approaches have contributed to our understanding of these two levels of genome architecture. We have emphasised our analysis with the aim of integrating information available for yeast, Arabidopsis, Drosophila, and mammalian cells. We consider that this comparative study helps define common and unique features in each system, providing a basis to better understand the complexity of genome organisation.

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States.

Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.

Handgrip strength values of Portuguese older adults: a population based study.

BACKGROUND: Handgrip strength is used to identify sarcopenia and frailty phenotypes, being a potential predictor of mortality in older adults. However, uniformity is lacking in the reference values. This study aimed to describe handgrip strength values of older population aged ≥65 years in Portugal, considering the possible influence of anthropometric parameters. METHODS: A cross-sectional study was conducted in Portugal, among 1500 older adults aged ≥65 years old, according to "The Nutrition UP 65 Study Protocol". Demographic data were collected and cognitive performance, subjective general health, physical activity, anthropometric parameters and nutritional status were assessed and analysed. Handgrip strength data was obtained with a Jamar dynamometer. A Pubmed/Medline search was carried out to compare handgrip strength data between Portuguese older adults and other older populations. RESULTS: Handgrip strength was higher among men than among women (30.3 ± 9.2 Kgf vs 18 ± 5.4 Kgf, p < 0.001, respectively). In general, handgrip strength values of Portuguese older adults were lower than other older populations. In our sample, age, cognitive and nutritional status, self-reported sitting time and practice of physical activity were significantly correlated with handgrip strength in both sexes. Concerning anthropometric parameters, height was the most significantly correlated with handgrip strength (r = 0.34, p < 0.001, in women and r = 0.40, p < 0.001, in men). CONCLUSION: This study described, for the first time, handgrip strength values of Portuguese population aged ≥65 years, according to age and to sex-specific tertiles of height. The definition of handgrip strength reference values in this age group merits further reflection.

Measuring Torque and Temperature in a Rotating Shaft Using Commercial SAW Sensors.

Real-time monitoring of torque in a rotating shaft is not easy to implement with technologies such as optic fiber sensors or strain gages. Surface acoustic wave (SAW) sensors are wireless and passive and can be used to monitor strain in moving parts. Commercial solutions (sensors, antennas and interrogation unit) can easily be purchased from some companies; however, they are not customized and may not meet the specificity of the measurements. In order to evaluate the adequacy of commercial off-the-shelf (COTS) solutions, temperature and strain sensors fabricated by SENSeOR (Besançon, France) were mounted on a load cell. The sensors were calibrated using a thermal chamber and a universal testing machine. The load cell was then assembled together with a steel shaft that rotated at different speeds inside an oven. The commercial antennas were replaced with an RF (radio frequency) coupler and the sensors were interrogated with the commercial interrogation unit. The influence of rotation in the accuracy on the measurements, as well as the adequacy of the sensors structure, was evaluated. It can be concluded that SAW sensors can be used to measure temperature or torque in a rotating environment; however, some customization of the components is required in order to overcome the limitations posed by COTS sensing solutions.

Links between genome replication and chromatin landscapes.

Post-embryonic organogenesis in plants requires the continuous production of cells in the organ primordia, their expansion and a coordinated exit to differentiation. Genome replication is one of the most important processes that occur during the cell cycle, as the maintenance of genomic integrity is of primary relevance for development. As it is chromatin that must be duplicated, a strict coordination occurs between DNA replication, the deposition of new histones, and the introduction of histone modifications and variants. In turn, the chromatin landscape affects several stages during genome replication. Thus, chromatin accessibility is crucial for the initial stages and to specify the location of DNA replication origins with different chromatin signatures. The chromatin landscape also determines the timing of activation during the S phase. Genome replication must occur fully, but only once during each cell cycle. The re-replication avoidance mechanisms rely primarily on restricting the availability of certain replication factors; however, the presence of specific histone modifications are also revealed as contributing to the mechanisms that avoid re-replication, in particular for heterochromatin replication. We provide here an update of genome replication mostly focused on data from Arabidopsis, and the advances that genomic approaches are likely to provide in the coming years. The data available, both in plants and animals, point to the relevance of the chromatin landscape in genome replication, and require a critical evaluation of the existing views about the nature of replication origins, the mechanisms of origin specification and the relevance of epigenetic modifications for genome replication.

Evaluating the phylogenetic signal limit from mitogenomes, slow evolving nuclear genes, and the concatenation approach. New insights into the Lacertini radiation using fast evolving nuclear genes and species trees.

Estimating the phylogeny of lacertid lizards, and particularly the tribe Lacertini has been challenging, possibly due to the fast radiation of this group resulting in a hard polytomy. However this is still an open question, as concatenated data primarily from mitochondrial markers have been used so far whereas in a recent phylogeny based on a compilation of these data within a squamate supermatrix the basal polytomy seems to be resolved. In this study, we estimate phylogenetic relationships between all Lacertini genera using for the first time DNA sequences from five fast evolving nuclear genes (acm4, mc1r, pdc, ßfib and reln) and two mitochondrial genes (nd4 and 12S). We generated a total of 529 sequences from 88 species and used Maximum Likelihood and Bayesian Inference methods based on concatenated multilocus dataset as well as a coalescent-based species tree approach with the aim of (i) shedding light on the basal relationships of Lacertini (ii) assessing the monophyly of genera which were previously questioned, and (iii) discussing differences between estimates from this and previous studies based on different markers, and phylogenetic methods. Results uncovered (i) a new phylogenetic clade formed by the monotypic genera Archaeolacerta, Zootoca, Teira and Scelarcis; and (ii) support for the monophyly of the Algyroides clade, with two sister species pairs represented by western (A. marchi and A. fitzingeri) and eastern (A. nigropunctatus and A. moreoticus) lineages. In both cases the members of these groups show peculiar morphology and very different geographical distributions, suggesting that they are relictual groups that were once diverse and widespread. They probably originated about 11-13 million years ago during early events of speciation in the tribe, and the split between their members is estimated to be only slightly older. This scenario may explain why mitochondrial markers (possibly saturated at higher divergence levels) or slower nuclear markers used in previous studies (likely lacking enough phylogenetic signal) failed to recover these relationships. Finally, the phylogenetic position of most remaining genera was unresolved, corroborating the hypothesis of a hard polytomy in the Lacertini phylogeny due to a fast radiation. This is in agreement with all previous studies but in sharp contrast with a recent squamate megaphylogeny. We show that the supermatrix approach may provide high support for incorrect nodes that are not supported either by original sequence data or by new data from this study. This finding suggests caution when using megaphylogenies to integrate inter-generic relationships in comparative ecological and evolutionary studies.

The CDK regulators Cdh1 and Sic1 promote efficient usage of DNA replication origins to prevent chromosomal instability at a chromosome arm.

Robustness and completion of DNA replication rely on redundant DNA replication origins. Reduced efficiency of origin licensing is proposed to contribute to chromosome instability in CDK-deregulated cell cycles, a frequent alteration in oncogenesis. However, the mechanism by which this instability occurs is largely unknown. Current models suggest that limited origin numbers would reduce fork density favouring chromosome rearrangements, but experimental support in CDK-deregulated cells is lacking. We have investigated the pattern of origin firing efficiency in budding yeast cells lacking the CDK regulators Cdh1 and Sic1. We show that each regulator is required for efficient origin activity, and that both cooperate non-redundantly. Notably, origins are differentially sensitive to CDK deregulation. Origin sensitivity is independent on normal origin efficiency, firing timing or chromosomal location. Interestingly, at a chromosome arm, there is a shortage of origin firing involving active and dormant origins, and the extent of shortage correlates with the severity of CDK deregulation and chromosome instability. We therefore propose that CDK deregulation in G1 phase compromises origin redundancy by decreasing the number of active and dormant origins, leading to origin shortage and increased chromosome instability.

On the opportunistic nature of transcription and replication initiation in the metazoan genome.

Cellular identity and its response to external or internal signalling variations are encoded in a cell's genome as regulatory information. The genomic regions that specify this type of information are highly variable and degenerated in their sequence determinants, as it is becoming increasingly evident through the application of genome-scale methods to study gene expression. Here, we speculate that the same scenario applies to the regulatory regions controlling where DNA replication starts in the metazoan genome. We propose that replication origins cannot be defined as unique genomic features, but rather that DNA synthesis initiates opportunistically from accessible DNA sites, making cells highly robust and adaptable to environmental or developmental changes.

A Rare Cause of Vitamin B12 Deficiency in the Pediatric Age.

Vitamin B12 plays an important role in DNA synthesis, hematopoiesis, and neuronal mechanisms, and its deficiency can be associated with insufficient intake or poor absorption and autoimmune and genetic diseases. Although rare, excessive, and chronic alcohol consumption may also justify a deficiency in this vitamin. We present a case of a 17-year-old Iraqi adolescent refugee in Portugal with a deficiency of vitamin B12 due to excessive and chronic alcohol consumption. Although intramuscular (IM) supplementation with cyanocobalamin is the most used, it was decided to initiate oral supplementation. After four months, vitamin B12 levels were replenished. With this clinical case, we aim to raise awareness of the cause of cyanocobalamin deficiency, which although rare in pediatric age should be considered in adolescents, given the possibility of risky behaviors in this age group. Additionally, given the therapeutic options, we have found that oral administration of vitamin B12 has been effective, as reported in the literature.