Proteomic associations with forced expiratory volume - a Mendelian randomisation study.

A decline in forced expiratory volume (FEV1) is a hallmark of obstructive respiratory diseases, an important cause of morbidity among the elderly. While some data exist on biomarkers that are related to FEV1, we sought to do a systematic analysis of causal relations of biomarkers with FEV1. Data from the general population-based AGES-Reykjavik study were used. Proteomic measurements were done using 4,782 DNA aptamers (SOMAmers). Data from 1,648 participants with spirometric data were used to assess the association of SOMAmer measurements with FEV1 using linear regression. Bi-directional Mendelian randomisation (MR) analyses were done to assess causal relations of observationally associated SOMAmers with FEV1, using genotype and SOMAmer data from 5,368 AGES-Reykjavik participants and genetic associations with FEV1 from a publicly available GWAS (n = 400,102). In observational analyses, 473 SOMAmers were associated with FEV1 after multiple testing adjustment. The most significant were R-Spondin 4, Alkaline Phosphatase, Placental Like 2 and Retinoic Acid Receptor Responder 2. Of the 235 SOMAmers with genetic data, eight were associated with FEV1 in MR analyses. Three were directionally consistent with the observational estimate, Thrombospondin 2 (THBS2), Endoplasmic Reticulum Oxidoreductase 1 Beta and Apolipoprotein M. THBS2 was further supported by a colocalization analysis. Analyses in the reverse direction, testing whether changes in SOMAmer levels were caused by changes in FEV1, were performed but no significant associations were found after multiple testing adjustments. In summary, this large scale proteogenomic analyses of FEV1 reveals protein markers of FEV1, as well as several proteins with potential causality to lung function.

Optical fiber bundles: Ultra-slim light field imaging probes.

Optical fiber bundle microendoscopes are widely used for visualizing hard-to-reach areas of the human body. These ultrathin devices often forgo tunable focusing optics because of size constraints and are therefore limited to two-dimensional (2D) imaging modalities. Ideally, microendoscopes would record 3D information for accurate clinical and biological interpretation, without bulky optomechanical parts. Here, we demonstrate that the optical fiber bundles commonly used in microendoscopy are inherently sensitive to depth information. We use the mode structure within fiber bundle cores to extract the spatio-angular description of captured light rays-the light field-enabling digital refocusing, stereo visualization, and surface and depth mapping of microscopic scenes at the distal fiber tip. Our work opens a route for minimally invasive clinical microendoscopy using standard bare fiber bundle probes. Unlike coherent 3D multimode fiber imaging techniques, our incoherent approach is single shot and resilient to fiber bending, making it attractive for clinical adoption.

A dual-mode mobile phone microscope using the onboard camera flash and ambient light.

Mobile phone microscopes are a natural platform for point-of-care imaging, but current solutions require an externally powered illumination source, thereby adding bulk and cost. We present a mobile phone microscope that uses the internal flash or sunlight as the illumination source, thereby reducing complexity whilst maintaining functionality and performance. The microscope is capable of both brightfield and darkfield imaging modes, enabling microscopic visualisation of samples ranging from plant to mammalian cells. We describe the microscope design principles, assembly process, and demonstrate its imaging capabilities through the visualisation of unlabelled cell nuclei to observing the motility of cattle sperm and zooplankton.

Magnetic field-induced enhancement of the nitrogen-vacancy fluorescence quantum yield.

The nitrogen-vacancy (NV) centre in diamond is a unique optical defect that is used in many applications today and methods to enhance its fluorescence brightness are highly sought after. We observed experimentally an enhancement of the NV quantum yield by up to 7% in bulk diamond caused by an external magnetic field relative to the field-free case. This observation is rationalised phenomenologically in terms of a magnetic field dependence of the NV excited state triplet-to-singlet transition rate. The theoretical model is in good qualitative agreement with the experimental results at low excitation intensities. Our results significantly contribute to our fundamental understanding of the photophysical properties of the NV defect in diamond.

Evaluation of different time schedules in training with the Da Vinci simulator.

BACKGROUND: This prospective study analyzed the effect of different time schedules in training on the main performance outcomes: overall score, time to complete, and economy of motion. METHODS: The study was performed on the da Vinci Skills Simulator from December 2014 to April 2016. Forty robotic novices were randomized into two groups of 20 participants, which trained in the same three exercises but with different intervals between their training sessions. Each group performed training in Peg Board 1 in their first week, Match Board 2 in their second week, and Ring and Rail 2 in their third week. On their last day, Needle Targeting and Energy Dissection 2, for which no previous training had been received, were performed. Regarding the different training intervals, group 1 trained each exercise six times in a row once a week. Group 2 performed their training once a day for 5 days. Technical performance parameters were recorded by the Mimics simulator software for further analysis. In addition, the participants were asked to fill out a questionnaire concerning the robotics training. RESULTS: Group 2 performed significantly better compared to group 1 in the main metrics in the more advanced exercises. For the easier exercises, the training frequency did not lead to significant differences in performance outcome. A significant skills gain was seen between the first and last training sessions for all exercises in both groups. CONCLUSIONS: Performance in the final exercise NT was significantly better in group 2 than group 1. Regarding ED 2, no difference was found between the two groups. As the training of group 2 led to significantly better outcomes, we suggest that, especially for advanced exercises, it seems to be more favorable to perform training every day for a short period than to train once a week six times in a row.

Biologia reprodutiva e ausência de frutificação de Aloe saponaria (Aiton) Haw. (Xanthorrhoeaceae) fora do local de origem / Reproductive biology and absence of fruiting of Aloe saponaria (Aiton) Haw. (Xanthorrhoeaceae) outside its place of origin

RESUMO O gênero Aloe, originário principalmente da África, tem atualmente uma ampla distribuição no mundo. No entanto, são poucas as regiões que têm realizado estudos quanto ao sistema reprodutivo. O objetivo do presente trabalho foi analisar as características e o comportamento reprodutivo de Aloe saponaria em Florianópolis, Santa Catarina. Foram conduzidos estudos sobre sua morfologia e biologia floral, visitantes florais e sistema reprodutivo. Esta espécie apresentou uma inflorescência por planta, com um comprimento de 105 ± 0,1 cm e 267 ± 92,7 flores. A razão pólen/óvulo sugere que a espécie é xenogâmica. O volume e concentração de sólidos solúveis totais do néctar potencial foi 16,6 ± 6,3 μL e 22 ± 2,4 °Brix respectivamente. O néctar instantâneo não apresentou diferenças significativas nos períodos avaliados (9:00h e 15:00h) e o estigma permaneceu receptivo até o segundo dia após a antese. Foram coletados 110 insetos visitantes florais, dos quais 61,8% foram indivíduos de Trigona spinipes. Entretanto, nos testes de polinização não foi observada frutificação efetiva, indicando que a propagação vegetativa é o principal tipo de reprodução usado nessa população. Isto pode estar relacionado a um mecanismo de autoincompatibilidade esporofítica, a anormalidades cromossômicas durante a formação do pólen, as condições climáticas, e a escassa variabilidade genética no local de estudo.

ABSTRACT The Aloe genus, originating mainly from Africa, currently has a wide distribution in the world. However, in few regions studies about the reproductive system have been carried on. The aim e of this study was to analyze the characteristics and reproductive performance of the Aloesaponaria in Florianópolis, Santa Catarina. The morphology, floral biology, flower visitors and the reproductive system were determined. The plants presented an inflorescence per plant, with 105 ± 0,1 cm in length and 267 ± 92.7 flowers. The pollen/ovule ratio suggested that the species is xenogamic. The volume and concentration of total soluble solids in the potential nectar were 16.6 ± 6.3 μL and 22 ± 2.4°Brix, respectively. The instant nectar showed no significant differences between the evaluated periods (9:00h and 15:00h) and the stigma remained receptive until the second day the after anthesis. 110 insects were collected, from which 61.8% were from theTrigona spinipesspecies. However, in the pollination tests the fruit set was not observation, indicating that vegetative propagation is the main type of reproduction used by this population. This may be related to a mechanism of sporophytic self-incompatibility, to chromosomal abnormalities during the formation of pollen, to weather conditions, and to the low genetic variability at the study site.

Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya.

The Kenyan East African zebu cattle are valuable and widely used genetic resources. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at genome-wide level the genetic composition and population structure of the East African Shorthorn Zebu (EASZ) of western Kenya. A total of 548 EASZ from 20 sub-locations were genotyped using the Illumina BovineSNP50 v. 1 beadchip. STRUCTURE analysis reveals admixture with Asian zebu, African and European taurine cattle. The EASZ were separated into three categories: substantial (⩾12.5%), moderate (1.56%

Multivariate analyses of immune reconstitution in children after allo-SCT: risk-estimation based on age-matched leukocyte sub-populations.

The speed of immune recovery after allo-SCT is of central importance to overcome infectious complications and relapse. To evaluate the immune reconstitution of pediatric patients concerning overall survival, we developed a three-component multivariate model and generated a reference domain of ellipsoidal shape on the basis of normal leukocyte subtype values of 100 healthy children and adolescents. The leukocyte subtypes include absolute nos. of leukocytes, CD14(+) monocytes, lymphocytes, CD3(+) T cells, CD3(+)CD4(+) helper T cells, CD3(+)CD8(+) cytotoxic T cells, CD3(-)CD56(+) natural killer-cells and CD19(+) B cells, all of which are correlated, thus, requiring the application of multivariate as opposed to multiple univariate modeling. According to their immune reconstitution, 32 pediatric patients post allo-SCT were classified into low-risk and high-risk groups on the basis of our new model. Therefore, we evaluated if the patients reached the ellipsoid of normal leukocyte sub-population values post SCT. We detected a significantly higher number of long-time survivors among the low-risk group compared with the high-risk group at days 200 (P=0.001) and 300 (P<0.0001). This is superior to our previously published univariate analysis. Combined with the clinical observation, a classification into risk groups based on an extended patient cohort may represent a predictor for complications.

Adaptive evolution of interferon-gamma in Glire lineage and evidence for a recent selective sweep in Mus. m. domesticus.

Interferon-gamma plays a key role in the immune response against intracellular pathogens. Its gene is located inside a cluster of cytokines from the interleukin-10 family. A comparison of the coding sequences in the mammalian Glire lineage indicates a possible action of positive Darwinian selection promoting rapid amino-acid changes in the branch leading to murine rodents represented by Mus and Rattus. Looking at genomic diversity of this gene inside the genus Mus, we could propose that a recent selective sweep has affected M. m. domesticus, this subspecies harbouring predominantly a single Ifng haplotype that differs from that of the other subspecies by a unique amino-acid difference in a key position of the molecule. The sweep seems to have affected a region of at most 50 kb as recombinants could be found at flanking conserved non-coding sequences. Functional differences were clearly apparent in cis-regulation of Ifng transcription between the domesticus and the musculus-type haplotypes. As the presence of the musculus haplotype in a predominantly domesticus background seems to promote susceptibility to chronic infection by Theiler's virus, these findings open interesting avenues for documenting immune system gene co-evolution.

Genetic variation and phylogeography of free-living mouse species (genus Mus) in the Balkans and the Middle East.

This work presents a study of the distribution and pattern of variation throughout the ranges of three free-living mouse species of the genus Mus-M. macedonicus, M. spicilegus, and a M. cypriacus - based on sequencing of two segments of the mitochondrial DNA (mtDNA) control region. The study shows a similar level of variability in the three species and suggests their recent population expansion. The highest proportion of variation is found within populations indicating low genetic structuring. Phylogenetic analysis confirms the significant divergence of a mitochondrial lineage of M. macedonicus from Israel, recently described as a new subspecies, M. macedonicus spretoides. Conversely, no genetic hiatus is revealed between European and Asian populations of M. macedonicus macedonicus. Although phylogenetic relationships among M. spicilegus populations could not be unravelled precisely, the results suggest a recent westward expansion of the species. The mtDNA divergence between M. macedonicus and M. spicilegus is 7.3%, suggesting their split between c. 700,000 and 1 million years ago. These dates correspond with a coalescent estimate about 720,000 years ago. On the other hand, M. cypriacus appeared almost twice as divergent from the former species (4.5%) as from the latter (8.8%) suggesting a divergence of c. 430,000-610,000 years ago (coalescent approximately 490,000 years ago) and 830,000-1.2 million years ago (coalescent approximately 780,000 years ago), respectively. Approximate times of population expansion have also been estimated for all taxa and groups of populations. Existence of several glacial refuges and various colonization scenarios are discussed; since all estimated divergence times fall within interglacial periods it seems that climatic oscillations did not play a crucial role in the evolution of the three species.

Immune recovery in children undergoing allogeneic stem cell transplantation: absolute CD8+ CD3+ count reconstitution is associated with survival.

To evaluate the correlation between kinetics of immune reconstitution and survival, we prospectively evaluated lymphocyte subsets in 32 paediatric patients undergoing allogeneic stem cell transplantation (SCT) for haematological malignancies. Four-colour flow cytometric analysis was performed at short intervals with a median follow-up of 4 years post SCT. A total of 50% of patients reached age-matched 5th percentile of natural killer, cytotoxic T, B and helper T cells 4, 9, 20 and 28 weeks after SCT, respectively, which increased to more than 80% within 1 year after SCT. Transplantation of peripheral blood stem cells (PBSC) seemed to elicit the fastest reconstitution of CD3+, CD4+ CD3+, CD8+ CD3+ and naïve T cells compared to bone marrow (BM) or CD34-selected PBSC, which did not differ. Most importantly, we observed a significantly higher number of survivors among patients whose CD8+ CD3+ absolute counts rose above the 5th percentile of age-matched normal levels during the first year post SCT compared to patients who never reached these levels (19/25 vs 0/7, P<0.001). This was still present in both subgroups, BM- and CD34-selected grafts (P=0.03, 0.02). These results from a small patient sample underline the importance of particular lymphocyte subsets for the outcome of children undergoing SCT. A larger study with detailed subset analysis is underway.

A strategy for probing the function of noncoding RNAs finds a repressor of NFAT.

Noncoding RNA molecules (ncRNAs) have been implicated in numerous biological processes including transcriptional regulation and the modulation of protein function. Yet, in spite of the apparent abundance of ncRNA, little is known about the biological role of the projected thousands of ncRNA genes present in the human genome. To facilitate functional analysis of these RNAs, we have created an arrayed library of short hairpin RNAs (shRNAs) directed against 512 evolutionarily conserved putative ncRNAs and, via cell-based assays, we have begun to determine their roles in cellular pathways. Using this system, we have identified an ncRNA repressor of the nuclear factor of activated T cells (NFAT), which interacts with multiple proteins including members of the importin-beta superfamily and likely functions as a specific regulator of NFAT nuclear trafficking.

Mouse biodiversity in the genomic era.

Comparative genomics has developed by comparison of distantly related genomes, for which the link between the reported evolutionary changes and species development/physiology/ecology is not obvious. It is argued that the mouse (genus Mus) is an optimal model for microevolutionary genomics in vertebrates. This is because the mouse genome sequence, physical and genetic map have been completed, because mouse genetics, morpho-anatomy, pathology, behavior and ecology are well-studied, and because the Mus genus is a diverse, well- documented taxon, allowing comparative studies at the level of individual, population, subspecies, and species. The potential of the interaction between mouse genome and mouse biodiversity is illustrated by recent studies of speciation in the house mouse Mus musculus, and studies about the evolution of isochores, the peculiar pattern of GC-content variation across mammalian genomes.

Divergent genetic and epigenetic post-zygotic isolation mechanisms in Mus and Peromyscus.

Interspecific hybridization in the rodent genera Peromyscus and Mus results in abnormal placentation. In the Peromyscus interspecies hybrids, abnormal allelic interaction between an X-linked locus and the imprinted paternally expressed Peg3 locus was shown to cause the placental defects. In addition, loss-of-imprinting (LOI) of Peg3 was positively correlated with increased placental size. As in extreme cases this placental dysplasia constitutes a post-zygotic barrier against interspecies hybridization, this finding was the first direct proof that imprinted genes may be important in speciation and thus in evolution. In the Mus interspecies hybrids, a strong role of an X-linked locus in placental dysplasia has also been detected. However, here we show by backcross and allele specific expression analyses that neither LOI of Peg3 nor abnormal interactions between Peg3 and an X-linked locus are involved in generating placental dysplasia in Mus hybrids, although the placental phenotypes observed in the two genera seem to be identical. In contrast to this, another dysgenesis effect common to Peromyscus and Mus hybrids, altered foetal growth, is caused at least in part by the same X-chromosomal regions in both genera. These findings first underline the strong involvement of the X-chromosome in the genetics of speciation. Secondly, they indicate that disruption of epigenetic states, such as LOI, at specific loci may be involved in hybrid dysgenesis effects in one group, but not in another. Thus, we conclude that even in closely related groups divergent molecular mechanisms may be involved in the production of phenotypically similar post-zygotic barriers against hybridization.

Sequence, structure and expression of the hemolymph juvenile hormone binding protein gene in the tobacco hornworm, Manduca sexta.

The hemolymph juvenile hormone binding protein (hJHBP) gene of Manduca sexta is a key target of its specific ligand, juvenile hormone (JH). While the cDNA for hJHBP has been partially characterized, little is known about the hJHBP gene structure or its promoter(s) and enhancers(s). Previous studies have demonstrated that JH stimulates a rapid accumulation of hJHBP mRNA in the fat body. To better understand the underlying molecular events affecting regulation, we sequenced the M. sexta hJHBP gene and its mRNA transcript, characterized its genomic organization, and determined the spatial and temporal expression patterns of the hJHBP gene. The gene is composed of 5 exons spanning 6.7 kb. Southern blot analysis indicates that the gene is present as a single copy. The earliest expression of hJHBP occurs 24 to 48 h after fertilization. Distribution studies indicate that fat body is the only site for hJHBP expression. Elements displaying similarity with sequences of other lepidopteran genes were discovered outside the open reading frame and may represent mobile insertion elements.

Two deeply divergent mitochondrial clades in the wild mouse Mus macedonicus reveal multiple glacial refuges south of Caucasus.

A survey of 77 individuals covering the range of Mus macedonicus from Georgia in the East to Greece and Bulgaria in the West and Israel in the South has shown the existence of two deeply divergent mitochondrial clades. The southern clade was until now undetected and characterises mice from Israel. Nuclear genes also show some amount of regional differentiation tending to separate the southern M. macedonicus from the northern ones. These results point towards the fact that the eastern Mediterranean short-tailed mouse, which was seen as a fairly homogeneous monotypic species, has in fact a more complex phylogeographic history than has been suspected, and that it warrants the existence of two subspecies. The reasons for this non-uniformity probably ought to be looked for in the history of faunal movements linked to glacial periods, underlining the possible existence of at least two refugia south of the Caucasus.

Evidence for a mitochondrial lineage originating from the Arabian peninsula in the Madagascar house mouse (Mus musculus).

Various subspecies of the house mouse (Mus musculus sensu lato) are known to have contributed to its worldwide expansion. However, the origin of mice on some larger islands such as Madagascar has remained unknown, with several sources being possible. In order to classify the Malagasy house mouse, individuals were trapped in 13 different localities distributed throughout the island. For 33 individuals the control region (D-Loop) of the mitochondrial DNA was partially sequenced and 21 males were typed for a Zfy-2 polymorphism of the Y chromosome. Malagasy mt DNA lineages constitute a narrow monophyletic group which suggests a recent and probably single origin, and are very close to the gentilulus mitochondrial lineages from Yemen. This was supported by the fact that all the males have the domesticus type Y chromosome, like gentilulus. From these results, it can be inferred that the Malagasy house mice originate probably from the Arabian peninsula in a single colonisation wave, unlike its human population. Our results provide a better molecular description of the Yemeni-Malagasy mitochondrial clade which clearly belongs to the Mus musculus radiation.

The cAMP signal transduction pathway mediates resistance to dicarboximide and aromatic hydrocarbon fungicides in Ustilago maydis.

The cAMP signal transduction pathway mediates the switch between yeast-like and filamentous growth and influences both sexual development and pathogenicity in the smut fungus Ustilago maydis. Signaling via cAMP may also play a role in fungicide resistance in U. maydis. In particular, the adr1 gene, which encodes the catalytic subunit of the U. maydis cAMP-dependent protein kinase (PKA), is implicated in resistance to the dicarboximide and aromatic hydrocarbon fungicides. In this study, we examined the sensitivity of PKA to vinclozolin and could not demonstrate direct inhibition of protein kinase activity. However, we did find that mutants with disruptions in the ubc1 gene, which encodes the regulatory subunit of PKA, were resistant to both vinclozolin and chloroneb. We also found that these fungicides altered the morphology of both wild-type and ubc1 mutant cells. In addition, strains that are defective in ubc1 display osmotic sensitivity, a property often associated with vinclozolin and chloroneb resistance in other fungi.

Genetic and developmental analysis of X-inactivation in interspecific hybrid mice suggests a role for the Y chromosome in placental dysplasia.

It has been shown previously that abnormal placental growth, i.e., hyper- and hypoplasia, occurs in crosses and backcrosses between different mouse (Mus) species. A locus that contributes to this abnormal development has been mapped to the X chromosome. Unexpectedly, an influence of fetal sex on placental development has been observed, in that placentas attached to male fetuses tended to exhibit a more pronounced phenotype than placentas attached to females. Here, we have analyzed this sex dependence in more detail. Our results show that differences between male and female placental weights are characteristic of interspecific matings and are not observed in intraspecific Mus musculus matings. The effect is retained in congenic lines that contain differing lengths of M. spretus-derived X chromosome. Expression of the X-linked gene Pgk1 from the maternal allele only and lack of overall activity of two paternally inherited X-linked transgenes indicate that reactivation or lack of inactivation of the paternal X chromosome in trophoblasts of interspecific hybrids is not a frequent occurrence. Thus, the difference between male and female placentas seems not to be caused by faulty preferential X-inactivation. Therefore, these data suggest that the sex difference of placental weights in interspecific hybrids is caused by interactions with the Y chromosome.

Dose-dependent effects of endotoxin on human sleep.

The role of the central nervous system in the host response to infection and inflammation and modulation of these responses by the hypothalamic-pituitary-adrenal system are well established. In animals, activation of host defense mechanisms increases non-rapid eye movement (NREM) sleep amount and intensity, which, in turn, are thought to support host defense, or the body's ability to defend itself against challenges to its immune system. In humans, the evidence is conflicting. Therefore, we investigated the effects of three placebo-controlled doses of endotoxin on host response, including nocturnal sleep in healthy volunteers. Administered before nocturnal sleep onset, endotoxin dose dependently increased rectal temperature, heart rate, and the plasma levels of tumor necrosis factor (TNF)-alpha, soluble TNF receptors, interleukin (IL)-1 receptor antagonist, IL-6, and cortisol. The lowest dose reliably increased circulating levels of cytokines and soluble cytokine receptors, but it did not affect rectal temperature, heart rate, or cortisol. This subtle host defense activation increased deep NREM sleep amount, often referred to as slow-wave sleep (stages 3 and 4), and intensity (delta power). Conversely, the highest dose of endotoxin disrupted sleep. Whereas it is well established that the endocrine and thermoregulatory systems are very sensitive to endotoxin, this study shows that human sleep-wake behavior is even more sensitive to activation of host defense mechanisms.