A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses.

Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples

Drying banana seeds for ex situ conservation

The ability of seeds to withstand drying is fundamental to ex situ seed conservation but drying responses are not well known for most wild species including crop wild relatives. We look at drying responses of seeds of Musa acuminata and Musa balbisiana, the two primary wild relatives of bananas and plantains, using the following four experimental approaches: (i)We equilibrated seeds to a range of relative humidity (RH) levels using non-saturated lithium chloride solutions and subsequently measured moisture content (MC) and viability. At each humidity levelwe tested viability using embryo rescue (ER), tetrazolium chloride staining and germination in an incubator.We found that seed viabilitywas not reduced when seedswere dried to 4% equilibrium relative humidity (eRH; equating to 2.5% MC). (ii)We assessed viability ofmature and less mature seeds using ER and germination in the soil and tested responses to drying. Findings showed that seeds must be fully mature to germinate and immature seeds had negligible viability. (iii) We dried seeds extracted from ripe/unripe fruit to 35–40% eRH at different rates and tested viability with germination tests in the soil. Seeds from unripe fruit lost viability when dried and especially when dried faster; seeds from ripe fruit only lost viability when fast dried. (iv) Finally, we dried and re-imbibed mature and less mature seeds and measured embryo shrinkage and volume change using X-ray computer tomography. Embryos of less mature seeds shrank significantly when dried to 15% eRH from 0.468 to 0.262 mm3, but embryos of mature seeds did not. Based on our results, mature seeds from ripe fruit are desiccation tolerant to moisture levels required for seed genebanking but embryos from immature seeds are mechanistically less able to withstand desiccation, especially when water potential gradients are high

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Type I primary hyperoxaluria in pediatric patients: Renal sonographic patterns

OBJECTIVE. Our aim was to review the sonographic features of type I primary hyperoxaluria in children and to correlate the sonographic patterns with the clinical development of end-stage renal disease (ESRD). MATERIALS AND METHODS. We performed a retrospective analysis of the clinical and imaging files of 13 patients with type I primary hyperoxaluria who were treated in one institution and of the sonographic patterns and the clinical follow-up reports. RESULTS. We encountered the following two sonographic patterns: medullary nephrocalcinosis in eight patients and cortical nephrocalcinosis in five patients. The sonographic appearance of cortical nephrocalcinosis is quite specific: a hyperechoic peripheral renal cortex with acoustic shadowing behind it. Medullary nephrocalcinosis is less specific because there are many other causes of hyperechoic pyramids. All patients with medullary nephrocalcinosis developed lithiasis during the course of the disease. All patients with cortical nephrocalcinosis but only two of eight with medullary nephrocalcinosis developed ESRD. CONCLUSION. Sonography can be used differentiate the two patterns of type 1 primary hyperoxaluria. The cortical nephrocalcinosis type carries a higher risk of developing ESRD. © American Roentgen Ray Society.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Research Panel, Moderated by Jacqueline Lynch

Albert E.J. Janssens How ideas from Feuerstein, Costa, Haywood and the neuroscience help by teaching children living in poverty Abstract: 1.Problem definition and research question: In Belgium most of the children living in poverty have bad school-results. What are the reasons for it and what can schools do to avoid this? The project-plan (2013 – 2017): Confronting the mindset of teachers concerning ‘poverty and development’ with interviews of the poor. (2013 – 2014) Assessment of 20 low-SES and 20 high-SES children to see the differences in results when the test needs little language and little ‘school knowledge’. With materials of dynamic assessment of D. Tzuriel). (2015) The pretest of 160 children was followed by a learning phase of 13 weeks to half of the group and coaching of the class-teachers. After 13 weeks there was a post test for all the children. (2016 – 2017) Carlos A. Osorio and Maria Renard Exploring the role of cognition and emotions on innovation learning and performance Abstract: This paper summarizes our exploration about the role of individual and team’s cognition and emotions on innovation learning performance. Based on an integrative review of the literature and action research, we examine the mobilization of fifteen competencies among twenty-eight stages of an innovation process with 1,176 participants between 2013 and 2017. This analysis was performed based on knowledge about the effect 46 critical decisions, and nearly fifty common technical mistakes along week-long experimental programs. Our results show that, regardless of industry, personal traits, gender or technical background, some specific tasks generate higher levels of frustration and types of mistakes in development teams. We identified how various cognitive and emotional limitations affect technical performance, and explored the effectiveness of preemptive actions for “troubleshooting” cognitive and emotional response under high uncertainty. We argue that project failure results from the accumulative effect of mistakes in decision-making under uncertainty, which in turn result from failures to learn and the effects of biased sense-making and inadequate response to challenges. We propose understanding innovation as a learning process under risk and uncertainty; where complex, conflicting, inaccurate and incomplete information becomes available incrementally through mechanisms of selective search and sense-making (individual and collective). As result, cognitive biases, inertia and overload affect substantive and procedural rationality limiting a team’s ability to learn and achieve superior technical results. Under highly uncertain and fast-pacing environments, technical tasks relying on synthesis capabilities tend to generate higher levels of frustration. Increased frustration lead to cognitive overload, thus increasing the frequency of mistakes and diminishing an individual’s performance, and affecting a team’s social cognition. We propose that ex-ante team configuration by explicit psychological variables and on-purpose generation of a noisy, risky and ambiguous climate reinforces the dynamics between cognition and emotions deepening significant innovation learning, positively affecting how a team represents the problem at hand, devise and manages the appropriate courses of action (process and methods) for solving it. Michelle Cumming Role of Stress, Stress Regulation, and Executive Function on Behavior: Similarities and Differences Between Middle Schoolers with and Without Significant Behavior Problems Abstract Executive functioning (EF), school-based stress, and stress regulation abilities may be key to the development and escalation of behavior problems during adolescence. We conducted a study with 79 middle schoolers with and without significant emotional and behavioral problems investigating relationships among these variables. Students with significant behavior problems had higher peer stress, lower EF skills, and used less effective stress regulation than matched peers. School stress predicted behavior problems in both groups and stress regulation served as an important mediator. Findings highlight important implications for school-based programming

To study and determine the role of anterior segment optical coherence tomography and ultrasound biomicroscopy in corneal and conjunctival tumors

Purpose. To analyze and describe corneal and conjunctival tumor thickness and internal characteristics and extension in depth and size and shape measured by two noninvasive techniques, anterior segment optical coherence tomography (AS-OCT) and ultrasound biomicroscopy (UBM). Design. Systematic review. Methods. This systematic review is based on a comprehensive search of 4 databases (Medline, Embase, Web of Science, and Cochrane Library). Articles published between January 1, 1999, and December 31, 2015, were included. We searched for articles using the following search terms in various combinations: “optical coherence tomography”, “ultrasound biomicroscopy”, “corneal neoplasm”, “conjunctival neoplasm”, “eye”, “tumor” and “anterior segment tumors”. Inclusion criteria were as follows: UBM and/or AS-OCT was used; the study included corneal or conjunctival tumors; and the article was published in English, French, Dutch, or German. Results. There were 14 sources selected. Discussion. Several studies on the quality of AS-OCT and UBM show that these imaging techniques provide useful information about the internal features, extension, size, and shape of tumors. Yet there is no enough evidence on the advantages and disadvantages of UBM and AS-OCT in certain tumor types. Conclusion. More comparative studies are needed to investigate which imaging technique is most suitable for a certain tumor type

Nutrient‑related metabolite profiles explain differences in body composition and size in Nile tilapia (Oreochromis niloticus) from different lakes

This study investigated how metabolite analysis can explain differences in tissue composition and size in fish from different habitats. We, therefore, studied Nile tilapia (Oreochromis niloticus) from three Ethiopian lakes (Gilgel Gibe, Ziway, and Langano) using dried bloodspot (DBS) analysis of carnitine esters and free amino acids. A total of sixty (N = 60) Nile tilapia samples were collected comprising twenty (n = 20) fish from each lake. The proximate composition of the targeted tissues (muscle, skin, gill, gut, and liver) were analyzed. The DBS samples were analyzed for acylcarnitine and free amino acid profiles using quantitative electrospray tandem mass spectrometry. Metabolite ratios were calculated from relevant biochemical pathways that could identify relative changes in nutrient metabolism. The mean weight of Nile tilapia sampled from each lake showed weight variation among the lakes, fish from Lake Ziway were largest (178 g), followed by Gilgel Gibe reservoir (134 g) and Lake Langano (118 g). Fish from Gilgel Gibe showed significantly higher fat composition in all tissues (P < 0.05) except the liver in which no significant variation was observed. The source of fish affected the tissue fat composition. Marked differences were observed in Nile tilapia metabolic activity between the lakes. For instance, the lower body weight and condition of the fish in Lake Langano coincided with several metabolite ratios pointing to a low flow of glucogenic substrate to the citric acid cycle. The low propionyl to acetylcarnitine ratio (C3:C2) in Gilgel Gibe fish is indicating that more of the available acetyl CoA is not led into the citric acid cycle, but instead will be used for fat synthesis. The metabolic markers for lipogenesis and metabolic rate could explain the high-fat concentration in several parts of the body composition of fish from Gilgel Gibe. Our results show that nutrition-related blood metabolite ratios are useful to understand the underlying metabolic events leading to the habitat-dependent differences in the growth of Nile tilapia, and by extension, other species

Skin barrier dysfunction in non-lesional atopic eczema: the role of stratum corneum lipids

Dermatology and Venereolog