ALBERT

Beschreibung: Motivation: Large phylogenies are being built today to study virus evolution, trace the origin of epidemics, establish the mode of transmission and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e.g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance. Results: We propose a new method for obtaining such groups, which we call phylotypes, from a phylogeny having taxa (strains) annotated with extrinsic traits. Phylotypes are subsets of taxa with close phylogenetic relationships and common trait values. The method combines ancestral trait reconstruction using parsimony, with combinatorial and numerical criteria measuring tree shape characteristics and the diversity and separation of the potential phylotypes. A shuffling procedure is used to assess the statistical significance of phylotypes. All algorithms have linear time complexity. This results in low computing times, typically a few minutes for the larger data sets with a number of shuffling steps. Two HIV-1 data sets are analyzed, one of which is large, containing 〉3000 strains of HIV-1 subtype C collected worldwide, where the method shows its ability to recover known clusters and transmission routes, and to detect new ones. Availability: This method and companion tools are implemented in an interactive Web interface ( www.phylotype.org ), which provides a wide choice of graphical views and output formats, and allows for exploratory analyses of large data sets. Contact: francois.chevenet@ird.fr , gascuel@lirmm.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Global warming affects carbon cycling in freshwater ecosystems, which both emit and bury substantial amounts of carbon. Most studies focus on the effect of warming on overall carbon emissions, while net effects on carbon budgets may strongly depend on burial in sediments. We showed that year‐round warming in a shallow macrophyte‐dominated mesocosm experiment doubled the carbon stock in plant biomass, increased sedimentation, and enhanced decomposition of plant detritus. These enhanced carbon fluxes compensated each other so that burial remained similar between treatments. This indicates that warming can increase the turnover of organic carbon, while not necessarily affecting net carbon burial. Abstract Temperatures have been rising throughout recent decades and are predicted to rise further in the coming century. Global warming affects carbon cycling in freshwater ecosystems, which both emit and bury substantial amounts of carbon on a global scale. Currently, most studies focus on the effect of warming on overall carbon emissions from freshwater ecosystems, while net effects on carbon budgets may strongly depend on burial in sediments. Here, we tested whether year‐round warming increases the production, sedimentation, or decomposition of particulate organic carbon and eventually alters the carbon burial in a typical shallow freshwater system. We performed an indoor experiment in eight mesocosms dominated by the common submerged aquatic plant Myriophyllum spicatum testing two temperature treatments: a temperate seasonal temperature control and a warmed (+4°C) treatment (n = 4). During a full experimental year, the carbon stock in plant biomass, dissolved organic carbon in the water column, sedimented organic matter, and decomposition of plant detritus were measured. Our results showed that year‐round warming nearly doubled the final carbon stock in plant biomass from 6.9 ± 1.1 g C in the control treatment to 12.8 ± 0.6 g C (mean ± SE), mainly due to a prolonged growing season in autumn. DOC concentrations did not differ between the treatments, but organic carbon sedimentation increased by 60% from 96 ± 9.6 to 152 ± 16 g C m−2 yaer−1 (mean ± SE) from control to warm treatments. Enhanced decomposition of plant detritus in the warm treatment, however, compensated for the increased sedimentation. As a result, net carbon burial was 40 ± 5.7 g C m−2 year−1 in both temperature treatments when fluxes were combined into a carbon budget model. These results indicate that warming can increase the turnover of organic carbon in shallow macrophyte‐dominated systems, while not necessarily affecting net carbon burial on a system scale.

Beschreibung: The spatially and temporally variable parameters and inputs to complex groundwater models typically result in long runtimes which hinder comprehensive calibration, sensitivity and uncertainty analysis. Surrogate modeling aims to provide a simpler, and hence faster, model which emulates the specified output of a more complex model in function of its inputs and parameters. In this review paper, we summarize surrogate modeling techniques in three categories: data-driven, projection, and hierarchical-based approaches. Data-driven surrogates approximate a groundwater model through an empirical model that captures the input-output mapping of the original model. Projection based models reduce the dimensionality of the parameter space by projecting the governing equations onto a basis of orthonormal vectors. In hierarchical or multi-fidelity methods the surrogate is created by simplifying the representation of the physical system, such as by ignoring certain processes, or reducing the numerical resolution. In discussing the application to groundwater modeling of these methods, we note several imbalances in the existing literature: a large body of work on data-driven approaches seemingly ignores major drawbacks to the methods; only a fraction of the literature focuses on creating surrogates to reproduce outputs of fully distributed groundwater models, despite these being ubiquitous in practice; and a number of the more advanced surrogate modeling methods are yet to be fully applied in a groundwater modeling context. This article is protected by copyright. All rights reserved.

Beschreibung: We studied the effect of waves on submerged macrophytes and hypothesized that exposure to large wave forces can hamper seedling establishment. In an indoor experiment in cylindrical mesocosms we tested whether large wave forces indeed inhibited the establishment of Chara globularis and Potamogeton pusillus from the propagule bank. We mimicked the effect of wave forces by generating a circular flow that caused resuspension of the sediment. Four treatments were applied, consisting of different repetition frequencies of resuspension events. Emergence and early growth of both species were monitored over 8 weeks. The resuspension treatments significantly reduced the emergence of both species, by 91% and 45% on average for Chara sp. and P. pusillus , respectively. We analysed field observations on the two species in the lakes of the IJsselmeer area in the Netherlands to evaluate whether wave forces may also inhibit establishment of macrophytes in the field. The field data seemed to support the hypothesis as both species hardly occurred in areas where a large bottom shear stress had occurred in spring, according to simulations with the SWAN wave model. The calculated maximum bottom shear stress correlated well with the occurrence of both Chara sp. and P. pusillus in the field. Regressions showed that this effect of wave forces was additional to the effect of light availability. Our study indicates that large wave forces may inhibit the establishment of macrophytes in large lakes. Reducing large wave forces can therefore potentially promote macrophyte development in these large lakes.

Beschreibung: To address the problem of indoor fungal growth, understanding the influence of moisture conditions on the fungal colonization process is crucial. This paper explores the influence of past moisture conditions on current processes. Specifically, it studies the growth and water sorption of conidia of Penicillium rubens formed at lower water activities (ranging from 0.86 to 0.99). For the first time, dynamic vapor sorption (DVS) is applied as a tool to quantify the water sorption of conidia as a function of the water activity at conidiation. Furthermore, growth experiments on agar and gypsum substrates are reported that relate hyphal growth rates of the mycelium from pretreated conidia to the water activity at conidiation. No effect of the conidiation water activity on mycelial growth rates is found on either gypsum or agar. It is found, however, that conidia formed at lower activities have a higher dry weight and attract more water from humid air. It is shown that both phenomena can be explained by conidia from lower activities carrying higher amounts of compatible solutes, glycerol in particular. The enhanced sorption observed in this study might constitute a mechanism through which solute reserves contribute to survival during the early steps of fungal colonization. The sorption behavior of conidia of Penicillium rubens that were formed under harsh moisture conditions was studied using a dynamic vapor sorption apparatus. It is found that conidia formed at low water activity will attract many times their own volume in water from humid air. From analysis of the sorption isotherms, it is deduced that this enhanced sorption behavior must be caused by large amounts of intra- and extracellular glycerol that was stored during sporulation.

Beschreibung: AnkyrinG, encoded by the ANK3 gene, is involved in neuronal development and signaling. It has previously been implicated in bipolar disorder and schizophrenia by association studies. Most recently, de novo missense mutations in this gene were identified in autistic patients. However, the causative nature of these mutations remained controversial. Here, we report inactivating mutations in the Ankyrin 3 ( ANK3 ) gene in patients with severe cognitive deficits. In a patient with a borderline intelligence, severe attention deficit hyperactivity disorder (ADHD), autism and sleeping problems, all isoforms of the ANK3 gene, were disrupted by a balanced translocation. Furthermore, in a consanguineous family with moderate intellectual disability (ID), an ADHD-like phenotype and behavioral problems, we identified a homozygous truncating frameshift mutation in the longest isoform of the same gene, which represents the first reported familial mutation in the ANK3 gene. The causality of ANK3 mutations in the two families and the role of the gene in cognitive function were supported by memory defects in a Drosophila knockdown model. Thus we demonstrated that ANK3 plays a role in intellectual functioning. In addition, our findings support the suggested association of ANK3 with various neuropsychiatric disorders and illustrate the genetic and molecular relation between a wide range of neurodevelopmental disorders.

Beschreibung: Aureobasidium melanogenum is the main fungus found in a spontaneously formed biofilm on a oil-treated wood. This dark colored biofilm functions as a protective coating. To better understand biofilm formation, in this study A. melanogenum was cultured on olive oil and raw linseed oil. Metabolic activity and oil conversion were measured. The results show that A. melanogenum is able to grow on linseed oil and olive oil as a single carbon source. The fungus produces the enzyme lipase to convert the oil into fatty acids and glycerol. Metabolic activity and oil conversion were equal on linseed oil and olive oil. The fungus was not able to grow on severe cross-linked linseed oil, meaning that the degree of cross-linking of the oil is important for growth of A. melanogenum . Dark coloring of the colony was seen on linseed oil, which might be a stress response on the presence of autoxidation products in linseed oil. The colony on olive oil showed delayed melanin production indicating an inhibitory effect of olive oil on melanin production. A uniform dark colored biofilm containing Aureobasidium melanogenum on oil-impregnated wood can be used as an environmentally friendly protective coating. For large-scale application, better understanding of the formation process is needed. This study focuses on the effect of oil type and cross-linking on growth of A. melanogenum .

Beschreibung: Plasmodium falciparum , the major cause of malaria morbidity and mortality worldwide, is only distantly related to other human malaria parasites and has thus been placed in a separate subgenus, termed Laverania . Parasites morphologically similar to P. falciparum have been identified in African apes, but only one other Laverania species, Plasmodium reichenowi from chimpanzees, has been formally described. Although recent studies have pointed to the existence of additional Laverania species, their precise number and host associations remain uncertain, primarily because of limited sampling and a paucity of parasite sequences other than from mitochondrial DNA. To address this, we used limiting dilution polymerase chain reaction to amplify additional parasite sequences from a large number of chimpanzee and gorilla blood and fecal samples collected at two sanctuaries and 30 field sites across equatorial Africa. Phylogenetic analyses of more than 2,000 new sequences derived from the mitochondrial, nuclear, and apicoplast genomes revealed six divergent and well-supported clades within the Laverania parasite group. Although two of these clades exhibited deep subdivisions in phylogenies estimated from organelle gene sequences, these sublineages were geographically defined and not present in trees from four unlinked nuclear loci. This greatly expanded sequence data set thus confirms six, and not seven or more, ape Laverania species, of which P. reichenowi , Plasmodium gaboni , and Plasmodium billcollinsi only infect chimpanzees, whereas Plasmodium praefalciparum, Plasmodium adleri , and Pladmodium blacklocki only infect gorillas. The new sequence data also confirm the P. praefalciparum origin of human P. falciparum .

Beschreibung: : RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface. Availability and implementation: Source code, binaries and documentation are available on http://rega.kuleuven.be/cev/regadb . RegaDB is written in the Java programming language, using a web-service-oriented architecture. Contact: pieter.libin@rega.kuleuven.be