First Miocene fossils of Vivianiaceae shed new light on phylogeny, divergence times, and historical biogeography of Geraniales

The origin of Geraniales (approximately 900 species in three families: Geraniaceae, Melianthaceae, and Vivianiaceae) is traced back to the Cretaceous of Gondwana, yet their geotemporal history is largely unknown because of a limited fossil record and incomplete phylogenies. In the present study, we provide the first fossil record of Vivianiaceae and a highly resolved molecular phylogeny for all extant Geraniales genera. Our results support the hypothesis that five (instead of three) families should be recognized in the order Geraniales: Francoaceae A. Juss. (Francoa, Greyia, Tetilla), Geraniaceae Juss. (Erodium, Geranium, Monsonia, Pelargonium), Hypseocharitaceae Wedd. (monogeneric), Melianthaceae Horan. (Bersama, Melianthus), and Vivianiaceae Klotzsch (Balbisia, Rhynchotheca, Viviania). The four major lineages (i.e. Geraniaceae, Francoaceae+Melianthaceae, Hypseocharitaceae, Vivianiaceae) all originated within a narrow time frame during the Eocene (36.9-49.9Mya) based on the five fossil calibration points. The divergence of most of the extant genera occurred much later, from the Miocene onwards. The South American-South African disjunction in Francoaceae apparently goes back to long distance dispersal with an estimated divergence time of the lineages in the Middle Miocene [11.2 (5.9-17.7)Mya]. Diversification in Melianthus appears to be much more recent than previously assumed [starting approximately 3.4 (1.9-5.2)Mya rather than approximately 8-20Mya]. However, divergence of the Andean Hypseocharis lineage [36.9 (31.9-42.8)Mya] significantly predates the main Andean uplift: Current distributions likely go back to northward migrations and subsequent extinctions in Patagonia. Similarly, Rhynchotheca, Balbisia, and Viviania have a current southern distribution limit >10°N of the fossil finds, indicating a massive northward displacement. The present evidence suggests that niche conservatism likely played a major role in the historical biogeography of Geraniales. © 2012 The Linnean Society of London.Fil: Palazzesi, Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Argentina. Freie Universität Berlin; AlemaniaFil: Gottschling, Marc. Ludwig Maximilians Universitat; AlemaniaFil: Barreda, Viviana Dora. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; ArgentinaFil: Weigend, M. Freie Universität Berlin; Alemani

The troublesome kernel: why deep learning for inverse problems is typically unstable

There is overwhelming empirical evidence that Deep Learning (DL) leads to unstable methods in applications ranging from image classification and computer vision to voice recognition and automated diagnosis in medicine. Recently, a similar instability phenomenon has been discovered when DL is used to solve certain problems in computational science, namely, inverse problems in imaging. In this paper we present a comprehensive mathematical analysis explaining the many facets of the instability phenomenon in DL for inverse problems. Our main results not only explain why this phenomenon occurs, they also shed light as to why finding a cure for instabilities is so difficult in practice. Additionally, these theorems show that instabilities are typically not rare events - rather, they can occur even when the measurements are subject to completely random noise - and consequently how easy it can be to destablise certain trained neural networks. We also examine the delicate balance between reconstruction performance and stability, and in particular, how DL methods may outperform state-of-the-art sparse regularization methods, but at the cost of instability. Finally, we demonstrate a counterintuitive phenomenon: training a neural network may generically not yield an optimal reconstruction method for an inverse problem

Optical control of AMPA receptors using a photoswitchable quinoxaline-2,3-dione antagonist

AMPA receptors respond to the neurotransmitter glutamate and play a critical role in excitatory neurotransmission. They have been implicated in several psychiatric disorders and have rich pharmacology. Antagonists of AMPA receptors have been explored as drugs and one has even reached the clinic. We now introduce a freely diffusible photoswitchable antagonist that is selective for AMPA receptors and endows them with light-sensitivity. Our photoswitch, ShuBQX-3, is active in its dark-adapted trans-isoform but is significantly less active as its cis-isoform. ShuBQX-3 exhibits a remarkable red-shifting of its photoswitching properties through interactions with the AMPA receptor ligand binding site. Since it can be used to control action potential firing with light, it could emerge as a powerful tool for studying synaptic transmission with high spatial and temporal precision

Zygosity Determination in Twin Studies: a Validation of Zygosity Questionnaires Using DNA in the German TwinLife Study

Lenau F, Hahn E, Peters A-L, Gottschling J, Thiel W, Spinath FM. Zygosity Determination in Twin Studies: a Validation of Zygosity Questionnaires Using DNA in the German TwinLife Study. TwinLife Working Paper Series. Vol 01. Bielefeld: Project TwinLife "Genetic and social causes of life chances" (Universität Bielefeld / Universität des Saarlandes); 2017.Zygosity determination using similarity ratings is frequently applied in twin studies. A correct determination of zygosity is essential for the estimation of heritability and environmental influences on phenotypes. Therefore, the present study examined the validity of two similarity questionnaires used in the German TwinLife study, in which data from 4,097 twin pairs and their families were assessed: twin children’s zygosities were determined with the Zygosity Questionnaire for Young Twins, which was administered in parent-report form. For adolescent twins, the Self Report Zygosity Questionnaire was used. For the present validation analyses, DNA samples of N = 328 twin pairs were collected via buccal swabs. In this DNA subsample, questionnaires were filled out by parents for n = 212 (aged 4 to 12 years) twin pairs while self-reports were collected from n = 116 adolescent twins (16 to 23 years of age). Using DNA-based zygosity as criteria, correct classification rates of 97% for parent- and 92% for self-reports were established and cross-validated. Additionally, classification rates based on a single item and variants of questionnaire based zygosity determination used in other twin studies were calculated and compared. Implications of incorrectly classified zygosity on genetic and environmental estimates in twin studies are discussed

Candida albicans repetitive elements display epigenetic diversity and plasticity

Transcriptionally silent heterochromatin is associated with repetitive DNA. It is poorly understood whether and how heterochromatin differs between different organisms and whether its structure can be remodelled in response to environmental signals. Here, we address this question by analysing the chromatin state associated with DNA repeats in the human fungal pathogen Candida albicans. Our analyses indicate that, contrary to model systems, each type of repetitive element is assembled into a distinct chromatin state. Classical Sir2-dependent hypoacetylated and hypomethylated chromatin is associated with the rDNA locus while telomeric regions are assembled into a weak heterochromatin that is only mildly hypoacetylated and hypomethylated. Major Repeat Sequences, a class of tandem repeats, are assembled into an intermediate chromatin state bearing features of both euchromatin and heterochromatin. Marker gene silencing assays and genome-wide RNA sequencing reveals that C. albicans heterochromatin represses expression of repeat-associated coding and non-coding RNAs. We find that telomeric heterochromatin is dynamic and remodelled upon an environmental change. Weak heterochromatin is associated with telomeres at 30?°C, while robust heterochromatin is assembled over these regions at 39?°C, a temperature mimicking moderate fever in the host. Thus in C. albicans, differential chromatin states controls gene expression and epigenetic plasticity is linked to adaptation

The Ctf18 RFC-like complex positions yeast telomeres but does not specify their replication time

Peer reviewedPreprin

The dinophycean genus Azadinium and related species – morphological and molecular characterization, biogeography, and toxins

Peer-reviewed.Azaspiracids (AZAs) are the most recently discovered group of lipophilic marine biotoxins of microalgal origin. It took about twelve years from the first human poisoning event until a culprit for AZA production was unambiguously identified and described as a novel species, Azadinium spinosum, within a newly created genus. Since then, knowledge on the genus has increased considerably, and an update on the current circumscription of the genus is presented here including various aspects of morphology, phylogeny, biogeography, and toxin production. There are currently five described species: A. spinosum, A. obesum, A. poporum, A. caudatum, and A. polongum. As indicated by molecular sequence variation detected in field samples, there are probably more species to recognize. Moreover, Amphidoma languida has been described recently, and this species is the closest relative of Azadinium based on both molecular and morphological data. Amphidoma and Azadinium are now grouped in the family Amphidomataceae, which forms an independent lineage among other monophyletic major groups of dinophytes. Initially, azaspiracids have been detected in A. spinosum only, but AZA production within the Amphidomataceae appears complex and diverse: A new type of azaspiracid, with a number of structural variants, has been detected in A. poporum and Amphidoma languida, and AZA-2 has now been detected in Chinese strains of A. poporum

The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state

We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores whether the presence of multiple marks lead to a qualitatively different systems behavior. We find that having both modifications is important for the robustness of epigenetic silencing. Besides the silenced and transcriptionally active fate of chromatin, our model leads to a novel state with bivalent (i.e., both active and silencing) marks under certain perturbations (knock-out mutations, inhibition or enhancement of enzymatic activity). The bivalent state appears under several perturbations and is shown to result in patchy silencing. We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive responses. The design principles of the silencing system is systematically investigated and disparate experimental observations are assessed within a single theoretical framework. Specifically, we discuss the behavior of Sir protein recruitment, spreading and stability of silenced regions in commonly-studied mutants (e.g., sas2, dot1) illuminating the controversial role of Dot1 in the systems biology of yeast silencing.Comment: Supplementary Material, 14 page