Repeated evolution of a morphological novelty: Convergence of the inflated fruiting calyx in the Physalideae tribe (Solanaceae)

La evolución de nuevas morfologías del fruto ha sido considerada una pieza clave para el éxito de las angiospermas. La morfología de frutos es conocida por su extensa diversidad, pero también por su alto grado de convergencia. Entre los rasgos más llamativos, el cáliz fructífero inflado, donde el cáliz se expande para envolver completamente al fruto, ha evolucionado repetidamente en angiospermas y ha sido postulado como un promotor de la dispersión y protección del fruto. Con el objetivo de analizar la evolución de este rasgo morfológico en la tribu Physalideae (Solanaceae), usamos una nueva reconstrucción filogenética y un conjunto de métodos comparativos filogenéticos para inferir las ganancias y pérdidas evolutivas de este rasgo. Se reconstruyó la filogenia de Physalideae usando secuencias de cuatro regiones de ADN (ITS, LEAFY, trnL-F, waxy) y aplicando análisis de máxima verosimilitud e inferencia bayesiana. Se codificó al cáliz fructífero como acrescente cuando el incremento de la longitud del cáliz desde la flor al fruto es ≥50%, y se consideró inflado cuando el fruto es completamente cubierto por el cáliz y existe además un espacio entre éste y la baya. La selección del mejor modelo de evolución del cáliz fructífero acrescente e inflado fue realizada con un análisis de máxima verosimilitud. Usando este modelo, se estimaron los estados ancestrales junto con el número de ganancias y pérdidas de la acrescencia del cáliz fructífero y de su estado inflado mediante mapeo estocástico bayesiano. Además, se examinó la señal filogenética de la morfología del cáliz a través de dos métricas: el índice de parsimonia y la D de Fritz-Purvis.Resultados: Se presenta la primera filogenia de la tribu Physalideae densamente muestreada (~73% de las especies). Esta filogenia, con buen grado de resolución, demuestra la necesidad de revisión de múltiples taxones, incluyendo ocho géneros que no son monofiléticos según su actual circunscripción. La evolución del cáliz fructífero ha procedido mediante un modelo "paso a paso", desde no acrescente hacia acrescente, y luego, hacia un cáliz inflado. Además, estas transiciones son mayormente irreversibles. A lo largo de los 215 taxones muestreados de Physalideae, se infirieron 24 ganancias de la acrescencia del cáliz fructífero, 24 subsecuentes transiciones a un cáliz totalmente inflado y solo dos reversiones. Un promedio de 50 cambios en total fue estimado a lo largo del clado desde un ancestro con cáliz no acrescente. A pesar de su labilidad, el cáliz fructífero acrescente e inflado muestran una fuerte señal filogenética mediante ambas métricas evaluadas.Conclusiones: La filogenia presentada mejora la resolución de Physalideae y destaca la necesidad de re arreglos taxonómicos. Los análisis evolutivos revelaron que el cáliz fructífero inflado, considerado tan característico de Physalis, ha evolucionado numerosas veces y que la trayectoria hacia este fenotipo es generalmente direccional y mediante un modelo "paso a paso". Estos resultados proveen los conocimientos necesarios para el estudio de los mecanismos genéticos y de desarrollo responsables del origen repetido de este llamativo rasgo del fruto.Fil: Deanna, Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Barboza, Gloria Estela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Smith, S.. State University of Colorado at Boulder; Estados UnidosXXXVII Jornadas Argentinas de BotánicaTucumanArgentinaSociedad Argentina de Botanic

Lis1 and Ndel1 influence the timing of nuclear envelope breakdown in neural stem cells

Lis1 and Ndel1 are essential for animal development. They interact directly with one another and with cytoplasmic dynein. The developing brain is especially sensitive to reduced Lis1 or Ndel1 levels, as both proteins influence spindle orientation, neural cell fate decisions, and neuronal migration. We report here that Lis1 and Ndel1 reduction in a mitotic cell line impairs prophase nuclear envelope (NE) invagination (PNEI). This dynein-dependent process facilitates NE breakdown (NEBD) and occurs before the establishment of the bipolar spindle. Ndel1 phosphorylation is important for this function, regulating binding to both Lis1 and dynein. Prophase cells in the ventricular zone (VZ) of embryonic day 13.5 Lis1+/− mouse brains show reduced PNEI, and the ratio of prophase to prometaphase cells is increased, suggesting an NEBD delay. Moreover, prophase cells in the VZ contain elevated levels of Ndel1 phosphorylated at a key cdk5 site. Our data suggest that a delay in NEBD in the VZ could contribute to developmental defects associated with Lis1–Ndel1 disruption

Improving Biosecurity through Instructional Crisis Communication: Lessons Learned from the PEDv Outbreak

Crises, by their nature, demand effectively designed and quickly delivered instructional messages that compel stakeholders to take appropriate actions to protect themselves and their assets. The challenges of crisis communication are intensified in crises involving unanticipated and relatively unknown disease outbreaks with the potential to spread exponentially. This study assesses the communication challenges and opportunities in such volatile crises through an analysis of the Porcine Epidemic Diarrhea virus (PEDv) outbreak that severely threatened the United States pork industry in 2013 and 2014. Interviews were conducted with 13 individuals directly involved in developing and distributing risk and crisis biosecurity messages during the PEDv outbreak. Participants were selected based on affiliation with the National Pork Board, American Association of Swine Veterinarians, university extension, or their swine industry expertise. Four generalizable implications emerged: 1) the advantage of maintaining flexibility in crisis communication planning; 2) the value of audience analysis and message adaptation; 3) the importance of understanding not only what to do, but also why the recommended actions are essential; and 4) the utility of risk/crisis communication and education both prior to and during a crisis event

Regulation of Cytoplasmic Dynein ATPase by Lis1

Mutations in Lis1 cause classical lissencephaly, a developmental brain abnormality characterized by defects in neuronal positioning.Over the last decade, a clear link has been forged between Lis1 and the microtubule motor cytoplasmic dynein. Substantial evidenceindicates that Lis1 functions in a highly conserved pathway with dynein to regulate neuronal migration and other motile events. Yeasttwo-hybrid studies predict that Lis1 binds directly to dynein heavy chains (Sasaki et al., 2000; Tai et al., 2002), but the mechanistic significance of this interaction is not well understood. We now report that recombinant Lis1 binds to native brain dynein and significantly increases the microtubule-stimulated enzymatic activity of dynein in vitro. Lis1 does this without increasing the proportion of dynein that binds to microtubules, indicating that Lis1 influences enzymatic activity rather than microtubule association. Dynein stimulation in vitrois not a generic feature of microtubule-associated proteins, because tau did not stimulate dynein. To our knowledge, this is the firstindication that Lis1 or any other factor directly modulates the enzymatic activity of cytoplasmic dynein. Lis1 must be able to homodimerizeto stimulate dynein, because a C-terminal fragment (containing the dynein interaction site but missing the self-association domain)was unable to stimulate dynein. Binding and colocalization studies indicate that Lis1 does not interact with all dynein complexes foundin the brain.We propose a model in which Lis1 stimulates the activity of a subset of motors, which could be particularly important during neuronal migration and long-distance axonal transport

Extracellular Stimuli Specifically Regulate Localized Levels of Individual Neuronal mRNAs

Subcellular regulation of protein synthesis requires the correct localization of messenger RNAs (mRNAs) within the cell. In this study, we investigate whether the axonal localization of neuronal mRNAs is regulated by extracellular stimuli. By profiling axonal levels of 50 mRNAs detected in regenerating adult sensory axons, we show that neurotrophins can increase and decrease levels of axonal mRNAs. Neurotrophins (nerve growth factor, brainderived neurotrophic factor, and neurotrophin-3) regulate axonal mRNA levels and use distinct downstream signals to localize individual mRNAs. However, myelin-associated glycoprotein and semaphorin 3A regulate axonal levels of different mRNAs and elicit the opposite effect on axonal mRNA levels from those observed with neurotrophins. The axonal mRNAs accumulate at or are depleted from points of ligand stimulation along the axons. The translation product of a chimeric green fluorescent protein–β-actin mRNA showed similar accumulation or depletion adjacent to stimuli that increase or decrease axonal levels of endogenous β-actin mRNA. Thus, extracellular ligands can regulate protein generation within subcellular regions by specifically altering the localized levels of particular mRNAs

Cellular Ser/Thr-Kinase Assays Using Generic Peptide Substrates

High-throughput cellular profiling has successfully stimulated early drug discovery pipelines by facilitating targeted as well as opportunistic lead finding, hit annotation and SAR analysis. While automation-friendly universal assay formats exist to address most established drug target classes like GPCRs, NHRs, ion channels or Tyr-kinases, no such cellular assay technology is currently enabling an equally broad and rapid interrogation of the Ser/Thr-kinase space. Here we present the foundation of an emerging cellular Ser/Thr-kinase platform that involves a) coexpression of targeted kinases with promiscuous peptide substrates and b) quantification of intracellular substrate phosphorylation by homogeneous TR-FRET. Proof-of-concept data is provided for cellular AKT, B-RAF and CamK2δ assays. Importantly, comparable activity profiles were found for well characterized B-Raf inhibitors in TR-FRET assays relying on either promiscuous peptide substrates or a MEK1(WT) protein substrate respectively. Moreover, IC50-values correlated strongly between cellular TR-FRET assays and a gold standard Ba/F3 proliferation assay for B-Raf activity. Finally, we expanded our initial assay panel by screening a kinase-focused cDNA library and identified starting points for >20 cellular Ser/Thr-kinase assays

DDX3X suppresses the susceptibility of hindbrain lineages to medulloblastoma

DEAD-Box Helicase 3 X-Linked (DDX3X) is frequently mutated in the Wingless (WNT) and Sonic hedghog (SHH) subtypes of medulloblastoma—the commonest malignant childhood brain tumor, but whether DDX3X functions as a medulloblastoma oncogene or tumor suppressor gene is not known. Here, we show that Ddx3x regulates hindbrain patterning and development by controlling Hox gene expression and cell stress signaling. In mice predisposed to Wnt- or Shh medulloblastoma, Ddx3x sensed oncogenic stress and suppressed tumor formation. WNT and SHH medulloblastomas normally arise only in the lower and upper rhombic lips, respectively. Deletion of Ddx3x removed this lineage restriction, enabling both medulloblastoma subtypes to arise in either germinal zone. Thus, DDX3X is a medulloblastoma tumor suppressor that regulates hindbrain development and restricts the competence of cell lineages to form medulloblastoma subtypes

Uncovering the Genetic Landscape for Multiple Sleep-Wake Traits

Despite decades of research in defining sleep-wake properties in mammals, little is known about the nature or identity of genes that regulate sleep, a fundamental behaviour that in humans occupies about one-third of the entire lifespan. While genome-wide association studies in humans and quantitative trait loci (QTL) analyses in mice have identified candidate genes for an increasing number of complex traits and genetic diseases, the resources and time-consuming process necessary for obtaining detailed quantitative data have made sleep seemingly intractable to similar large-scale genomic approaches. Here we describe analysis of 20 sleep-wake traits from 269 mice from a genetically segregating population that reveals 52 significant QTL representing a minimum of 20 genomic loci. While many (28) QTL affected a particular sleep-wake trait (e.g., amount of wake) across the full 24-hr day, other loci only affected a trait in the light or dark period while some loci had opposite effects on the trait during the light vs. dark. Analysis of a dataset for multiple sleep-wake traits led to previously undetected interactions (including the differential genetic control of number and duration of REM bouts), as well as possible shared genetic regulatory mechanisms for seemingly different unrelated sleep-wake traits (e.g., number of arousals and REM latency). Construction of a Bayesian network for sleep-wake traits and loci led to the identification of sub-networks of linkage not detectable in smaller data sets or limited single-trait analyses. For example, the network analyses revealed a novel chain of causal relationships between the chromosome 17@29cM QTL, total amount of wake, and duration of wake bouts in both light and dark periods that implies a mechanism whereby overall sleep need, mediated by this locus, in turn determines the length of each wake bout. Taken together, the present results reveal a complex genetic landscape underlying multiple sleep-wake traits and emphasize the need for a systems biology approach for elucidating the full extent of the genetic regulatory mechanisms of this complex and universal behavior

Comparative genomics of Cluster O mycobacteriophages

Mycobacteriophages - viruses of mycobacterial hosts - are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages - Corndog, Catdawg, Dylan, Firecracker, and YungJamal - designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange

Genetic Variation in the Proximal Promoter of ABC and SLC Superfamilies: Liver and Kidney Specific Expression and Promoter Activity Predict Variation

Membrane transporters play crucial roles in the cellular uptake and efflux of an array of small molecules including nutrients, environmental toxins, and many clinically used drugs. We hypothesized that common genetic variation in the proximal promoter regions of transporter genes contribute to observed variation in drug response. A total of 579 polymorphisms were identified in the proximal promoters (−250 to +50 bp) and flanking 5′ sequence of 107 transporters in the ATP Binding Cassette (ABC) and Solute Carrier (SLC) superfamilies in 272 DNA samples from ethnically diverse populations. Many transporter promoters contained multiple common polymorphisms. Using a sliding window analysis, we observed that, on average, nucleotide diversity (π) was lowest at approximately 300 bp upstream of the transcription start site, suggesting that this region may harbor important functional elements. The proximal promoters of transporters that were highly expressed in the liver had greater nucleotide diversity than those that were highly expressed in the kidney consistent with greater negative selective pressure on the promoters of kidney transporters. Twenty-one promoters were evaluated for activity using reporter assays. Greater nucleotide diversity was observed in promoters with strong activity compared to promoters with weak activity, suggesting that weak promoters are under more negative selective pressure than promoters with high activity. Collectively, these results suggest that the proximal promoter region of membrane transporters is rich in variation and that variants in these regions may play a role in interindividual variation in drug disposition and response