Effects of Aneuploidy on Genome Structure, Expression, and Interphase Organization in Arabidopsis thaliana

Aneuploidy refers to losses and/or gains of individual chromosomes from the normal chromosome set. The resulting gene dosage imbalance has a noticeable affect on the phenotype, as illustrated by aneuploid syndromes, including Down syndrome in humans, and by human solid tumor cells, which are highly aneuploid. Although the phenotypic manifestations of aneuploidy are usually apparent, information about the underlying alterations in structure, expression, and interphase organization of unbalanced chromosome sets is still sparse. Plants generally tolerate aneuploidy better than animals, and, through colchicine treatment and breeding strategies, it is possible to obtain inbred sibling plants with different numbers of chromosomes. This possibility, combined with the genetic and genomics tools available for Arabidopsis thaliana, provides a powerful means to assess systematically the molecular and cytological consequences of aberrant numbers of specific chromosomes. Here, we report on the generation of Arabidopsis plants in which chromosome 5 is present in triplicate. We compare the global transcript profiles of normal diploids and chromosome 5 trisomics, and assess genome integrity using array comparative genome hybridization. We use live cell imaging to determine the interphase 3D arrangement of transgene-encoded fluorescent tags on chromosome 5 in trisomic and triploid plants. The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5. Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles. Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and progressive genome instability

Dispersal in the Ordovician: Speciation patterns and paleobiogeographic analyses of brachiopods and trilobites

The Middle to Late Ordovician was a time of profound biotic diversification, paleoecological change, and major climate shifts. Yet studies examining speciation mechanisms and drivers of dispersal are lacking. In this study, we use Bayesian phylogenetics and maximum likelihood analyses in the R package BioGeoBEARS to reanalyze ten published data matrices of brachiopods and trilobites and produce time-calibrated species-level phylogenetic hypotheses with estimated biogeographic histories. Recovered speciation and biogeographic patterns were examined within four time slices to test for changes in speciation type across major tectonic and paleoclimatic events. Statistical model comparison showed that biogeographic models that incorporate long-distance founder-event speciation best fit the data for most clades, which indicates that this speciation type, along with vicariance and traditional dispersal, were important for Paleozoic benthic invertebrates. Speciation by dispersal was common throughout the study interval, but notably elevated during times of climate change. Vicariance events occurred synchronously among brachiopod and trilobite lineages, indicating that tectonic, climate, and ocean processes affected benthic and planktotrophic larvae similarly. Middle Ordovician inter-oceanic dispersal in trilobite lineages was influenced by surface currents along with volcanic island arcs acting as “stepping stones” between areas, indicating most trilobite species may have had a planktic protaspid stage. These factors also influenced brachiopod dispersal across oceanic basins among Laurentia, Avalonia, and Baltica. These results indicate that gyre spin-up and intensification of surface currents were important dispersal mechanisms during this time. Within Laurentia, surface currents, hurricane tracks, and upwelling zones controlled dispersal among basins. Increased speciation during the Middle Ordovician provides support for climatic facilitators for diversification during the Great Ordovician Biodiversification Event. Similarly, increased speciation in Laurentian brachiopod lineages during the Hirnantian indicates that some taxa experienced speciation in relation to major climate changes. Overall, this study demonstrates the substantial power and potential for likelihood-based methods for elucidating biotic patterns during the history of life.This study was supported by NSF (EF-1206750, EAR-0922067 to A.L.S.) and the Dry Dredgers Paleontological Research Award, the Paleontological Society Arthur J. Boucot Award, and an Ohio University Graduate Alumni Research Grant to A.R.L. N.J.M. was supported by Discovery Early Career Researcher Award (DECRA) DE150101773, funded by the Australian Research Council, and by The Australian National University. He was also supported by the National Institute for Mathematical and Biological Synthesis (NIMBioS), an Institute sponsored by the National Science Foundation, the U.S. Department of Homeland Security, and the U.S. Department of Agriculture through NSF Awards #EFJ0832858 and DBI-1300426, with additional support from The University of Tennessee, Knoxville. In addition, a NIMBioS short-term visitor award allowed A.R.L. to visit NIMBioS to begin collaboration with N.J.M. This is a contribution to the International Geoscience Programme (IGCP) Projects 591- The Early to Middle Paleozoic Revolution and 653- The Onset of the Great Ordovician Biodiversification Event

Effect of Ceftazidime on Systemic Cytokine Concentrations in Rats

The effect of a single dose of ceftazidime on circulating concentrations of interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) in a rat model of sepsis was studied. IL-6 concentrations were significantly elevated (100 to 200 times the baseline) 6 h after ceftazidime administration in both septic and nonseptic (control) rats. TNF-α concentrations increased significantly in nonseptic (∼40 times the baseline) rats but not septic (∼2 to 3 times the baseline) rats. Ceftazidime administration was not associated with an increase in endotoxin concentrations. These findings suggest that ceftazidime modulation of proinflammatory cytokine concentrations may be independent of its antimicrobial properties

Safety and Pharmacokinetics of Multiple Doses of Intravenous Ofloxacin in Healthy Volunteers

The safety and pharmacokinetics of ofloxacin in 48 healthy male volunteers were studied in a two-center, randomized, double-blind, placebo-controlled study. Ofloxacin (200 or 400 mg) or placebo was administered as 1-h infusions every 12 h for 7 days. Plasma ofloxacin concentrations were measured by high-performance liquid chromatography. Mean harmonic half-lives ranged from 4.28 to 4.98 h in the 200-mg dosing group and from 5.06 to 6.67 h in the 400-mg dosing group. Intragroup comparisons of trough plasma concentration-versus-time data from study days 2 through 7 revealed that steady state was achieved by day 2 of both multiple-dose regimens. Intergroup comparisons of mean harmonic half-lives, the areas under the concentration-time curve from 0 to 12 and 0 to 60 h, clearance, and apparent volume of distribution (area method) revealed that the pharmacokinetics of ofloxacin are dose independent. Both ofloxacin dosage regimens appeared to be reasonably well tolerated. The two dosage regimens of ofloxacin, 200 or 400 mg every 12 h, appear to be safe and provide serum drug concentrations in excess of the MICs for most susceptible pathogens over the entire dosing interval

Evaluation of Potential LSST Spatial Indexing Strategies

The LSST requirement for producing alerts in near real-time, and the fact that generating an alert depends on knowing the history of light variations for a given sky position, both imply that the clustering information for all detections is available at any time during the survey. Therefore, any data structure describing clustering of detections in LSST needs to be continuously updated, even as new detections are arriving from the pipeline. We call this use case ''incremental clustering'', to reflect this continuous updating of clustering information. This document describes the evaluation results for several potential LSST incremental clustering strategies, using: (1) Neighbors table and zone optimization to store spatial clusters (a.k.a. Jim Grey's, or SDSS algorithm); (2) MySQL built-in R-tree implementation; (3) an external spatial index library which supports a query interface

Supporting Advocacy, Deliberation, and Civic Learning in the Classroom

We live, teach and learn in complicated times. As faculty in higher education, we have the opportunity to help uphold the civic purpose of higher education. We are accustomed to helping students navigate academic information, and to equipping them for more standard academic tasks. Through thoughtful course design, we can also help our students become better consumers and evaluators of less traditionally academic information: from critically interpreting what they read and see in the news media, to engaging the arguments of their friends, peers and family members. Further, we can challenge our students to use these evaluative skills to engage in debate and advocacy activities around critical issues of the day

Exceptional preservation of reproductive organs and giant sperm in Cretaceous ostracods

The bivalved crustacean ostracods have the richest fossil record of any arthropod group and display complex reproductive strategies contributing to their evolutionary success. Sexual reproduction involving giant sperm, shared by three superfamilies of living ostracod crustaceans, is among the most fascinating behaviours. However, the origin and evolution of this reproductive mechanism has remained largely unexplored because fossil preservation of such features is extremely rare. Here, we report exceptionally preserved ostracods with soft parts (appendages and reproductive organs) in a single piece of mid-Cretaceous Kachin amber (approximately 100 Myr old). The ostracod assemblage is composed of 39 individuals. Thirty-one individuals belong to a new species and genus, Myanmarcypris hui gen. et sp. nov., exhibiting an ontogenetic sequence from juveniles to adults (male and female). Seven individuals are assigned to Thalassocypria sp. (Cypridoidea, Candonidae, Paracypridinae) and one to Sanyuania sp. (Cytheroidea, Loxoconchidae). Our micro-CT reconstruction provides direct evidence of the male clasper, sperm pumps (Zenker organs), hemipenes, eggs and female seminal receptacles with giant sperm. Our results reveal that the reproduction behavioural repertoire, which is associated with considerable morphological adaptations, has remained unchanged over at least 100 million years—a paramount example of evolutionary stasis. These results also double the age of the oldest unequivocal fossil animal sperm. This discovery highlights the capacity of amber to document invertebrate soft parts that are rarely recorded by other depositional environments

Photosynthesis dependent acidification of perialgal vacuoles in theParamedum bursaria/Chlorella symbiosis. Visualization by monensin

After treatment with the carboxylic ionophore monensin theChlorella containing perialgal vacuoles of the greenParamecium bursaria swell. TheParamecium cells remain motile at this concentration for at least one day. The swelling is only observed in illuminated cells and can be inhibited by DCMU. We assume that during photosynthesis the perialgal vacuoles are acidified and that monensin exchanges H+ ions against monovalent cations (here K+). In consequence the osmotic value of the vacuoles increases. The proton gradient is believed to drive the transport of maltose from the symbiont into the host. Another but light independent effect of the monensin treatment is the swelling of peripheral alveoles of the ciliates, likewise indicating that the alveolar membrane contains an active proton pump