DNAReplication: a database of information and resources for the eukaryotic DNA replication community

DNAReplication (at http://www.dnareplication.net) has been set up as a freely available single resource to facilitate access to information on eukaryotic DNA replication. This database summarizes organism-sorted data on replication proteins in the categories of nomenclature, biochemical properties, motifs, interactions, modifications, structure, cell localization and expression, and general comments. Replication concepts are defined and a general model of the steps in DNA replication is presented. Links to relevant websites and homepages of replication labs are provided. The site also has an interactive section where links to recent replication papers are posted and readers are provided with the facility to post comments about each paper. The interactive and links pages are modified weekly and the whole site is updated annually

Dynamic, mating-induced gene expression changes in female head and brain tissues of Drosophila melanogaster

BACKGROUND: Drosophila melanogaster females show changes in behavior and physiology after mating that are thought to maximize the number of progeny resulting from the most recent copulation. Sperm and seminal fluid proteins induce post-mating changes in females, however, very little is known about the resulting gene expression changes in female head and central nervous system tissues that contribute to the post-mating response. RESULTS: We determined the temporal gene expression changes in female head tissues 0-2, 24, 48 and 72 hours after mating. Females from each time point had a unique post-mating gene expression response, with 72 hours post-mating having the largest number of genes with significant changes in expression. At most time points, genes expressed in the head fat body that encode products involved in metabolism showed a marked change in expression. Additional analysis of gene expression changes in dissected brain tissues 24 hours post-mating revealed changes in transcript abundance of many genes, notably, the reduced transcript abundance of genes that encode ion channels. CONCLUSIONS: Substantial changes occur in the regulation of many genes in female head tissues after mating, which might underlie aspects of the female post-mating response. These results provide new insights into the physiological and metabolic changes that accompany changes in female behaviors

Dynamic Recruitment of Licensing Factor Cdt1 to Sites of DNA Damage

For genomic integrity to be maintained, the cell cycle and DNA damage responses must be linked. Cdt1, a G1-specific cell-cycle factor, is targeted for proteolysis by the Cul4-Ddb1Cdt2 ubiquitin ligase following DNA damage. Using a laser nanosurgery microscope to generate spatially restricted DNA damage within the living cell nucleus, we show that Cdt1 is recruited onto damaged sites in G1 phase cells, within seconds of DNA damage induction. PCNA, Cdt2, Cul4, DDB1 and p21Cip1 also accumulate rapidly to damaged sites. Cdt1 recruitment is PCNA-dependent, whereas PCNA and Cdt2 recruitment are independent of Cdt1. Fitting of fluorescence recovery after photobleaching profiles to an analytic reaction-diffusion model shows that Cdt1 and p21Cip1 exhibit highly dynamic binding at the site of damage, whereas PCNA appears immobile. Cdt2 exhibits both a rapidly exchanging and an apparently immobile subpopulation. Our data suggest that PCNA provides an immobile binding interface for dynamic Cdt1 interactions at the site of damage, which leads to rapid Cdt1 recruitment to damaged DNA, preceding Cdt1 degradation

Coordinated SuperDARN THEMIS ASI observations of mesoscale flow bursts associated with auroral streamers

Nightside auroral zone localized flow channels, typically associated with auroral poleward boundary intensifications and streamers, are an important component of high‐latitude ionospheric plasma dynamics. We investigate the structure of these flow channels using two‐dimensional line‐of‐sight flow observations from the Super Dual Auroral Radar Network (SuperDARN) radars and auroral images from the Time History of Events and Macroscale Interactions during Substorms (THEMIS) ground‐based all‐sky imager (ASI) array. Radar echoes captured <~500 km horizontal distance from the radars were mainly used to detect small‐scale flow structures that would otherwise be missed or poorly resolved in long‐range radar echoes. After identifying 135 auroral streamers in the ASI images at close‐radar capture locations, we examined the associated ionospheric flow data in the radar echoes. Flow bursts and streamers are invariably correlated in all events. The flow bursts are often directed equatorward and appear simultaneously with the streamers. Equatorward flows are located just to the east of the streamers. Less frequently (~10% of the time), a poleward flow enhancement was detected even when a streamer propagated equatorward, the poleward flow enhancement being located to the west of the auroral streamer, or to the east of the equatorward flow enhancement, consistently with the spatial relationship between flow shear and upward field‐aligned currents in plasma sheet flow bursts. The azimuthal width of the flow channel is, on average, ~75 km, and the azimuthal offset of the equatorward flow channel relative to the auroral streamer is ~57 km eastward. This study demonstrates the capability of radar‐imager pairs for identifying the 2‐D structure of localized flows associated with plasma sheet flow bursts. Key Points Structure of flow channels using SuperDARN radars and THEMIS ASI is investigated Simultaneous flow bursts and streamers are invariably correlated in all events 3‐D structure of flows consistent with plasma flow shears around a BBF channelPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106072/1/jgra50744.pd

Expression pattern of four storage xyloglucan mobilization-related genes during seedling development of the rain forest tree Hymenaea courbaril L.

During seedling establishment, cotyledons of the rain forest tree Hymenaea courbaril mobilize storage cell wall xyloglucan to sustain growth. The polysaccharide is degraded and its products are transported to growing sink tissues. Auxin from the shoot controls the level of xyloglucan hydrolytic enzymes. It is not yet known how important the expression of these genes is for the control of storage xyloglucan degradation. In this work, partial cDNAs of the genes xyloglucan transglycosylase hydrolase (HcXTH1) and β-galactosidase (HcBGAL1), both related to xyloglucan degradation, and two other genes related to sucrose metabolism [alkaline invertase (HcAlkIN1) and sucrose synthase (HcSUS1)], were isolated. The partial sequences were characterized by comparison with sequences available in the literature, and phylogenetic trees were assembled. Gene expression was evaluated at intervals of 6 h during 24 h in cotyledons, hypocotyl, roots, and leaves, using 45-d-old plantlets. HcXTH1 and HcBGAL1 were correlated to xyloglucan degradation and responded to auxin and light, being down-regulated when transport of auxin was prevented by N-1-naphthylphthalamic acid (NPA) and stimulated by constant light. Genes related to sucrose metabolism, HcAlkIN1 and HcSUS1, responded to inhibition of auxin transport in consonance with storage mobilization in the cotyledons. A model is proposed suggesting that auxin and light are involved in the control of the expression of genes related to storage xyloglucan mobilization in seedlings of H. courbaril. It is concluded that gene expression plays a role in the control of the intercommunication system of the source–sink relationship during seeding growth, favouring its establishment in the shaded environment of the rain forest understorey

Acute interaction between hydrocortisone and insulin alters the plasma metabolome in humans

With the aim of identifying biomarkers of glucocorticoid action and their relationship with biomarkers of insulin action, metabolomic profiling was carried out in plasma samples from twenty healthy men who were administered either a low or medium dose insulin infusion (n = 10 each group). In addition, all subjects were given metyrapone (to inhibit adrenal cortisol secretion) +/-hydrocortisone (HC) in a randomised crossover design to produce low, medium and high glucocorticoid levels. The clearest effects of insulin were to reduce plasma levels of the branched chain amino acids (BCAs) leucine/isoleucine and their deaminated metabolites, and lowered free fatty acids and acylcarnitines. The highest dose of hydrocortisone increased plasma BCAs in both insulin groups but increased free fatty acids only in the high insulin group, however hydrocortisone did not affect the levels of acyl carnitines in either group. The clearest interaction between HC and insulin was that hydrocortisone produced an elevation in levels of BCAs and their metabolites which were lowered by insulin. The direct modulation of BCAs by glucocorticoids and insulin may provide the basis for improved in vivo monitoring of glucocorticoid and insulin action

The 17 March 2013 storm: Synergy of observations related to electric field modes and their ionospheric and magnetospheric Effects

The main phase of the 17 March 2013 storm had excellent coverage from groundâ based instruments and from lowâ and highâ altitude spacecraft, allowing for evaluation of the relations between major storm time phenomena that are often considered separately. The shock impact with its concurrent southward interplanetary magnetic field (IMF) immediately drove dramatic poleward expansion of the poleward boundary of the auroral oval (implying strong nightside reconnection), strong auroral activity, and strong penetrating midlatitude convection and ionospheric currents. This was followed by periods of southward IMF driving of electric fields that were at first relatively smooth as often employed in storm modeling but then became extremely bursty and structured associated with equatorward extending auroral streamers. The auroral oval did not expand much further poleward during these two latter periods, suggesting a lower overall nightside reconnection rate than that during the first period and approximate balance with dayside reconnection. Characteristics of these three modes of driving were reflected in horizontal and fieldâ aligned currents. Equatorward expansion of the auroral oval occurred predominantly during the structured convection mode, when electric fields became extremely bursty. The period of this third mode also approximately corresponded to the time of largest equatorward motion of the ionospheric trough, of apparent transport of high total electron content (TEC) features into the auroral oval from the polar cap, and of largest earthward injection of ions and electrons into the ring current. The enhanced responses of the aurora, currents, TEC, and the ring current indicate a common driving of all these storm time features during the bursty convection mode period.Key PointsStorm had excellent ground/space data coverage, allowing evaluation of relations between major storm phenomena often considered separatelyIdentified three southward IMF electric fields driving modes that were reflected in the aurora and ionospheric and fieldâ aligned currentsThe third mode was extremely bursty, giving common driving of auroral and current structures, TEC changes, and ring current injectionPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135355/1/jgra53033_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135355/2/jgra53033.pd