Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1

In eukaryotic Okazaki fragment processing, the RNA primer is displaced into a single-stranded flap prior to removal. Evidence suggests that some flaps become long before they are cleaved, and that this cleavage involves the sequential action of two nucleases. Strand displacement characteristics of the polymerase show that a short gap precedes the flap during synthesis. Using biochemical techniques, binding and cleavage assays presented here indicate that when the flap is ∼30 nt long the nuclease Dna2 can bind with high affinity to the flap and downstream double strand and begin cleavage. When the polymerase idles or dissociates the Dna2 can reorient for additional contacts with the upstream primer region, allowing the nuclease to remain stably bound as the flap is further shortened. The DNA can then equilibrate to a double flap that can bind Dna2 and flap endonuclease (FEN1) simultaneously. When Dna2 shortens the flap even more, FEN1 can displace the Dna2 and cleave at the flap base to make a nick for ligation

Distributed intelligence in pedestrian simulations

In order to accurately simulate pedestrian behaviour in complex situations, one is required to model both the physical environment and the strategic decision-making of individuals We present a method for integrating both of these model requirements, by distributing the computational complexity across discrete modules. These modules communicate with each other via XML messages. The approach also provides considerable flexibility for changing and evolving the model. The model is explained using an example of simulating hikers in the Swiss Alps.SNF, NFP 48, Habitats and Landscapes of the Alp

Programmed death-ligand 1 (PD-L1) expression in primary gastric adenocarcinoma and matched metastases.

BACKGROUND Combination of immunotherapy and chemotherapy is recommended for first line treatment of gastric adenocarcinoma (GC) patients with locally advanced unresectable disease or metastatic disease. However, data regarding the concordance rate between PD-L1 combined positive score (CPS) in primary GC and matched regional lymph node metastasis (LNmet) or matched distant metastasis (Dmet) is limited. METHODS Tissue microarray sections from primary resected GC, LNmet and Dmet were immunohistochemically stained with anti-PD-L1 (clone SP263). PD-L1 expression was scored separately in tumour cells and immune cells and compared between matched primary GC, LNmet and/or Dmet. CPS was calculated and results for CPS cut-offs 1 and 5 were compared between matched samples. RESULTS 275 PD-L1 stained GC were analysed. 189 primary GC had matched LNmet. CPS cut-off 1 concordance rate between primary GC and LNmet was 77%. 23 primary GC had matched Dmet but no matched LNmet, CPS cut-off 1 concordance rate was 70%. 63 primary GC had both matched LNmet and matched Dmet, CPS cut-off 1 concordance rate of 67%. CPS cut-off 5 results were similar. The proportion of PD-L1 positive tumour cells increased from primary GC (26%) to LNmet (42%) and was highest in Dmet (75%). CONCLUSION Our study showed up to 33% discordance of PD-L1 CPS between primary GC and LNmet and/or Dmet suggesting that multiple biopsies of primary GC and metastatic sites might need to be tested before considering treatment options. Moreover, this is the first study that seems to suggest that tumour cells acquire PD-L1 expression during disease progression

Size and frequency of natural forest disturbances and Amazon carbon balance

Forest inventory studies in the Amazon indicate a large terrestrial carbon sink. However, field plots may fail to represent forest mortality processes at landscape-scales of tropical forests. Here we characterize the frequency distribution of disturbance events in natural forests from 0.01 ha to 2,651 ha size throughout Amazonia using a novel combination of forest inventory, airborne lidar and satellite remote sensing data. We find that small-scale mortality events are responsible for aboveground biomass losses of B1.28 Pg C y 1 over the entire Amazon region. We also find that intermediate-scale disturbances account for losses of B0.01 Pg C y 1 , and that the largest-scale disturbances as a result of blow-downs only account for losses of B0.003 Pg C y 1 . Simulation of growth and mortality indicates that even when all carbon losses from intermediate and large-scale disturbances are considered, these are outweighed by the net biomass accumulation by tree growth, supporting the inference of an Amazon carbon sink

Questioning the Influence of Sunspots on Amazon Hydrology: Even a Broken Clock Tells the Right Time Twice a Day

It was suggested in a recent article that sunspots drive decadal variation in Amazon River flow. This conclusion was based on a novel time series decomposition method used to extract a decadal signal from the Amazon River record. We have extended this analysis back in time, using a new hydrological proxy record of tree ring oxygen isotopes (δ¹⁸OTR). Consistent with the findings of Antico and Torres, we find a positive correlation between sunspots and the decadal δ¹⁸OTR cycle from 1903 to 2012 (r = 0.60, p < 0.001). However, the relationship does not persist into the preceding century and even becomes weakly negative (r = −0.30, p = 0.11, 1799–1902). This result casts considerable doubt over the mechanism by which sunspots are purported to influence Amazon hydrology

Causal hierarchy within the thalamo-cortical network in spike and wave discharges

Background: Generalised spike wave (GSW) discharges are the electroencephalographic (EEG) hallmark of absence seizures, clinically characterised by a transitory interruption of ongoing activities and impaired consciousness, occurring during states of reduced awareness. Several theories have been proposed to explain the pathophysiology of GSW discharges and the role of thalamus and cortex as generators. In this work we extend the existing theories by hypothesizing a role for the precuneus, a brain region neglected in previous works on GSW generation but already known to be linked to consciousness and awareness. We analysed fMRI data using dynamic causal modelling (DCM) to investigate the effective connectivity between precuneus, thalamus and prefrontal cortex in patients with GSW discharges. Methodology and Principal Findings: We analysed fMRI data from seven patients affected by Idiopathic Generalized Epilepsy (IGE) with frequent GSW discharges and significant GSW-correlated haemodynamic signal changes in the thalamus, the prefrontal cortex and the precuneus. Using DCM we assessed their effective connectivity, i.e. which region drives another region. Three dynamic causal models were constructed: GSW was modelled as autonomous input to the thalamus (model A), ventromedial prefrontal cortex (model B), and precuneus (model C). Bayesian model comparison revealed Model C (GSW as autonomous input to precuneus), to be the best in 5 patients while model A prevailed in two cases. At the group level model C dominated and at the population-level the p value of model C was ∼1. Conclusion: Our results provide strong evidence that activity in the precuneus gates GSW discharges in the thalamo-(fronto) cortical network. This study is the first demonstration of a causal link between haemodynamic changes in the precuneus - an index of awareness - and the occurrence of pathological discharges in epilepsy. © 2009 Vaudano et al

Glycerol accelerates recovery of barrier function in vivo.

Two studies were performed to evaluate the influence of glycerolon the recovery of damaged stratum corneum barrier function.Measurements of transepidermal water loss and capacitancewere conducted in a 3-day follow-up after tape stripping (study1) and a 7-day follow-up after a barrier damage due to arepeated washing with sodium lauryl sulphate. In study 1 afaster barrier repair (transepidermal water loss) was monitoredin glycerol-treated sites. Significant differences between glycerolopen vs. untreated and glycerol occluded vs. untreated wereobserved at day 3. Stratum corneum hydration showedsignificantly higher values in the sites treated with glycer-olzocclusion, compared with all other sites. In study 2 a fasterbarrier repair was seen in glycerol-treated sites, with significantdifferences against untreated and base-treated sites 7 days afterthe end of the treatment. Stratum corneum hydration showedhighest values in the glycerol treated sites after 3 days oftreatment. Glycerol creates a stimulus for barrier repair andimproves the stratum corneum hydration; stratum corneumhydration is not strictly related to barrier homeostasis and canbe optimized by different mechanisms and pathways. Theobserved effects were based on the modulation of barrier repairand were not biased by the humectant effect of glycerol. As theglycerol-induced recovery of barrier function and stratumcorneum hydration were observed even 7 days after the endof treatment, glycerol can be regarded as a barrier stabilizingand moisturizing compound. Key words: tape stripping; SLSwashing; transepidermal water loss (TEWL); capacitance;occlusion; barrier repair.(Accepted May 19, 1999.)Acta Derm Venereol 1999; 79: 418–421.Joachim Fluhr, Department of Dermatology, KarlsruheHospital, Sta¨dt. Klinikum, Moltkestrasse 120, D-76133Karlsruhe, Germany.The mechanisms promoting barrier repair in vivo afterstripping of the stratum corneum (SC) and repeated irritationwith sodium lauryl sulphate (SLS) are not completely clear:the modulation of water flux is probably a key factor involvedin barrier repair (1–7). It is known, that glycerol represents ahygroscopic compound capable of absorbing water from theenvironment and deeper parts of the SC.The purpose of the present study was to evaluate in vivothe effects of glycerol and occlusion in the promotion ofbarrier repair. Two studies were performed to evaluate theeffect of a repeated application of glycerol on damaged SCbarrier. The barrier disruption was performed by tapestripping (study 1) and by repeated washing with SLS over4 days (study 2).MATERIALS AND METHOD

What drives interannual variation in tree ring oxygen isotopes in the Amazon?

Oxygen isotope ratios in tree rings (δ18OTR) from northern Bolivia record local precipitation δ18O and correlate strongly with Amazon basin-wide rainfall. While this is encouraging evidence that δ18OTR can be used for palaeoclimate reconstructions, it remains unclear whether variation in δ18OTR is truly driven by within-basin processes, thus recording Amazon climate directly, or if the isotope signal may already be imprinted on incoming vapour, perhaps reflecting a pan-tropical climate signal. We use atmospheric back-trajectories combined with satellite observations of precipitation, together with water vapour transport analysis to show that δ18OTR in Bolivia are indeed controlled by basin-intrinsic processes, with rainout over the basin the most important factor. Furthermore, interannual variation in basin-wide precipitation and atmospheric circulation are both shown to affect δ18OTR. These findings suggest δ18OTR can be reliably used to reconstruct Amazon precipitation, and have implications for the interpretation of other palaeoproxy records from the Amazon basin