Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses

Peer reviewedPublisher PD

A Complete Year of User Retrieval Sessions in a Social Sciences Academic Search Engine

In this paper, we present an open data set extracted from the transaction log of the social sciences academic search engine sowiport. The data set includes a filtered set of 484,449 retrieval sessions which have been carried out by sowiport users in the period from April 2014 to April 2015. We propose a description of interactions performed by the academic search engine users that can be used in different applications such as result ranking improvement, user modeling, query reformulation analysis, search pattern recognition.Comment: 6 pages, 2 figures, accepted short paper at the 21st International Conference on Theory and Practice of Digital Libraries (TPDL 2017

Event Structure at RHIC from p-p to Au-Au

Several correlation analysis techniques are applied to p-p and Au-Au collisions at RHIC. Strong large-momentum-scale correlations are observed which can be related to local charge and momentum conservation during hadronization and to minijet (minimum-bias parton fragment) correlations.Comment: 6 pages, 6 figures, 20th Winter Workshop on Nuclear Dynamics, Trelawny Beach, Jamaica, March 15-20, 200

BORIS/CTCFL is an RNA-binding protein that associates with polysomes

© 2013 Ogunkolade et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

An alternative approach to using LiDAR remote sensing data to predict stem diameter distributions across a temperate forest landscape

© 2017 by the authors. We apply a spatially-implicit, allometry-based modelling approach to predict stem diameter distributions (SDDs) from low density airborne LiDAR data in a heterogeneous, temperate forest in Ontario, Canada. Using a recently published algorithm that relates the density, size, and species of individual trees to the height distribution of first returns, we estimated parameters that succinctly describe SDDs that are most consistent with each 0.25-ha LiDAR tile across a 30,000 ha forest landscape. Tests with independent validation plots showed that the diameter distribution of stems was predicted with reasonable accuracy in most cases (half of validation plots had R2 ≥ 0.75, and another 23% had 0.5 ≤ R2 < 0.75). The predicted frequency of larger stems was much better than that of small stems (8 ≤ x < 11 cm diameter), particularly small conifers. We used the predicted SDDs to calculate aboveground carbon density (ACD; RMSE = 21.4 Mg C/ha), quadratic mean diameter (RMSE = 3.64 cm), basal area (RMSE = 6.99 m2/ha) and stem number (RMSE = 272 stems/ha). The accuracy of our predictions compared favorably with previous studies that have generally been undertaken in simpler conifer-dominated forest types. We demonstrate the utility of our results to spatial forest management planning by mapping SDDs, the proportion of broadleaves, and ACD at a 0.25 ha resolution

Methylated DNA recognition during the reversal of epigenetic silencing is regulated by cysteine and cerine residues in the Epstein-Barr Virus lytic switch protein

Epstein-Barr virus (EBV) causes infectious mononucleosis and is associated with various malignancies, including Burkitt's lymphoma and nasopharyngeal carcinoma. Like all herpesviruses, the EBV life cycle alternates between latency and lytic replication. During latency, the viral genome is largely silenced by host-driven methylation of CpG motifs and, in the switch to the lytic cycle, this epigenetic silencing is overturned. A key event is the activation of the viral BRLF1 gene by the immediate-early protein Zta. Zta is a bZIP transcription factor that preferentially binds to specific response elements (ZREs) in the BRLF1 promoter (Rp) when these elements are methylated. Zta's ability to trigger lytic cycle activation is severely compromised when a cysteine residue in its bZIP domain is mutated to serine (C189S), but the molecular basis for this effect is unknown. Here we show that the C189S mutant is defective for activating Rp in a Burkitt's lymphoma cell line. The mutant is compromised both in vitro and in vivo for binding two methylated ZREs in Rp (ZRE2 and ZRE3), although the effect is striking only for ZRE3. Molecular modeling of Zta bound to methylated ZRE3, together with biochemical data, indicate that C189 directly contacts one of the two methyl cytosines within a specific CpG motif. The motif's second methyl cytosine (on the complementary DNA strand) is predicted to contact S186, a residue known to regulate methyl-ZRE recognition. Our results suggest that C189 regulates the enhanced interaction of Zta with methylated DNA in overturning the epigenetic control of viral latency. As C189 is conserved in many bZIP proteins, the selectivity of Zta for methylated DNA may be a paradigm for a more general phenomenon