Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK.

Short-patch repair of DNA single-strand breaks and gaps (SSB) is coordinated by XRCC1, a scaffold protein that recruits the DNA polymerase and DNA ligase required for filling and sealing the damaged strand. XRCC1 can also recruit end-processing enzymes, such as PNK (polynucleotide kinase 3'-phosphatase), Aprataxin and APLF (aprataxin/PNK-like factor), which ensure the availability of a free 3'-hydroxyl on one side of the gap, and a 5'-phosphate group on the other, for the polymerase and ligase reactions respectively. PNK binds to a phosphorylated segment of XRCC1 (between its two C-terminal BRCT domains) via its Forkhead-associated (FHA) domain. We show here, contrary to previous studies, that the FHA domain of PNK binds specifically, and with high affinity to a multiply phosphorylated motif in XRCC1 containing a pSer-pThr dipeptide, and forms a 2:1 PNK:XRCC1 complex. The high-resolution crystal structure of a PNK-FHA-XRCC1 phosphopeptide complex reveals the basis for this unusual bis-phosphopeptide recognition, which is probably a common feature of the known XRCC1-associating end-processing enzymes

Expressed in the yeast Saccharomyces cerevisiae, human ERK5 is a client of the Hsp90 chaperone that complements loss of the Slt2p (Mpk1p) cell integrity stress-activated protein kinase

ERK5 is a mitogen-activated protein (MAP) kinase regulated in human cells by diverse mitogens and stresses but also suspected of mediating the effects of a number of oncogenes. Its expression in the slt2Delta Saccharomyces cerevisiae mutant rescued several of the phenotypes caused by the lack of Slt2p (Mpk1p) cell integrity MAP kinase. ERK5 is able to provide this cell integrity MAP kinase function in yeast, as it is activated by the cell integrity signaling cascade that normally activates Slt2p and, in its active form, able to stimulate at least one key Slt2p target (Rlm1p, the major transcriptional regulator of cell wall genes). In vitro ERK5 kinase activity was abolished by Hsp90 inhibition. ERK5 activity in vivo was also lost in a strain that expresses a mutant Hsp90 chaperone. Therefore, human ERK5 expressed in yeast is an Hsp90 client, despite the widely held belief that the protein kinases of the MAP kinase class are non-Hsp90-dependent activities. Two-hybrid and protein binding studies revealed that strong association of Hsp90 with ERK5 requires the dual phosphorylation of the TEY motif in the MAP kinase activation loop. These phosphorylations, at positions adjacent to the Hsp90-binding surface recently identified for a number of protein kinases, may cause a localized rearrangement of this MAP kinase region that leads to creation of the Hsp90-binding surface. Complementation of the slt2Delta yeast defect by ERK5 expression establishes a new tool with which to screen for novel agonists and antagonists of ERK5 signaling as well as for isolating mutant forms of ERK5

Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2.

Poly(ADP-ribose) polymerase-1 (PARP-1) has become an important pharmacological target in the treatment of cancer due to its cellular role as a 'DNA-strand break sensor', which leads in part to resistance to some existing chemo- and radiological treatments. Inhibitors have now been developed which prevent PARP-1 from synthesizing poly(ADP-ribose) in response to DNA-breaks and potentiate the cytotoxicity of DNA damaging agents. However, with the recent discoveries of PARP-2, which has a similar DNA-damage dependent catalytic activity, and additional members containing the 'PARP catalytic' signature, the isoform selectivity and resultant pharmacological effects of existing inhibitors are brought into question. We present here the crystal structure of the catalytic fragment of murine PARP-2, at 2.8 A resolution, and compare this to the catalytic fragment of PARP-1, with an emphasis on providing a possible framework for rational drug design in order to develop future isoform-specific inhibitors

The sensitivity of land emissivity estimates from AMSR-E at C and X bands to surface properties

Microwave observations at low frequencies exhibit more sensitivity to surface and subsurface properties with little interference from the atmosphere. The objective of this study is to develop a global land emissivity product using passive microwave observations from the Advanced Microwave Scanning Radiometer – Earth Observing System (AMSR-E) and to investigate its sensitivity to land surface properties. The developed product complements existing land emissivity products from SSM/I and AMSU by adding land emissivity estimates at two lower frequencies, 6.9 and 10.65 GHz (C- and X-band, respectively). Observations at these low frequencies penetrate deeper into the soil layer. Ancillary data used in the analysis, such as surface skin temperature and cloud mask, are obtained from International Satellite Cloud Climatology Project (ISCCP). Atmospheric properties are obtained from the TIROS Operational Vertical Sounder (TOVS) observations to determine the small upwelling and downwelling atmospheric emissions as well as the atmospheric transmission. A sensitivity test confirms the small effect of the atmosphere but shows that skin temperature accuracy can significantly affect emissivity estimates. Retrieved emissivities at C- and X-bands and their polarization differences exhibit similar patterns of variation with changes in land cover type, soil moisture, and vegetation density as seen at SSM/I-like frequencies (Ka and Ku bands). The emissivity maps from AMSR-E at these higher frequencies agree reasonably well with the existing SSM/I-based product. The inherent discrepancy introduced by the difference between SSM/I and AMSR-E frequencies, incidence angles, and calibration has been assessed. Significantly greater standard deviation of estimated emissivities compared to SSM/I land emissivity product was found over desert regions. Large differences between emissivity estimates from ascending and descending overpasses were found at lower frequencies due to the inconsistency between thermal IR skin temperatures and passive microwave brightness temperatures which can originate from below the surface. The mismatch between day and night AMSR-E emissivities is greater than ascending and descending differences of SSM/I emissivity. This is because of unique orbit time of AMSR-E (01:30 a.m./p.m. LT) while other microwave sensors have orbit time of 06:00 to 09:00 (a.m./p.m.). This highlights the importance of considering the penetration depth of the microwave signal and diurnal variability of the temperature in emissivity retrieval. The effect of these factors is greater for AMSR-E observations than SSM/I observations, as AMSR-E observations exhibit a greater difference between day and night measures. This issue must be addressed in future studies to improve the accuracy of the emissivity estimates especially at AMSR-E lower frequencies

Thinking About Causation : A Causal Language with Epistemic Operators

In this paper we propose a formal framework for modeling the interaction of causal and (qualitative) epistemic reasoning. To this purpose, we extend the notion of a causal model [11, 16, 17, 26] with a representation of the epistemic state of an agent. On the side of the object language, we add operators to express knowledge and the act of observing new information. We provide a sound and complete axiomatization of the logic, and discuss the relation of this framework to causal team semantics.Peer reviewe

Child–Adult Relationship Enhancement (CARE): An evidence-informed program for children with a history of trauma and other behavioral challenges

Child maltreatment impacts approximately two million children each year, with physical abuse and neglect the most common form of maltreatment. These children are at risk for mental and physical health concerns and the ability to form positive social relationships is also adversely affected. Child Adult Relationship Enhancement (CARE) is a set of skills designed to improve interactions of any adult and child or adolescent. Based on parent training programs, including the strong evidence-based treatment, Parent-Child Interaction Therapy (PCIT), CARE was initially developed to fill an important gap in mental health services for children of any age who are considered at-risk for maltreatment or other problems. CARE subsequently has been extended for use by adults who interact with children and youth outside of existing mental health therapeutic services as well as to compliment other services the child or adolescent may be receiving. Developed through discussions with Parent-Child Interaction Therapy (PCIT) therapists and requests for a training similar to PCIT for the non-mental health professional, CARE is not therapy, but is comprised of a set of skills that can support other services provided to families. Since 2006, over 2000 caregivers, mental health, child welfare, educators, and other professionals have received CARE training with a focus on children who are exposed to trauma and maltreatment. This article presents implementation successes and challenges of a trauma-informed training designed to help adults connect and enhance their relationships with children considered at-risk

Phosphorylation-dependent assembly of DNA damage response systems and the central roles of TOPBP1

The cellular response to DNA damage (DDR) that causes replication collapse and/or DNA double strand breaks, is characterised by a massive change in the post-translational modifications (PTM) of hundreds of proteins involved in the detection and repair of DNA damage, and the communication of the state of damage to the cellular systems that regulate replication and cell division. A substantial proportion of these PTMs involve targeted phosphorylation, which among other effects, promotes the formation of multiprotein complexes through the specific binding of phosphorylated motifs on one protein, by specialised domains on other proteins. Understanding the nature of these phosphorylation mediated interactions allows definition of the pathways and networks that coordinate the DDR, and helps identify new targets for therapeutic intervention that may be of benefit in the treatment of cancer, where DDR plays a key role. In this review we summarise the present understanding of how phosphorylated motifs are recognised by BRCT domains, which occur in many DDR proteins. We particularly focus on TOPBP1 – a multi-BRCT domain scaffold protein with essential roles in replication and the repair and signalling of DNA damage

Robust Inference of Trees

This paper is concerned with the reliable inference of optimal tree-approximations to the dependency structure of an unknown distribution generating data. The traditional approach to the problem measures the dependency strength between random variables by the index called mutual information. In this paper reliability is achieved by Walley's imprecise Dirichlet model, which generalizes Bayesian learning with Dirichlet priors. Adopting the imprecise Dirichlet model results in posterior interval expectation for mutual information, and in a set of plausible trees consistent with the data. Reliable inference about the actual tree is achieved by focusing on the substructure common to all the plausible trees. We develop an exact algorithm that infers the substructure in time O(m^4), m being the number of random variables. The new algorithm is applied to a set of data sampled from a known distribution. The method is shown to reliably infer edges of the actual tree even when the data are very scarce, unlike the traditional approach. Finally, we provide lower and upper credibility limits for mutual information under the imprecise Dirichlet model. These enable the previous developments to be extended to a full inferential method for trees.Comment: 26 pages, 7 figure

Picturing classical and quantum Bayesian inference

We introduce a graphical framework for Bayesian inference that is sufficiently general to accommodate not just the standard case but also recent proposals for a theory of quantum Bayesian inference wherein one considers density operators rather than probability distributions as representative of degrees of belief. The diagrammatic framework is stated in the graphical language of symmetric monoidal categories and of compact structures and Frobenius structures therein, in which Bayesian inversion boils down to transposition with respect to an appropriate compact structure. We characterize classical Bayesian inference in terms of a graphical property and demonstrate that our approach eliminates some purely conventional elements that appear in common representations thereof, such as whether degrees of belief are represented by probabilities or entropic quantities. We also introduce a quantum-like calculus wherein the Frobenius structure is noncommutative and show that it can accommodate Leifer's calculus of `conditional density operators'. The notion of conditional independence is also generalized to our graphical setting and we make some preliminary connections to the theory of Bayesian networks. Finally, we demonstrate how to construct a graphical Bayesian calculus within any dagger compact category.Comment: 38 pages, lots of picture