Regulatory Effects of the E. coli RecBCD Nuclease Domain on DNA Unwinding Kinetics

I have examined the effects of deleting the nuclease domain of the E. coli helicase RecBCD on the rates of ATP-independent DNA melting, single stranded (ss) DNA translocation, and double stranded (ds) DNA unwinding by RecBCD. The canonical role of the nuclease domain is DNA degradation, but the removal of this domain showed unexpected effects on other RecBCD activities including DNA binding, melting, and unwinding. This thesis presents a mechanistic study of DNA unwinding by RecBCD and a RecBCD variant with the nuclease domain deleted (RecBΔnucCD). I examined the rates of ssDNA translocation and dsDNA unwinding by RecBCD and RecBΔnucCD using fluorescence stopped-flow assays. Deletion of the nuclease domain does not significantly affect the rate of ssDNA translocation in either the 3’ to 5’ or 5’ to 3’ directions but slows the rate of dsDNA unwinding by 25-45%. These results are consistent with a model in which RecBCD unwinds dsDNA through iterations of binding free energy-driven ATP-independent DNA base pair melting and ATP hydrolysis driven ssDNA translocation along the melted base pairs. Slower unwinding by RecBΔnucCD is likely due to an effect on its ability to destabilize or melt the duplex DNA. I also examined the ability of RecBCD and RecBΔnucCD to initiate unwinding from DNA with blunt, partially pre-melted or fully pre-melted ends using fluorescence stopped-flow experiments. I found that RecBCD is able to initiate efficiently from all DNA end types. The rates of unwinding initiation by RecBΔnucCD, however, are up to 10-fold slower than RecBCD and are sensitive to DNA end type. Additionally, deletion of the nuclease domain decreases the fraction of initially productive RecBCD-DNA complexes. These results suggest DNA melting is necessary for efficient initiation of DNA unwinding, and the slow initiation by RecBΔnucCD emphasizes that the deletion of the nuclease domain decreases DNA melting by RecBCD. I also present preliminary single molecule total internal reflection fluorescence experiments designed to directly examine the extent and dynamics of ATP-independent DNA melting by RecBCD and RecBΔnucCD. These results were difficult to analyze and interpret due in large part to Cy3 protein induced fluorescence enhancement (PIFE) upon binding of RecBCD, which is then transferred to Cy5 via FRET. We, therefore, turned to ensemble fluorescence binding experiments to better understand the nature of the fluorescence signals that were observed in the smTIRF experiments. Results of these experiments suggest that using Cy5 and black hole quencher to label DNA may be a viable labeling scheme for measuring DNA melting by RecBCD. Additionally, careful fluorophore placement and fluorescence calibrations and corrections will be necessary to measure DNA melting. Combined, my results indicate that the nuclease domain has a role in regulating dsDNA unwinding and initiation, possibly through DNA melting and allosteric interactions within RecBCD

Intrinsically Disordered C-Terminal Tails of \u3cem\u3eE. coli\u3c/em\u3e Single-Stranded DNA Binding Protein Regulate Cooperative Binding to Single-Stranded DNA

The homotetrameric Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA replication, repair and recombination. E. coli SSB can bind to long single-stranded DNA (ssDNA) in multiple binding modes using all four subunits [(SSB)65 mode] or only two subunits [(SSB)35 binding mode], with the binding mode preference regulated by salt concentration and SSB binding density. These binding modes display very different ssDNA binding properties with the (SSB)35 mode displaying highly cooperative binding to ssDNA. SSB tetramers also bind an array of partner proteins, recruiting them to their sites of action. This is achieved through interactions with the last 9 amino acids (acidic tip) of the intrinsically disordered linkers (IDLs) within the four C-terminal tails connected to the ssDNA binding domains. Here, we show that the amino acid composition and length of the IDL affects the ssDNA binding mode preferences of SSB protein. Surprisingly, the number of IDLs and the lengths of individual IDLs together with the acidic tip contribute to highly cooperative binding in the (SSB)35 binding mode. Hydrodynamic studies and atomistic simulations suggest that the E. coli SSB IDLs show a preference for forming an ensemble of globular conformations, whereas the IDL from Plasmodium falciparum SSB forms an ensemble of more extended random coils. The more globular conformations correlate with cooperative binding

Sunitinib in patients with pre-treated pancreatic neuroendocrine tumors: A real-world study

Introduction: Besides data reported in a Phase-III trial, data on sunitinib in pancreatic Neuroendocrine Tumors (panNETs) are scanty. Aim: To evaluate sunitinib efficacy and tolerability in panNETs patients treated in a real-world setting. Patients and methods: Retrospective analysis of progressive panNETs treated with sunitinib. Efficacy was assessed by evaluating progression-free survival, overall survival, and disease control (DC) rate (stable disease (SD) + partial response + complete response). Data are reported as median (25th\ue2\u80\u9375th IQR). Results: Eighty patients were included. Overall, 71.1% had NET G2, 26.3% had NET G1, and 2.6% had NET G3 neoplasms. A total of 53 patients (66.3%) had received three or more therapeutic regimens before sunitinib, with 24 patients (30%) having been treated with four previous treatments. Median PFS was 10 months. Similar risk of progression was observed between NET G1 and NET G2 tumors (median PFS 11 months and 8 months, respectively), and between patients who had received \ue2\u89\ua5 3 vs \ue2\u89\ua4 2 therapeutic approaches before sunitinib (median PFS 9 months and 10 months, respectively). DC rate was 71.3% and SD was the most frequent observed response, occurring in 43 pts (53.8%). Overall, 59 pts (73.8%) experienced AEs, which were grade 1\ue2\u80\u932 in 43 of them (72.9%), grade 3 in 15 pts (25.4%), and grade 4 in one patient (1.7%). Six pts (7.5%) stopped treatment due to toxicity. Conclusions: The present real-world experience shows that sunitinib is a safe and effective treatment for panNETs, even in the clinical setting of heavily pre-treated, progressive diseases

Multidimensional Model of Racial Identity: A Reconceptualization of African American Racial Identity

Research on African American racial identity has utilized 2 distinct approaches. The mainstream approach has focused on universal properties associated with ethnic and racial identities. In contrast, the underground approach has focused on documenting the qualitative meaning of being African American, with an emphasis on the unique cultural and historical experiences of African Americans. The Multidimensional Model of Racial Identity (MMRI) represents a synthesis of the strengths of these two approaches. The underlying assumptions associated with the model are explored. The model proposes 4 dimensions of African American racial identity: salience, centrality, regard, and ideology. A description of these dimensions is provided along with a discussion of how they interact to influence behavior at the level of the event. We argue that the MMRI has the potential to make contributions to traditional research objectives of both approaches, as well as to provide the impetus to explore new questions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68695/2/10.1207_s15327957pspr0201_2.pd

Neuron-oligodendrocyte potassium shuttling at nodes of Ranvier protects against

Multiple sclerosis (MS) is a progressive inflammatory demyelinating disease of the CNS. Increasing evidence suggests that vulnerable neurons in MS exhibit fatal metabolic exhaustion over time, a phenomenon hypothesized to be caused by chronic hyperexcitability. Axonal Kv7 (outward-rectifying) and oligodendroglial Kir4.1 (inward-rectifying) potassium channels have important roles in regulating neuronal excitability at and around the nodes of Ranvier. Here, we studied the spatial and functional relationship between neuronal Kv7 and oligodendroglial Kir4.1 channels and assessed the transcriptional and functional signatures of cortical and retinal projection neurons under physiological and inflammatory demyelinating conditions. We found that both channels became dysregulated in MS and experimental autoimmune encephalomyelitis (EAE), with Kir4.1 channels being chronically downregulated and Kv7 channel subunits being transiently upregulated during inflammatory demyelination. Further, we observed that pharmacological Kv7 channel opening with retigabine reduced neuronal hyperexcitability in human and EAE neurons, improved clinical EAE signs, and rescued neuronal pathology in oligodendrocyte-Kir4.1-deficient (OL-Kir4.1-deficient) mice. In summary, our findings indicate that neuron-OL compensatory interactions promoted resilience through Kv7 and Kir4.1 channels and identify pharmacological activation of nodal Kv7 channels as a neuroprotective strategy against inflammatory demyelination

Anxiety and avoidance in psychogenic nonepileptic seizures: the role of implicit and explicit anxiety

This study examined implicit and explicit anxiety in individuals with epilepsy and psychogenic nonepileptic seizures (PNESs) and explored whether these constructs were related to experiential avoidance and seizure frequency. Based on recent psychological models of PNESs, it was hypothesized that nonepileptic seizures would be associated with implicit and explicit anxiety and experiential avoidance. Explicit anxiety was measured by the State-Trait Anxiety Inventory; implicit anxiety was measured by an Implicit Relational Assessment Procedure; and experiential avoidance was measured with the Multidimensional Experiential Avoidance Questionnaire. Although both groups with epilepsy and PNESs scored similarly on implicit measures of anxiety, significant implicit–explicit anxiety discrepancies were only identified in patients with PNESs (p < .001). In the group with PNESs (but not in the group with epilepsy), explicit anxiety correlated with experiential avoidance (r = .63, p < .01) and frequency of seizures (r = .67, p < .01); implicit anxiety correlated with frequency of seizures only (r = .56, p < .01). Our findings demonstrate the role of implicit anxiety in PNESs and provide additional support for the contribution of explicit anxiety and experiential avoidance to this disorder

Cluster Lensing And Supernova survey with Hubble (CLASH): An Overview

The Cluster Lensing And Supernova survey with Hubble (CLASH) is a 524-orbit multi-cycle treasury program to use the gravitational lensing properties of 25 galaxy clusters to accurately constrain their mass distributions. The survey, described in detail in this paper, will definitively establish the degree of concentration of dark matter in the cluster cores, a key prediction of CDM. The CLASH cluster sample is larger and less biased than current samples of space-based imaging studies of clusters to similar depth, as we have minimized lensing-based selection that favors systems with overly dense cores. Specifically, twenty CLASH clusters are solely X-ray selected. The X-ray selected clusters are massive (kT > 5 keV; 5 - 30 x 10^14 M_solar) and, in most cases, dynamically relaxed. Five additional clusters are included for their lensing strength (Einstein radii > 35 arcsec at z_source = 2) to further quantify the lensing bias on concentration, to yield high resolution dark matter maps, and to optimize the likelihood of finding highly magnified high-redshift (z > 7) galaxies. The high magnification, in some cases, provides angular resolutions unobtainable with any current UVOIR facility and can yield z > 7 candidates bright enough for spectroscopic follow-up. A total of 16 broadband filters, spanning the near-UV to near-IR, are employed for each 20-orbit campaign on each cluster. These data are used to measure precise (sigma_phz < 0.02(1+z)) photometric redshifts for dozens of newly discovered multiply-lensed images per cluster. Observations of each cluster are spread over 8 epochs to enable a search, primarily in the parallel fields, for Type Ia supernovae at z > 1 to improve constraints on the time dependence of the dark energy equation of state and the evolution of such supernovae in an epoch when the universe is matter dominated.Comment: Accepted for publication in the Astrophysical Journal Supplements, 22 pages, 16 figures. Updated Tables 3,4,8 and figures 6 and 8 to reflect replacement of Abell 963 with Abell 1423 in CLASH survey. A963 cannot be observed with WFC3 due to the lack of usable guide star

Rare germline copy number variants (CNVs) and breast cancer risk.

Funder: CIHRGermline copy number variants (CNVs) are pervasive in the human genome but potential disease associations with rare CNVs have not been comprehensively assessed in large datasets. We analysed rare CNVs in genes and non-coding regions for 86,788 breast cancer cases and 76,122 controls of European ancestry with genome-wide array data. Gene burden tests detected the strongest association for deletions in BRCA1 (P = 3.7E-18). Nine other genes were associated with a p-value < 0.01 including known susceptibility genes CHEK2 (P = 0.0008), ATM (P = 0.002) and BRCA2 (P = 0.008). Outside the known genes we detected associations with p-values < 0.001 for either overall or subtype-specific breast cancer at nine deletion regions and four duplication regions. Three of the deletion regions were in established common susceptibility loci. To the best of our knowledge, this is the first genome-wide analysis of rare CNVs in a large breast cancer case-control dataset. We detected associations with exonic deletions in established breast cancer susceptibility genes. We also detected suggestive associations with non-coding CNVs in known and novel loci with large effects sizes. Larger sample sizes will be required to reach robust levels of statistical significance

Relapses and treatment-related events contributed equally to poor prognosis in children with ABL-class fusion positive B-cell acute lymphoblastic leukemia treated according to AIEOP-BFM protocols

ABL-class fusions other than BCR-ABL1 characterize around 2–3% of precursor B-cell acute lymphoblastic leukemia. Case series indicated that patients suffering from these subtypes have a dismal outcome and may benefit from the introduction of tyrosine kinase inhibitors. We analyzed clinical characteristics and outcome of 46 ABL-class fusion positive cases other than BCR-ABL1 treated according to AIEOP-BFM (Associazione Italiana di Ematologia-Oncologia Pediatrica-Berlin-Frankfurt-Münster) ALL 2000 and 2009 protocols; 13 of them received a tyrosine kinase inhibitor (TKI) during different phases of treatment. ABL-class fusion positive cases had a poor early treatment response: minimal residual disease levels of ≥5×10−4 were observed in 71.4% of patients after induction treatment and in 51.2% after consolidation phase. For the entire cohort of 46 cases, the 5-year probability of event-free survival was 49.1+8.9% and that of overall survival 69.6+7.8%; the cumulative incidence of relapse was 25.6+8.2% and treatment-related mortality (TRM) 20.8+6.8%. One out of 13 cases with TKI added to chemotherapy relapsed while eight of 33 cases without TKI treatment suffered from relapse, including six in 17 patients who had not received hematopoietic stem cell transplantation. Stem cell transplantation seems to be effective in preventing relapses (only three relapses in 25 patients), but was associated with a very high TRM (6 patients). These data indicate a major need for an early identification of ABL-class fusion positive acute lymphoblastic leukemia cases and to establish a properly designed, controlled study aimed at investigating the use of TKI, the appropriate chemotherapy backbone and the role of hematopoietic stem cell transplantation. (Registered at: clinicaltrials.gov identifier: NTC00430118, NCT00613457, NCT01117441)