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1.  Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding 
Cell host & microbe  2015;18(6):723-735.
SUMMARY
Several systems-level datasets designed to dissect host-pathogen interactions during influenza A infection have been reported. However, apparent discordance among these data has hampered their full utility toward advancing mechanistic and therapeutic knowledge. To collectively reconcile these datasets, we performed a meta-analysis of data from eight published RNAi screens and integrated these data with three protein interaction datasets, including one generated within the context of this study. Further integration of these data with global virus-host interaction analyses revealed a functionally validated biochemical landscape of the influenza-host interface, which can be queried through a simplified and customizable web portal (http://www.metascape.org/IAV). Follow-up studies revealed that the putative ubiquitin ligase UBR4 associates with the viral M2 protein and promotes apical transport of viral proteins. Taken together, the integrative analysis of influenza OMICs datasets illuminates a viral-host network of high-confidence human proteins that are essential for influenza A virus replication.
Graphical Abstract
doi:10.1016/j.chom.2015.11.002
PMCID: PMC4829074  PMID: 26651948
2.  Dust deposition on the decks of the Mars Exploration Rovers: 10 years of dust dynamics on the Panoramic Camera calibration targets 
Abstract
The Panoramic Cameras on NASA's Mars Exploration Rovers have each returned more than 17,000 images of their calibration targets. In order to make optimal use of this data set for reflectance calibration, a correction must be made for the presence of air fall dust. Here we present an improved dust correction procedure based on a two‐layer scattering model, and we present a dust reflectance spectrum derived from long‐term trends in the data set. The dust on the calibration targets appears brighter than dusty areas of the Martian surface. We derive detailed histories of dust deposition and removal revealing two distinct environments: At the Spirit landing site, half the year is dominated by dust deposition, the other half by dust removal, usually in brief, sharp events. At the Opportunity landing site the Martian year has a semiannual dust cycle with dust removal happening gradually throughout two removal seasons each year. The highest observed optical depth of settled dust on the calibration target is 1.5 on Spirit and 1.1 on Opportunity (at 601 nm). We derive a general prediction for dust deposition rates of 0.004 ± 0.001 in units of surface optical depth deposited per sol (Martian solar day) per unit atmospheric optical depth. We expect this procedure to lead to improved reflectance‐calibration of the Panoramic Camera data set. In addition, it is easily adapted to similar data sets from other missions in order to deliver improved reflectance calibration as well as data on dust reflectance properties and deposition and removal history.
Key Points
We present an improved method for dust‐correcting calibration target imagesThe maximum deposited optical depth is 1.5 for Spirit and 1.1 for OpportunityThe two MER landing sites exhibit very different dust histories
doi:10.1002/2014EA000073
PMCID: PMC5125412  PMID: 27981072
Mars; dust; calibration; reflectance; camera
3.  Asymmetric Synthesis of β-Amino Amides by Catalytic Enantioconvergent 2-Aza-Cope Rearrangement 
Journal of the American Chemical Society  2015;137(46):14574-14577.
Dynamic kinetic resolutions of α-stereogenic-β-formyl amides in asymmetric 2-aza-Cope rearrangements are described. Chiral phosphoric acids catalyze this rare example of a non-hydrogenative DKR of a β-oxo acid derivative. The [3,3]-rearrangement occurs with high diastereo- and enantiocontrol, forming β-imino amides that can be deprotected to the primary β-amino amide or reduced to the corresponding diamine.
doi:10.1021/jacs.5b09593
PMCID: PMC4661081  PMID: 26561873
4.  Discovery and SAR of Novel 2,3‐Dihydroimidazo[1,2‐c]quinazoline PI3K Inhibitors: Identification of Copanlisib (BAY 80‐6946) 
Chemmedchem  2016;11(14):1517-1530.
Abstract
The phosphoinositide 3‐kinase (PI3K) pathway is aberrantly activated in many disease states, including tumor cells, either by growth factor receptor tyrosine kinases or by the genetic mutation and amplification of key pathway components. A variety of PI3K isoforms play differential roles in cancers. As such, the development of PI3K inhibitors from novel compound classes should lead to differential pharmacological and pharmacokinetic profiles and allow exploration in various indications, combinations, and dosing regimens. A screening effort aimed at the identification of PI3Kγ inhibitors for the treatment of inflammatory diseases led to the discovery of the novel 2,3‐dihydroimidazo[1,2‐c]quinazoline class of PI3K inhibitors. A subsequent lead optimization program targeting cancer therapy focused on inhibition of PI3Kα and PI3Kβ. Herein, initial structure–activity relationship findings for this class and the optimization that led to the identification of copanlisib (BAY 80‐6946) as a clinical candidate for the treatment of solid and hematological tumors are described.
doi:10.1002/cmdc.201600148
PMCID: PMC5094563  PMID: 27310202
phosphoinositide 3-kinase; copanlisib; lipid kinases; PI3K inhibitors; X-ray crystallography
5.  Enantioselective reductive multicomponent coupling reactions between isatins and aldehydes† 
A metal-free stereoselective reductive coupling reaction between isatins and aldehydes is reported. The reaction relies on commercial diethyl phosphite (∼€70 kg−1) as the stoichiometric reductant. Base-catalyzed Pudovik addition and phosphonate/phosphate rearrangement achieved polarity inversion on the isatin, and the derived carbanions were trapped by aldehydes with subsequent dialkoxyphosphinyl migration. Chiral iminophosphoranes were used as basic catalysts to achieve high diastereo- and enantioselectivities with excellent yields.
doi:10.1039/C5SC02170G
PMCID: PMC4618493  PMID: 26508995
6.  Randomized Trial of Lenalidomide Alone Versus Lenalidomide Plus Rituximab in Patients With Recurrent Follicular Lymphoma: CALGB 50401 (Alliance) 
Journal of Clinical Oncology  2015;33(31):3635-3640.
Purpose
Lenalidomide and rituximab (LR) are active agents in follicular lymphoma (FL). Combination regimens have not been previously assessed in randomized studies.
Patients and Methods
The Cancer and Leukemia Group B (Alliance) 50401 trial is a randomized phase II trial studying rituximab (375 mg/m2 weekly for 4 weeks), lenalidomide (15 mg per day on days 1 to 21, followed by 7 days of rest, in cycle 1 and then 20 mg per day on days 1 to 21, followed by 7 days of rest, in cycles 2 to 12), or LR. The rituximab-alone arm was discontinued as a result of poor accrual. Eligibility included recurrent FL and prior rituximab with time to progression of ≥ 6 months from last dose. Aspirin or heparin was recommended for patients at high thrombosis risk.
Results
Ninety-one patients (lenalidomide, n = 45; LR, n = 46) received treatment; median age was 63 years (range, 34 to 89 years), and 58% were intermediate or high risk according to the Follicular Lymphoma International Prognostic Index. In the lenalidomide and LR arms, grade 3 to 4 adverse events occurred in 58% and 53% of patients, with 9% and 11% of patients experiencing grade 4 toxicity, respectively; grade 3 to 4 adverse events included neutropenia (16% v 20%, respectively), fatigue (9% v 13%, respectively), and thrombosis (16% [n = 7] v 4% [n = 2], respectively; P = .157). Thirty-six percent of lenalidomide patients and 63% of LR patients completed 12 cycles. Lenalidomide alone was associated with more treatment failures, with 22% of patients discontinuing treatment as a result of adverse events. Dose-intensity exceeded 80% in both arms. Overall response rate was 53% (20% complete response) and 76% (39% complete response) for lenalidomide alone and LR, respectively (P = .029). At the median follow-up of 2.5 years, median time to progression was 1.1 year for lenalidomide alone and 2 years for LR (P = .0023).
Conclusion
LR is more active than lenalidomide alone in recurrent FL with similar toxicity, warranting further study in B-cell non-Hodgkin lymphoma as a platform for addition of novel agents.
doi:10.1200/JCO.2014.59.9258
PMCID: PMC4622102  PMID: 26304886
7.  Nrf2—a therapeutic target for the treatment of neurodegenerative diseases 
Free radical biology & medicine  2015;88(Pt B):253-267.
The brain is very sensitive to changes in redox status; thus maintaining redox homeostasis in the brain is critical for the prevention of accumulating oxidative damage. Aging is the primary risk factor for developing neurodegenerative diseases. In addition to age, genetic and environmental risk factors have also been associated with disease development. The primary reactive insults associated with the aging process are a result of oxidative stress (OS) and nitrosative stress (NS). Markers of increased oxidative stress, protein and DNA modification, inflammation, and dysfunctional proteostasis have all been implicated in contributing to the progression of neurodegeneration. The ability of the cell to combat OS/NS and maintain a clearance mechanism for misfolded aggregating proteins determines whether or not it will survive. A critical pathway in this regard is the Nrf2 (nuclear factor erythroid 2-related factor 2)- antioxidant response element (ARE) pathway. Nrf2 activation has been shown to mitigate a number of pathologic mechanisms associated with Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, Huntington's disease, and multiple sclerosis. This review will focus on the role of Nrf2 in these diseases and the potential for Nrf2 activation to mitigate disease progression.
doi:10.1016/j.freeradbiomed.2015.07.147
PMCID: PMC4809057  PMID: 26281945
8.  Asymmetric Total Synthesis of the Indole Diterpene Alkaloid Paspaline 
The Journal of organic chemistry  2015;80(19):9740-9766.
An enantioselective synthesis of the indole diterpenoid natural product paspaline is disclosed. Critical to this approach was the implementation of stereoselective desymmetrization reactions to assemble key stereocenters of the molecule. The design and execution of these tactics are described in detail, and a thorough analysis of observed outcomes is presented, ultimately providing the title compound in high stereopurity. This synthesis provides a novel template for preparing key stereocenters in this family of molecules, and the reactions developed en route to paspaline present a series of new synthetic disconnections in preparing steroidal natural products.
doi:10.1021/acs.joc.5b01844
PMCID: PMC4598058  PMID: 26398568
9.  A Scalable Protocol for the Regioselective Alkylation of 2-Methylcyclohexane-1,3-dione with Unactivated sp3 Electrophiles 
A method for the C-selective alkylation of 2-methylcyclohexane-1,3-dione with unactivated sp3 electrophiles is accomplished via alkylation and subsequent deprotection of the derived ketodimethyl hydrazones. The present method provides a high-yielding entry to dialkyl cycloalkanones that cannot be accessed via direct alkylation of 2-methylcyclohexane-1,3-dione. The title reaction may be useful in the scalable preparation of terpene and steroidal building blocks in the arena of natural product synthesis.
doi:10.1055/s-0035-1560186
PMCID: PMC4625839  PMID: 26525231
alkylation; regioselectivity; hydrazones; ketones; alkyl halides; steroids; terpenoids
10.  Check the score: Field validation of Street Smart Walk Score in Alberta, Canada 
Preventive Medicine Reports  2016;4:532-539.
Walk Score® is a proprietary walkability metric that ranks locations by proximity to destinations, with emerging health promotion applications for increasing walking as physical activity. Currently, field validations of Walk Score® have only occurred in metropolitan regions of the United States; moreover, many studies employ an earlier Walk Score® version utilizing straight line distance. To address this gap, we conducted a field validation of the newest, network-based metric for three municipal types along a rural-urban continuum in Alberta, Canada. In 2015, using street-level systematic observations collected in Bonnyville, Medicine Hat, and North Central Edmonton in 2008 (part of the Community Health and the Built Environment (CHBE) project), we reverse engineered 2181 scores with the network Walk Score® algorithm. We computed means, 95% confidence intervals, and t-tests (α = 0.05) for both sets of scores. Applying the Clifford-Richardson adjustment for spatial autocorrelation, we calculated Spearman's Rank Correlation Coefficients (rho, rs) and adjusted p-values to measure the strength of association between the derived scores and original network scores provided by Walk Score®. Spearman's rho for scores were very high for Bonnyville (rs = 0.950, adjusted p < 0.001), and high for Medicine Hat (rs = 0.790, adjusted p < 0.001) and North Central Edmonton (rs = 0.763, adjusted p < 0.001). High to very high correlations between derived scores and Walk Scores® field validated this metric across small, medium, and large population centres in Alberta, Canada. However, we suggest caution in interpreting Walk Score® for planning and evaluating health promotion interventions, since the strength of association between destinations and walking may vary across different municipal types.
Highlights
•Physical inactivity linked to chronic disease can be addressed by increasing walking.•Understanding walkability can support health promotion policies and interventions.•Walk Score provides a uniquely accessible and generalizable metric for walkability•Walk Score has been field validated in urban America but not internationally.•We validated Walk Score in Alberta, Canada using field observation and correlation.
doi:10.1016/j.pmedr.2016.09.010
PMCID: PMC5065046  PMID: 27752462
ABL, Average Block Length; BMI, Body Mass Index; CHBE, Community Health and the Built Environment; CI, Confidence Interval; CSRS, Canadian Spatial Reference System; GIS, Geographic Information System; ID, Intersection Density; IMI, Irvine-Minnesota Inventory; NAD, North American Datum; NC, North Central; NRN, National Road Network; SS, Street Smart; TM, Transverse Mercator; Chronic disease; Geographic mapping; Health promotion; Validation studies; Walking
11.  Decrease of miR-146a is associated with the aggressiveness of human oral squamous cell carcinoma 
Archives of oral biology  2015;60(9):1416-1427.
With the aim to identify microRNAs that may contribute to oral squamous cell carcinoma (OSCC) progression, we compared the microRNA expression profiles of two related cell lines that form tumors with differential aggressiveness. A panel of 28 microRNAs was found to be more than 1.5-fold altered, among which miR-146a was the most significantly changed (-4.6-fold). Loss of miR-146a expression was validated in human high-grade tumors, while normal oral mucosa retained expression, using fluorescence in situ hybridization on a tissue microarray. Restoration of miR-146a in SCC25 and UMSCC1 cells decreased in vitro invasive activity, suppressed tumor growth in vivo, and decreased the incidence of UMSCC1 lung metastasis. The transcription factor Sox2 was found to be a putative target of miR-146a. In conclusion, the loss or decrease of miR-146a is a new feature that is associated with more aggressive behavior in oral squamous carcinoma.
doi:10.1016/j.archoralbio.2015.06.007
PMCID: PMC4536106  PMID: 26159827
oral cancer; microRNA; miR-146a; metastasis
12.  A qualitative study examining healthcare managers and providers’ perspectives on participating in primary care implementation research 
Background
Primary care reforms should be supported by high-quality evidence across the entire life cycle of research. Front-line healthcare providers play an increasing role in implementation research. We recently evaluated two interventions for people with type 2 diabetes (T2D) in partnership with four Primary Care Networks (PCNs) in Alberta, Canada. Here, we report healthcare professionals perspectives on participating in primary care implementation research.
Methods
Guided by the RE-AIM framework, we collected qualitative data before, during, and after both interventions. We conducted 34 in-person or telephone interviews with 17 individual PCN professionals. We used content analysis to identify emerging codes and concepts.
Results
Two major themes emerged from the data. First, healthcare managers were eager to conduct implementation research in a primary care setting. Second, regardless of willingness to conduct research, there were challenges to implementing experimental study designs for both interventions. PCN professionals presumed the interventions were better than usual care, expressed role conflict, and reported administrative burdens related to research participation. Perceptions of patient vulnerability and an obligation to intervene exacerbated these issues.
Conclusions
Healthcare professionals with limited practical research experience might not foresee the challenges in implementing experimental study designs in primary care settings to generate high-quality evidence. These issues are intensified when healthcare professionals perceive target patient populations as vulnerable and in need of intervention based on the presenting illness. Possible solutions include further research training, involving healthcare professionals in study design development, and using non-clinical staff to conduct research activities, particularly among acutely unwell patient populations.
doi:10.1186/s12913-016-1577-1
PMCID: PMC4965883  PMID: 27473755
Primary care; Implementation research; Qualitative study; Healthcare provider perspectives; Experimental study design
13.  Incident Infection and Resistance Mutation Analysis of Dried Blood Spots Collected in a Field Study of HIV Risk Groups, 2007-2010 
PLoS ONE  2016;11(7):e0159266.
Objective
To assess the utility of cost-effective dried blood spot (DBS) field sampling for incidence and drug resistance surveillance of persons at high risk for HIV infection.
Methods
We evaluated DBS collected in 2007–2010 in non-clinical settings by finger-stick from HIV-positive heterosexuals at increased risk of HIV infection (n = 124), men who have sex with men (MSM, n = 110), and persons who inject drugs (PWID, n = 58). Relative proportions of recent-infection findings among risk groups were assessed at avidity index (AI) cutoffs of ≤25%, ≤30%, and ≤35%, corresponding to an infection mean duration of recency (MDR) of 220.6, 250.4, and 278.3 days, respectively. Drug resistance mutation prevalence was compared among the risk groups and avidity indices.
Results
HIV antibody avidity testing of all self-reported ARV-naïve persons (n = 186) resulted in 9.7%, 11.3% and 14.0% with findings within the 221, 250, and 278-day MDRs, respectively. The proportion of ARV-naïve MSM, heterosexuals, and PWID reporting only one risk category who had findings below the suggested 30% AI was 23.1%, 6.9% and 3.6% (p<0.001), respectively. MSM had the highest prevalence of drug resistance and the only cases of transmitted multi-class resistance. Among the ARV-experienced, MSM had disproportionately more recent-infection results than did heterosexuals and PWID.
Conclusions
The disproportionately higher recent-infection findings for MSM as compared to PWID and heterosexuals increased as the MDR window increased. Unreported ARV use might explain greater recent-infection findings and drug resistance in this MSM population. DBS demonstrated utility in expanded HIV testing; however, optimal field handling is key to accurate recent-infection estimates.
doi:10.1371/journal.pone.0159266
PMCID: PMC4944983  PMID: 27415433
14.  Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection 
Cell host & microbe  2015;18(1):109-121.
SUMMARY
Chlamydia trachomatis is a leading cause of genital and ocular infections for which no vaccine exists. Upon entry into host cells, C. trachomatis resides within a membrane bound compartment—the inclusion--and secretes inclusion membrane proteins (Incs) that are thought to modulate the host-bacterium interface. To expand our understanding of Inc function(s), we subjected putative C. trachomatis Incs to affinity purification-mass spectroscopy (AP-MS). We identified Inc-human interactions for 38/58 Incs with enrichment in host processes consistent with Chlamydia’s intracellular lifecycle. There is significant overlap between Inc targets and viral proteins, suggesting common pathogenic mechanisms among obligate intracellular microbes. IncE binds to sorting nexins (SNXs) 5/6, components of the retromer, resulting in SNX5/6 relocalization to the inclusion membrane and enhanced inclusion membrane tubulation. Depletion of retromer components enhances progeny production, revealing that retromer restricts Chlamydia infection. This study demonstrates the value of proteomics in unveiling host-pathogen interactions in genetically challenging microbes.
Graphical abstract
doi:10.1016/j.chom.2015.06.004
PMCID: PMC4540348  PMID: 26118995
15.  Non-degradative Ubiquitination of Protein Kinases 
PLoS Computational Biology  2016;12(6):e1004898.
Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation. In contrast to other common post-translational modifications, such as phosphorylation, little is known about how non-degradative ubiquitination modulates protein structure, dynamics, and function. Due to the wealth of knowledge concerning protein kinase structure and regulation, we examined kinase ubiquitination using ubiquitin remnant immunoaffinity enrichment and quantitative mass spectrometry to identify ubiquitinated kinases and the sites of ubiquitination in Jurkat and HEK293 cells. We find that, unlike phosphorylation, ubiquitination most commonly occurs in structured domains, and on the kinase domain, ubiquitination is concentrated in regions known to be important for regulating activity. We hypothesized that ubiquitination, like other post-translational modifications, may alter the conformational equilibrium of the modified protein. We chose one human kinase, ZAP-70, to simulate using molecular dynamics with and without a monoubiquitin modification. In Jurkat cells, ZAP-70 is ubiquitinated at several sites that are not sensitive to proteasome inhibition and thus may have other regulatory roles. Our simulations show that ubiquitination influences the conformational ensemble of ZAP-70 in a site-dependent manner. When monoubiquitinated at K377, near the C-helix, the active conformation of the ZAP-70 C-helix is disrupted. In contrast, when monoubiquitinated at K476, near the kinase hinge region, an active-like ZAP-70 C-helix conformation is stabilized. These results lead to testable hypotheses that ubiquitination directly modulates kinase activity, and that ubiquitination is likely to alter structure, dynamics, and function in other protein classes as well.
Author Summary
Attachment of ubiquitin to another protein is typically used to mark the protein for degradation by the proteasome. However, recent studies show that many proteins are tagged with ubiquitin and not degraded. We hypothesized that ubiquitin can regulate the protein it is attached to by changing its structure and dynamics. We performed proteomics experiments to identify all of the kinase proteins tagged by ubiquitin in a human cell line as well as the site of ubiquitination. We found that kinases are often ubiquitinated in structured regions important for regulation and activity. We then performed molecular dynamics simulations of one kinase, ZAP-70, to see if a ubiquitin tag could affect the kinase structure. We found that ubiquitin does affect the structure of ZAP-70, and the effect depends on where the ubiquitin is attached. At K377, ubiquitin changes the ZAP-70 structure to resemble the inactive state, while ubiquitin attached at K476, on the other side of the protein, has the opposite effect. These simulations indicate that ubiquitin, like other post-translational modifications, may alter the structure and dynamics of proteins in ways that impact activity and function.
doi:10.1371/journal.pcbi.1004898
PMCID: PMC4890936  PMID: 27253329
16.  Severe Obesity Is Associated With Increased Risk of Early Complications and Extended Length of Stay Following Coronary Artery Bypass Grafting Surgery 
Background
Better understanding of the relationship between obesity and postsurgical adverse outcomes is needed to provide quality and efficient care. We examined the relationship of obesity with the incidence of early adverse outcomes and in‐hospital length of stay following coronary artery bypass grafting surgery.
Methods and Results
We analyzed data from 7560 patients who underwent coronary artery bypass grafting. Using body mass index (BMI; in kg/m2) of 18.5 to 24.9 as a reference, the associations of 4 BMI categories (25.0–29.9, 30.0–34.9, 35.0–39.9, and ≥40.0) with rates of operative mortality, overall early complications, subgroups of early complications (ie, infection, renal and pulmonary complications), and length of stay were assessed while adjusting for clinical covariates. There was no difference in operative mortality; however, higher risks of overall complications were observed for patients with BMI 35.0 to 39.9 (adjusted odds ratio 1.35, 95% CI 1.11–1.63) and ≥40.0 (adjusted odds ratio 1.56, 95% CI 1.21–2.01). Subgroup analyses identified obesity as an independent risk factor for infection (BMI 30.0–34.9: adjusted odds ratio 1.60, 95% CI 1.24–2.05; BMI 35.0–39.9: adjusted odds ratio 2.34, 95% CI 1.73–3.17; BMI ≥40.0: adjusted odds ratio 3.29, 95% CI 2.30–4.71). Median length of stay was longer with BMI ≥40.0 than with BMI 18.5 to 24.9 (median 7.0 days [interquartile range 5 to 10] versus 6.0 days [interquartile range 5 to 9], P=0.026).
Conclusions
BMI ≥40.0 was an independent risk factor for longer length of stay, and infection was a potentially modifiable risk factor. Greater perioperative attention and intervention to control the risks associated with infection and length of stay in patients with BMI ≥40.0 may improve patient care quality and efficiency.
doi:10.1161/JAHA.116.003282
PMCID: PMC4937271  PMID: 27250114
cardiovascular disease; diabetes mellitus; health outcomes; infection; surgery; Cost-Effectiveness; Quality and Outcomes
17.  Lineage-Specific Viral Hijacking of Non-Canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity 
Cell reports  2015;11(8):1236-1250.
SUMMARY
HIV-1 encodes the accessory protein Vif, which hijacks a host Cullin-RING ubiquitin ligase (CRL) complex as well as the non-canonical cofactor CBFβ, to antagonize APOBEC3 antiviral proteins. Non-canonical cofactor recruitment to CRL complexes by viral factors, to date, has only been attributed to HIV-1 Vif. To further study this phenomenon, we employed a comparative approach combining proteomic, biochemical, structural, and virological techniques to investigate Vif complexes across the lentivirus genus, including primate (HIV-1, SIVmac) and non-primate (FIV, BIV, and MVV) viruses. We find that CBFβ is completely dispensable for the activity of non-primate lentiviral Vif proteins. Furthermore, we find that BIV Vif requires no cofactor, and that MVV Vif requires a novel cofactor, Cyclophilin A (CYPA), for stable CRL complex formation and anti-APOBEC3 activity. We propose modular conservation of Vif complexes allows for potential exaptation of novel functions through the acquisition of non-CRL associated host cofactors while preserving anti-APOBEC3 activity.
Graphical Abstract
doi:10.1016/j.celrep.2015.04.038
PMCID: PMC4613747  PMID: 25981045
18.  A Cyclic Peptide Mimic of the β-Amyloid Binding Domain on Transthyretin 
ACS chemical neuroscience  2015;6(5):778-789.
Self-association of β-amyloid (Aβ) into oligomers and fibrils is associated with Alzheimer’s disease (AD), motivating the search for compounds that bind to and inhibit Aβ oligomerization and/or neurotoxicity. Peptides are an attractive class of such compounds, with potential advantages over small molecules in affinity and specificity. Self-complementation and peptide library screening are two strategies that have been employed in the search for peptides that bind to Aβ. Alternatively, one could design Aβ-binding peptides based on knowledge of complementary binding proteins. One candidate protein, transthyretin (TTR), binds Aβ, inhibits aggregation, and reduces its toxicity. Previously, strand G of TTR was identified as part of a specific Aβ binding domain, and G16, a 16-mer peptide with a sequence that spans strands G and H of TTR, was synthesized and tested. Although both TTR and G16 bound to Aβ, they differed significantly in their effect on Aβ aggregation, and G16 was less effective than TTR at protecting neurons from Aβ toxicity. G16 lacks the β-strand/loop/β-strand structure of TTR’s Aβ binding domain. To enforce proper residue alignment, we transplanted the G16 sequence onto a β-hairpin template. Two peptides with 18 and 22 amino acids were synthesized using an orthogonally protected glutamic acid derivative, and an N-to-C cyclization reaction was carried out to further restrict conformational flexibility. The cyclized 22-mer (but not the noncyclized 22-mer nor the 18-mer) strongly suppressed Aβ aggregation into fibrils, and protected neurons against Aβ toxicity. The imposition of structural constraints generated a much-improved peptidomimetic of the Aβ binding epitope on TTR.
Graphical Abstract
doi:10.1021/cn500272a
PMCID: PMC4797071  PMID: 25713928
Beta-amyloid; transthyretin; cyclic peptide; Alzheimer’s disease; peptidomimetics; amyloid fibrils
19.  Increasing AIP Macrocycle Size Reveals Key Features of agr Activation in S. aureus 
The agr locus in the commensal human pathogen, Staphylococcus aureus, is a two-promoter regulon with allelic variability that produces a quorum-sensing circuit involved in regulating virulence within the bacterium. Secretion of unique autoinducing peptides (AIPs) and detection of their concentration via AgrC, a transmembrane receptor histidine kinase, coordinates local bacterial population density with global changes in gene expression. The finding that staphylococcal virulence can be inhibited through antagonism of this quorum-sensing pathway has fueled tremendous interest in understanding the structure-activity relationships underlying the AIP-AgrC interaction. The defining structural feature of the AIP is a 16-membered, thiolactone-containing macrocycle. Surprisingly, the importance of ring size on agr activation or inhibition has not been explored. In this study, we address this deficiency through the synthesis and functional analysis of AIP analogs featuring enlarged and reduced macrocycles. Notably, this study is the first to interrogate AIP function using both established cell-based reporter gene assays and newly developed in vitro AgrC-I binding and autophosphorylation activity assays. Based on our data, we present a model for robust agr activation involving a cooperative, 3-points-of-contact interaction between the AIP macrocycle and AgrC.
doi:10.1002/cbic.201500006
PMCID: PMC4589298  PMID: 25801678
Quorum Sensing; Autoinducing Peptides; Structure-activity relationships; Biological activity; Bacterial virulence
20.  Tensor-Based Morphometry Reveals Volumetric Deficits in Moderate=Severe Pediatric Traumatic Brain Injury 
Journal of Neurotrauma  2016;33(9):840-852.
Abstract
Traumatic brain injury (TBI) can cause widespread and prolonged brain degeneration. TBI can affect cognitive function and brain integrity for many years after injury, often with lasting effects in children, whose brains are still immature. Although TBI varies in how it affects different individuals, image analysis methods such as tensor-based morphometry (TBM) can reveal common areas of brain atrophy on magnetic resonance imaging (MRI), secondary effects of the initial injury, which will differ between subjects. Here we studied 36 pediatric moderate to severe TBI (msTBI) participants in the post-acute phase (1–6 months post-injury) and 18 msTBI participants who returned for their chronic assessment, along with well-matched controls at both time-points. Participants completed a battery of cognitive tests that we used to create a global cognitive performance score. Using TBM, we created three-dimensional (3D) maps of individual and group differences in regional brain volumes. At both the post-acute and chronic time-points, the greatest group differences were expansion of the lateral ventricles and reduction of the lingual gyrus in the TBI group. We found a number of smaller clusters of volume reduction in the cingulate gyrus, thalamus, and fusiform gyrus, and throughout the frontal, temporal, and parietal cortices. Additionally, we found extensive associations between our cognitive performance measure and regional brain volume. Our results indicate a pattern of atrophy still detectable 1-year post-injury, which may partially underlie the cognitive deficits frequently found in TBI.
doi:10.1089/neu.2015.4012
PMCID: PMC4860661  PMID: 26393494
MRI; pediatric; tensor based morphometry; traumatic brain injury
21.  A Global and Local Desymmetrization Approach to the Synthesis of Steroidal Alkaloids: Stereocontrolled Total Synthesis of Paspaline 
A stereocontrolled total synthesis of the indole diterpenoid natural product paspaline is described. Key steps include a highly diastereoselective enzymatic desymmetrization, substrate-directed epoxidation, Ireland-Claisen rearrangement, and diastereotopic group selective C–H acetoxylation to assemble the target with excellent stereofidelity. The route and results described herein outline complementary conceptual disconnections in the arena of steroid natural product synthesis.
doi:10.1021/jacs.5b02631
PMCID: PMC4409926  PMID: 25856767
22.  Volumetric measurement of rock movement using photogrammetry 
NIOSH ground control safety research program at Spokane, Washington, is exploring applications of photogrammetry to rock mass and support monitoring. This paper describes two ways photogrammetric techniques are being used. First, photogrammetric data of laboratory testing is being used to correlate energy input and support deformation. This information can be used to infer remaining support toughness after ground deformation events. This technique is also demonstrated in a field application. Second, field photogrammetric data is compared to crackmeter data from a deep underground mine. Accuracies were found to average 8 mm, but have produced results within 0.2 mm of true displacement, as measured by crackmeters. Application of these techniques consists of monitoring overall fault activity by monitoring multiple points around the crackmeter. A case study is provided in which a crackmeter is clearly shown to have provided insufficient information regarding overall fault ground deformation. Photogrammetry is proving to be a useful ground monitoring tool due to its unobtrusiveness and ease of use.
doi:10.1016/j.ijmst.2015.11.020
PMCID: PMC4837642  PMID: 27110429
Photogrammetry; Ground control; Monitoring; Deep vein mining; Volume calculation; Crackmeter
23.  Preparation and biological evaluation of synthetic and polymer-encapsulated congeners of the antitumor agent pactamycin: Insight into functional group effects and biological activity 
Bioorganic & medicinal chemistry  2015;23(8):1849-1857.
The synthesis and biological analysis of a number of novel congeners of the aminocyclopentitol pactamycin is described. Specific attention was paid to the preparation of derivatives at crucial synthetic branch points of the parent structure, and biological assays revealed a number of insights into the source of pactamycin’s biological activity. Additionally, the encapsulation of pactamycin and select derivatives into the PRINT© nanoparticle technology was investigated as a proof-of-concept, and evidence of bioactivity modulation through nanoparticle delivery is demonstrated. This work has provided heretofore unrealized access to a large number of novel compounds for further evaluation.
doi:10.1016/j.bmc.2015.02.022
PMCID: PMC4380168  PMID: 25792144
Pactamycin; Nanoparticles; Structure activity relationships; Structural derivatization
24.  NF-κB activating complex engaged in response to EGFR oncogene inhibition drives tumor cell survival and residual disease in lung cancer 
Cell reports  2015;11(1):98-110.
Summary
Although oncogene-targeted therapy often elicits profound initial tumor responses in patients, responses are generally incomplete because some tumor cells survive initial therapy as residual disease that enables eventual acquired resistance. The mechanisms underlying tumor cell adaptation and survival during initial therapy are incompletely understood. Here, through the study of EGFR-mutant lung adenocarcinoma we show that NF-κB signaling is rapidly engaged upon initial EGFR inhibitor treatment to promote tumor cell survival and residual disease. EGFR oncogene inhibition induced an EGFR-TRAF2-RIP1-IKK complex that stimulated an NF-κB-mediated transcriptional survival program. The direct NF-κB inhibitor PBS-1086 suppressed this adaptive survival program and increased the magnitude and duration of initial EGFR inhibitor response in multiple NSCLC models, including a patient-derived xenograft. These findings unveil NF-κB activation as a critical adaptive survival mechanism engaged by EGFR oncogene inhibition and provide rationale for EGFR and NF-κB co-inhibition to eliminate residual disease and enhance patient responses.
doi:10.1016/j.celrep.2015.03.012
PMCID: PMC4394036  PMID: 25843712
25.  WHITE MATTER INTEGRITY IN TRAUMATIC BRAIN INJURY: EFFECTS OF PERMISSIBLE FIBER TURNING ANGLE 
Traumatic brain injury (TBI) is the leading cause of death and disability in children. Diffusion weighted imaging (DWI) methods have been shown to be especially sensitive to white matter abnormalities in TBI. We used our newly developed autoMATE algorithm (automated multi-atlas tract extraction) to map altered WM integrity in TBI. Even so, tractography methods include a free parameter that limits the maximum permissible turning angles for extracted fibers, with little investigation of how this may affect statistical group comparisons. Here, we examined WM integrity calculated over a range of fiber turning angles to determine to what extent this parameter affects our ability to detect group differences. Fiber turning angle threshold has a subtle, but sometimes significant, effect on the differences we were able to detect between TBI and healthy children.
doi:10.1109/ISBI.2015.7164023
PMCID: PMC4578174  PMID: 26413206
High angular resolution diffusion imaging (HARDI); traumatic brain injury; tractography; fiber turning angle

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