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2.  Trisomy 8 Acute Myeloid Leukemia Analysis Reveals New Insights of DNA Methylome with Identification of HHEX as Potential Diagnostic Marker 
Biomarkers in Cancer  2015;7:1-6.
Trisomy 8 acute myeloid leukemia (AML) is the commonest numerical aberration in AML. Here we present a global analysis of trisomy 8 AML using methylated DNA immunoprecipitation-sequencing (MeDIP-seq). The study is based on three diagnostic trisomy 8 AML and their parallel relapse status in addition to nine non-trisomic AML and four normal bone marrows (NBMs). In contrast to non-trisomic DNA samples, trisomy 8 AML showed a characteristic DNA methylation distribution pattern because an increase in the frequency of the hypermethylation signals in chromosome 8 was associated with an increase in the hypomethylation signals in the rest of the chromosomes. Chromosome 8 hypermethylation signals were found mainly in the CpG island (CGI) shores and interspersed repeats. Validating the most significant differentially methylated CGI (P = 7.88 × 10−11) identified in trisomy 8 AML demonstrated a specific core region within the gene body of HHEX, which was significantly correlated with HHEX expression in both diagnostic and relapse trisomy 8 AMLs. Overall, the existence of extra chromosome 8 was associated with a global impact on the DNA methylation distribution with identification of HHEX gene methylation as a potential diagnostic marker for trisomy 8 AML.
PMCID: PMC4315123
trisomy 8; MeDIP-seq; CGI shores; HHEX
3.  Basal and treatment-induced activation of AKT mediates resistance to cell death by AZD6244 (ARRY-142886) in Braf-mutant human cutaneous melanoma cells 
Cancer research  2010;70(21):8736-8747.
The majority of melanomas demonstrate constitutive activation of the RAS-RAF-MEK-MAPK pathway. AZD6244 is a selective MEK1/2 inhibitor which markedly reduces tumor P-MAPK levels, but it produced few clinical responses in melanoma patients. An improved understanding of the determinants of resistance to AZD6244 may lead to improved patient selection and effective combinatorial approaches. The effects of AZD6244 on cell growth and survival were tested in a total of 14 Braf-mutant and 3 wild-type human cutaneous melanoma cell lines. Quantitative assessment of phospho-protein levels in the Braf-mutant cell lines by reverse phase protein array (RPPA) analysis showed no significant association between P-MEK or P-MAPK levels and AZD6244 sensitivity, but activation-specific markers in the PI3K-AKT pathway correlated with resistance. We also identified resistant cell lines without basal activation of the PI3K-AKT pathway. RPPA characterization of the time-dependent changes in signaling pathways revealed that AZD6244 produced durable and potent inhibition of P-MAPK in sensitive and resistant Braf-mutant cell lines, but several resistant lines demonstrated AZD6244-induced activation of AKT. In contrast, sensitive cell lines demonstrated AZD6244 treatment-induced upregulation of PTEN protein and mRNA expression. Inhibition of AKT, TORC1/2, or IGF1R blocked AZD6244-induced activation of AKT and resulted in synergistic cell killing with AZD6244. These findings identify basal and treatment-induced regulation of the PI3K-AKT pathway as a critical regulator of AZD6244 sensitivity in Braf-mutant cutaneous melanoma cells, the novel regulation of PTEN expression by AZD6244 in sensitive cells, and suggest new combinatorial approaches for patients.
PMCID: PMC4286702  PMID: 20959481
AZD6244; AZD8055; MEK; BRAF; MAPK; AKT; PTEN; melanoma
4.  Development, Characterization, and Reversal of Acquired Resistance to the MEK1 Inhibitor Selumetinib (AZD6244) in an In Vivo Model of Childhood Astrocytoma 
The BT-40 low-grade childhood astrocytoma xenograft model expresses mutated BRAFV600E and is highly sensitive to the MEK inhibitor selumetinib (AZD6244). In this study we developed and characterized selumetinib resistance and explored approaches to circumventing the mechanism(s) of acquired resistance.
Experimental Design
BT-40 xenografts were selected in vivo for selumetinib resistance. Resistant tumors were obtained and characterized, as were tumors that reverted to sensitivity. Characterization included expression-profiling, assessment of MEK signature and compensatory pathways, MEK inhibition, BRAF expression, and cytokine levels. Combination treatment of BT-40/AZD resistant tumors with the MEK inhibitor and a STAT3 inhibitor (LLL12) was assessed.
Resistance was unstable, tumors reverting to selumetinib sensitivity when passaged in untreated mice, and MEK was equally inhibited in sensitive and resistant tumors by selumetinib. Drug resistance was associated with an enhanced MEK signature, and increased IL6 and IL8 expression. Selumetinib treatment induced phosphorylation of STAT3(Y705) only in resistant xenografts, and similar results were observed in BRAFV600E astrocytic cell lines intrinsically resistant to selumetinib. Treatment of BT-40 resistant tumors with selumetinib or LLL12 had no significant effect, whereas combined treatment induced complete regressions of BT-40/AZD resistant xenografts.
Resistance to selumetinib selected in vivo in BT-40 tumor xenografts was unstable. In resistant tumors selumetinib activated STAT3, and combined treatment with selumetinib and LLL12, induced complete responses in resistant BT-40 tumors. These results suggest dual targeting BRAF(V600E) signaling and STAT3 signaling may be effective in selumetinib-resistant tumors, or may retard or prevent onset of resistance.
PMCID: PMC4086218  PMID: 24132923
5.  Leveraging practice-based research networks to accelerate implementation and diffusion of chronic kidney disease guidelines in primary care practices: a prospective cohort study 
Four practice-based research networks (PBRNs) participated in a study to determine whether networks could increase dissemination, implementation, and diffusion of evidence-based treatment guidelines for chronic kidney disease by leveraging early adopter practices.
Motivated practices from four PBRNs received baseline and periodic performance feedback, academic detailing, and weekly practice facilitation for 6 months during wave I of the study. Each wave I practice then recruited two additional practices (wave II), which received performance feedback and academic detailing and participated in monthly local learning collaboratives led by the wave I clinicians. They received only monthly practice facilitation. The primary outcomes were adherence to primary care-relevant process-of-care recommendations from the National Kidney Foundation Kidney Disease Outcomes Quality Initiative Guidelines. Performance was determined retrospectively by medical records abstraction. Practice priority, change capacity, and care process content were measured before and after the interventions.
Following the intervention, wave I practices increased the use of ACEIs/ARBs, discontinuation of NSAIDs, testing for anemia, and testing and/or treatment for vitamin D deficiency. Most were able to recruit two additional practices for wave II, and wave II practices also increased their use of ACEIs/ARBs and testing and/or treatment of vitamin D deficiency.
With some assistance, early adopter practices can facilitate the diffusion of evidence-based approaches to other practices. PBRNs are well-positioned to replicate this process for other evidence-based innovations.
Electronic supplementary material
The online version of this article (doi:10.1186/s13012-014-0169-x) contains supplementary material, which is available to authorized users.
PMCID: PMC4245828  PMID: 25416998
Implementation; Diffusion; Primary care; Practice-based research network; Chronic kidney disease
6.  Osteoblasts from osteoarthritis patients show enhanced susceptibility to Ross River virus infection associated with delayed type I interferon responses 
Virology Journal  2014;11(1):189.
Arthritogenic alphaviruses such as Ross River virus (RRV) and chikungunya virus (CHIKV) have caused widespread outbreaks of chronic polyarthritis. The inflammatory responses in alphavirus-induced arthritis and osteoarthritis (OA) share many similar features, which suggests the possibility of exacerbated alphavirus-induced bone pathology in individuals with pre-existing OA. Here, we investigated the susceptibility of osteoblasts (OBs) from OA patients to RRV infection and dissected the immune mechanisms elicited from infection.
Primary hOBs obtained from trabecular bone of healthy donors and OA patients were infected with RRV. Infectivity and viral replication were determined using flow cytometry and plaque assay, respectively. Real-time PCR was performed to determine expression kinetics of type I interferon (IFN)-related immune mediators and osteotropic factors.
OA hOBs showed enhanced RRV infectivity and replication during infection, which was associated with delayed induction of IFN-β and RIG-I expression. Enhanced susceptibility of OA hOBs to RRV was associated with a more pronounced increase in RANKL/OPG ratio and expression of osteotropic factors (IL-6, IL-1β, TNF-α and CCL2) in comparison to RRV-infected healthy hOBs.
Delayed activation of type I IFN-signalling pathway may have contributed to enhanced susceptibility to RRV infection in hOBs from OA patients. RRV-induced increases in RANKL/OPG ratio and expression of osteotropic factors that favour bone resorption, which may be exacerbated during osteoarthritis. This study provides the novel insight that osteoarthritis may be a risk factor for exacerbated arthritogenic alphaviral infection.
PMCID: PMC4252017  PMID: 25407789
Ross River virus; Human osteoblasts; RANKL/OPG ratio; Osteotropic factors
8.  Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28 
Nucleic Acids Research  2014;42(20):12885-12898.
Yeast Prp28 is a DEAD-box pre-mRNA splicing factor implicated in displacing U1 snRNP from the 5′ splice site. Here we report that the 588-aa Prp28 protein consists of a trypsin-sensitive 126-aa N-terminal segment (of which aa 1–89 are dispensable for Prp28 function in vivo) fused to a trypsin-resistant C-terminal catalytic domain. Purified recombinant Prp28 and Prp28-(127–588) have an intrinsic RNA-dependent ATPase activity, albeit with a low turnover number. The crystal structure of Prp28-(127–588) comprises two RecA-like domains splayed widely apart. AMPPNP•Mg2+ is engaged by the proximal domain, with proper and specific contacts from Phe194 and Gln201 (Q motif) to the adenine nucleobase. The triphosphate moiety of AMPPNP•Mg2+ is not poised for catalysis in the open domain conformation. Guided by the Prp28•AMPPNP structure, and that of the Drosophila Vasa•AMPPNP•Mg2+•RNA complex, we targeted 20 positions in Prp28 for alanine scanning. ATP-site components Asp341 and Glu342 (motif II) and Arg527 and Arg530 (motif VI) and RNA-site constituent Arg476 (motif Va) are essential for Prp28 activity in vivo. Synthetic lethality of double-alanine mutations highlighted functionally redundant contacts in the ATP-binding (Phe194-Gln201, Gln201-Asp502) and RNA-binding (Arg264-Arg320) sites. Overexpression of defective ATP-site mutants, but not defective RNA-site mutants, elicited severe dominant-negative growth defects.
PMCID: PMC4227776  PMID: 25303995
9.  Health Literacy and Urbanicity Among Cancer Patients 
Low health literacy is associated with inadequate health care utilization and poor health outcomes, particularly among elderly persons. There is a dearth of research exploring the relationship between health literacy and place of residence (urbanicity). This study examined the association between urbanicity and health literacy, as well as factors related to low health literacy, among cancer patients.
A cross-sectional survey was conducted with a population-based sample of 1,841 cancer patients in Wisconsin. Data on sociodemographics, urbanicity, clinical characteristics, insurance status, and health literacy were obtained from the state’s cancer registry and participants’ answers to a mailed questionnaire. Partially and fully adjusted multivariate logistic regression models were fitted to examine: 1) the association between urbanicity and health literacy, and 2) the role of socioeconomic status as a possible mediator of this relationship.
Rural cancer patients had a 33% (95% CI: 1.06–1.67) higher odds of having lower levels of health literacy than their counterparts in more urbanized areas of Wisconsin. The association between urbanicity and health literacy attenuated after controlling for socioeconomic status.
Level of urbanicity was significantly related to health literacy. Socioeconomic status fully mediated the relationship between urbanicity and health literacy. These results call for policies and interventions to assess and address health literacy barriers among cancer patients in rural areas.
PMCID: PMC3989904  PMID: 24088213
cancer; health disparities; health literacy; rural; socioeconomic status
10.  Infrared and Visible Absolute and Difference Spectra of Bacteriorhodopsin Photocycle Intermediates 
Applied spectroscopy  2011;65(9):1029-1045.
We have used new kinetic fitting procedures to obtain IR absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear algebra-based procedures of Hendler et al. (2001) J. Phys. Chem. B, 105, 3319–3228, for obtaining clean absolute visible spectra of bR photocycle intermediates, were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its MF and MS components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm−1 for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the MF pathway of the parallel cycles model of the photocycle.
PMCID: PMC4167422  PMID: 21929858
kinetic analysis; reversible homogeneous model; parallel cycles; arginine 82 deprotonation; proton release group (PRG); flash photolysis; purple membrane
11.  Overcoming endocrine resistance due to reduced PTEN levels in estrogen receptor-positive breast cancer by co-targeting mammalian target of rapamycin, protein kinase B, or mitogen-activated protein kinase kinase 
Activation of the phosphatidylinositol 3-kinase (PI3K) pathway in estrogen receptor α (ER)-positive breast cancer is associated with reduced ER expression and activity, luminal B subtype, and poor outcome. Phosphatase and tensin homolog (PTEN), a negative regulator of this pathway, is typically lost in ER-negative breast cancer. We set out to clarify the role of reduced PTEN levels in endocrine resistance, and to explore the combination of newly developed PI3K downstream kinase inhibitors to overcome this resistance.
Altered cellular signaling, gene expression, and endocrine sensitivity were determined in inducible PTEN-knockdown ER-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer cell and/or xenograft models. Single or two-agent combinations of kinase inhibitors were examined to improve endocrine therapy.
Moderate PTEN reduction was sufficient to enhance PI3K signaling, generate a gene signature associated with the luminal B subtype of breast cancer, and cause endocrine resistance in vitro and in vivo. The mammalian target of rapamycin (mTOR), protein kinase B (AKT), or mitogen-activated protein kinase kinase (MEK) inhibitors, alone or in combination, improved endocrine therapy, but the efficacy varied by PTEN levels, type of endocrine therapy, and the specific inhibitor(s). A single-agent AKT inhibitor combined with fulvestrant conferred superior efficacy in overcoming resistance, inducing apoptosis and tumor regression.
Moderate reduction in PTEN, without complete loss, can activate the PI3K pathway to cause endocrine resistance in ER-positive breast cancer, which can be overcome by combining endocrine therapy with inhibitors of the PI3K pathway. Our data suggests that the ER degrader fulvestrant, to block both ligand-dependent and -independent ER signaling, combined with an AKT inhibitor is an effective strategy to test in patients.
Electronic supplementary material
The online version of this article (doi:10.1186/s13058-014-0430-x) contains supplementary material, which is available to authorized users.
PMCID: PMC4303114  PMID: 25212826
12.  Synthesis, characterisation, and preliminary anti-cancer photodynamic therapeutic in vitro studies of mixed-metal binuclear ruthenium(II)-vanadium(IV) complexes 
We report the synthesis and characterisation of mixed-metal binuclear ruthenium(II)-vanadium(IV) complexes, which were used as potential photodynamic therapeutic agents for melanoma cell growth inhibition. The novel complexes, [Ru(pbt)2(phen2DTT)](PF6)2•1.5H2O 1 (where phen2DTT = 1,4-bis(1,10-phenanthrolin-5-ylsulfanyl)butane-2,3-diol and pbt = 2-(2'-pyridyl)benzothiazole) and [Ru(pbt)2(tpphz)](PF6)2•3H2O 2 (where tpphz = tetrapyrido[3,2-a:2′,3′-c:3″,2″-h:2‴,3‴-j]phenazine) were synthesised and characterised. Compound 1 was reacted with [VO(sal-L-tryp)(H2O)] (where sal-L-tryp = N-salicylidene-L-tryptophanate) to produce [Ru(pbt)2(phen2DTT)VO(sal-L-tryp)](PF6)2•5H2O 4; while [VO(sal-L-tryp)(H2O)] was reacted with compound 2 to produce [Ru(pbt)2(tpphz)VO(sal-L-tryp)](PF6)2•6H2O 3. All complexes were characterised by elemental analysis, HRMS, ESI MS, UV-visible absorption, ESR spectroscopy, and cyclic voltammetry, where appropriate. In vitro cell toxicity studies (with the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric assay) via dark and light reaction conditions were carried out with sodium diaqua-4,4',4”,4”'tetrasulfophthalocyaninecobaltate(II) (Na4[Co(tspc)(H2O)2]), [VO(sal-L-tryp)(phen)]•H2O, and the chloride salts of complexes 3 and 4. Such studies involved A431, human epidermoid carcinoma cells; human amelanotic malignant melanoma cells; and HFF, non-cancerous human skin fibroblast cells. Both chloride salts of complexes 3 and 4 were found to be more toxic to melanoma cells than to non-cancerous fibroblast cells, and preferentially led to apoptosis of the melanoma cells over non-cancerous skin cells. The anti-cancer property of the chloride salts of complexes 3 and 4 was further enhanced when treated cells were exposed to light, while no such effect was observed on non-cancerous skin fibroblast cells. ESR and 51V NMR spectroscopic studies were also used to assess the stability of the chloride salts of complexes 3 and 4 in aqueous media at pH 7.19. This research illustrates the potential for using mixed-metal binuclear ruthenium(II)-vanadium(IV) complexes fighting skin cancer.
PMCID: PMC3751419  PMID: 23783642
13.  Further Studies with Isolated Absolute IR Spectra of Bacteriorhodopsin Photocycle Intermediates: Conformational changes and possible role of a new proton-binding center 
Applied spectroscopy  2013;67(1):73-85.
We recently published procedures describing the isolation of absolute IR spectra for all of the intermediates of the bacteriorhodopsin photocycle, and from these to obtain transitional difference spectra between consecutive intermediates (Hendler et al. Applied Spectroscopy, 65, 1029-1045 (2011)).
In that work, we concentrated mainly on proton-binding centers and the route of proton transport across the membrane. In the current communication we use isolated spectra for the Amide I, Amide II, and Amide III envelopes to obtain quantitative information on the extents of conformational change accompanying each transition in the photocycle. Our main finding is that most of the conformational changes occur in the conversion of the MF intermediate to N.
In the earlier publication, a new proton acceptor, absorbing at 1650 cm−1 was identified which appeared to accept a proton from Asp96COOH during the transformation of †BR* to L. Below, we present evidence which supports this interpretation and propose a possible role for this new component.
PMCID: PMC4151312  PMID: 23317674
14.  Identifying Health Literacy and Health System Navigation Needs Among Rural Cancer Patients: Findings from the Rural Oncology Literacy Enhancement Study (ROLES) 
Rural residence is associated with disparities in cancer-related outcomes. Guided by the Chronic Care Model (CCM), the Rural Oncology Literacy Enhancement Study (ROLES) assessed health literacy and patient navigation needs among rural cancer patients. A mixed methods (qualitative and quantitative) approach was used, including: in-depth interviews, health literacy assessments, and phone surveys with cancer patients (N=53) from 5 oncology clinics in rural Wisconsin; focus groups and selfadministered surveys with staff (N=41) in these clinics. Within four dimensions of the CCM (community resources, self-management support, delivery system design, and decision support), this study uncovered multiple unmet navigation needs, health literacy limitations, and barriers to quality cancer care. System-level implementation of patient navigation and health literacy best practices could contribute to improved cancer care and patient outcomes among rural populations. Further research identifying effective interventions that reduce cancer disparities among rural cancer patients is necessary.
PMCID: PMC3755018  PMID: 23813542
15.  Accuracy assessment of Tri-plane B-mode ultrasound for non-invasive 3D kinematic analysis of knee joints 
Currently the clinical standard for measuring the motion of the bones in knee joints with sufficient precision involves implanting tantalum beads into the bones. These beads appear as high intensity features in radiographs and can be used for precise kinematic measurements. This procedure imposes a strong coupling between accuracy and invasiveness. In this paper, a tri-plane B-mode ultrasound (US) based non-invasive approach is proposed for use in kinematic analysis of knee joints in 3D space.
The 3D analysis is performed using image processing procedures on the 2D US slices. The novelty of the proposed procedure and its applicability to the unconstrained 3D kinematic analysis of knee joints is outlined. An error analysis for establishing the method’s feasibility is included for different artificial compositions of a knee joint phantom. Some in-vivo and in-vitro scans are presented to demonstrate that US scans reveal enough anatomical details, which further supports the experimental setup used using knee bone phantoms.
The error between the displacements measured by the registration of the US image slices and the true displacements of the respective slices measured using the precision mechanical stages on the experimental apparatus is evaluated for translation and rotation in two simulated environments. The mean and standard deviation of errors are shown in tabular form. This method provides an average measurement precision of less than 0.1 mm and 0.1 degrees, respectively.
In this paper, we have presented a novel non-invasive approach to measuring the motion of the bones in a knee using tri-plane B-mode ultrasound and image registration. In our study, the image registration method determines the position of bony landmarks relative to a B-mode ultrasound sensor array with sub-pixel accuracy. The advantages of our proposed system over previous techniques are that it is non-invasive, does not require the use of ionizing radiation and can be used conveniently if miniaturized.
PMCID: PMC4162952  PMID: 25159051
Motion analysis; Ultrasound; Image registration; Knee joint diagnostics
16.  Activity of the Monocarboxylate Transporter 1 inhibitor AZD3965 in Small Cell Lung Cancer 
The monocarboxylate transporter 1 (MCT1) inhibitor AZD3965 is undergoing Phase I evaluation in the UK. AZD3965 is proposed, via lactate transport modulation, to kill tumor cells reliant on glycolysis. We investigated the therapeutic potential of AZD3965 in small cell lung cancer (SCLC) seeking rationale for clinical testing in this disease and putative predictive biomarkers for trial use.
Experimental Design
AZD3965 sensitivity was determined for 7 SCLC cell lines, in normoxia and hypoxia, and for a tumor xenograft model. Proof of mechanism was sought via changes in intracellular/tumor lactate. Expression of MCT1 and related transporter MCT4 were assessed by western blot. Drug resistance was investigated via MCT4 siRNAi and overexpression. The expression and clinical significance of MCT1 and MCT4 were explored in a tissue microarray from 78 SCLC patients.
AZD3965 sensitivity varied in vitro and was highest in hypoxia. Resistance in hypoxia was associated with increased MCT4 expression. In vivo, AZD3965 reduced tumor growth and increased intra-tumor lactate. In the tissue microarray, high MCT1 expression was associated with worse prognosis (p=0.014). MCT1 and hypoxia marker CA IX expression in the absence of MCT4 was observed in 21% of SCLC tumors.
This study provides a rationale to test AZD3965 in SCLC patients. Our results suggest that patients with tumors expressing MCT1 and lacking in MCT4 are most likely to respond.
PMCID: PMC3929348  PMID: 24277449
17.  Development of a Rapid Serological Assay for the Diagnosis of Strongyloidiasis Using a Novel Diffraction-Based Biosensor Technology 
Strongyloidiasis is a persistent human parasitic infection caused by the intestinal nematode, Strongyloides stercoralis. The parasite has a world-wide distribution, particularly in tropical and subtropical regions with poor sanitary conditions. Since individuals with strongyloidiasis are typically asymptomatic, the infection can persist for decades without detection. Problems arise when individuals with unrecognized S. stercoralis infection are immunosuppressed, which can lead to hyper-infection syndrome and disseminated disease with an associated high mortality if untreated. Therefore a rapid, sensitive and easy to use method of diagnosing Strongyloides infection may improve the clinical management of this disease.
Methodology/Principal Findings
An immunological assay for diagnosing strongyloidiasis was developed on a novel diffraction-based optical bionsensor technology. The test employs a 31-kDa recombinant antigen called NIE derived from Strongyloides stercoralis L3-stage larvae. Assay performance was tested using retrospectively collected sera from patients with parasitologically confirmed strongyloidiasis and control sera from healthy individuals or those with other parasitoses including schistosomiasis, trichinosis, echinococcosis or amebiasis who were seronegative using the NIE ELISA assay. If we consider the control group as the true negative group, the assay readily differentiated S. stercoralis-infected patients from controls detecting 96.3% of the positive cases, and with no cross reactivity observed in the control group These results were in excellent agreement (κ = 0.98) with results obtained by an NIE-based enzyme-linked immunosorbent assay (ELISA). A further 44 sera from patients with suspected S. stercoralis infection were analyzed and showed 91% agreement with the NIE ELISA.
In summary, this test provides high sensitivity detection of serum IgG against the NIE Strongyloides antigen. The assay is easy to perform and provides results in less than 30 minutes, making this platform amenable to rapid near-patient screening with minimal technical expertise.
Author Summary
A rapid and sensitive serodiagnostic assay for strongyloidiasis based on a 31-kDa recombinant antigen from Strongyloides stercoralis (NIE) was developed using a novel diffraction-based optical biosensor technology. Assay performance was tested using retrospectively collected sera from patients with parasitologically confirmed strongyloidiasis (n = 54) and control sera from healthy individuals (n = 7) or those with other parasitoses including schistosomiasis, trichinosis, echinococcosis or amebiasis (n = 40). If we consider the control group as the true negative group, the assay readily differentiated S. stercoralis-infected patients from controls detecting 96.3% of the positive cases, and with no cross reactivity observed in the control group. These results were in excellent agreement (κ = 0.98) with results obtained by an NIE-based enzyme-linked immunosorbent assay (ELISA). A further 44 sera from patients with suspected S. stercoralis infection were analyzed and showed 91% agreement with the NIE ELISA. This test provides high sensitivity detection of serum IgG against the NIE Strongyloides antigen. The assay is easy to perform and provides results in less than 30 minutes, making this platform amenable to rapid near-patient screening with minimal technical expertise.
PMCID: PMC4125104  PMID: 25102174
18.  The Effects of Acute Stress-Induced Sleep Disturbance on Acoustic Trauma-Induced Tinnitus in Rats 
BioMed Research International  2014;2014:724195.
Chronic tinnitus is a debilitating condition and often accompanied by anxiety, depression, and sleep disturbance. It has been suggested that sleep disturbance, such as insomnia, may be a risk factor/predictor for tinnitus-related distress and the two conditions may share common neurobiological mechanisms. This study investigated whether acute stress-induced sleep disturbance could increase the susceptibility to acoustic trauma-induced tinnitus in rats. The animals were exposed to unilateral acoustic trauma 24 h before sleep disturbance being induced using the cage exchange method. Tinnitus perception was assessed behaviourally using a conditioned lick suppression paradigm 3 weeks after the acoustic trauma. Changes in the orexin system in the hypothalamus, which plays an important role in maintaining long-lasting arousal, were also examined using immunohistochemistry. Cage exchange resulted in a significant reduction in the number of sleep episodes and acoustic trauma-induced tinnitus with acoustic features similar to a 32 kHz tone at 100 dB. However, sleep disturbance did not exacerbate the perception of tinnitus in rats. Neither tinnitus alone nor tinnitus plus sleep disturbance altered the number of orexin-expressing neurons. The results suggest that acute sleep disturbance does not cause long-term changes in the number of orexin neurons and does not change the perception of tinnitus induced by acoustic trauma in rats.
PMCID: PMC4137606  PMID: 25162023
19.  The ABC-F protein EttA gates ribosome entry into the translation elongation cycle 
ABC-F proteins have evaded functional characterization even though they comprise one of the most widely distributed branches of the ATP-binding cassette (ABC) superfamily. Herein, we demonstrate that YjjK, the most prevalent eubacterial ABC-F protein, gates ribosome entry into the translation elongation cycle through a nucleotide-dependent interaction sensitive to ATP/ADP ratio. Accordingly, we rename this protein Energy-dependent Translational Throttle A (EttA). We determined the crystal structure of Escherichia coli EttA and used it to design mutants for biochemical studies, including enzymological assays of the initial steps of protein synthesis. These studies suggest that EttA may regulate protein synthesis in energy-depleted cells, which have a low ATP/ADP ratio. Consistent with this inference, ΔettA cells exhibit a severe fitness defect in long-term stationary phase. These studies demonstrate that an ABC-F protein regulates protein synthesis via a novel mechanism sensitive to cellular energy status.
PMCID: PMC4101993  PMID: 24389466
Protein synthesis; translational regulation; ABC-F protein family; YjjK; ATP/ADP ratio; stationary phase fitness; X-ray crystallography
20.  Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial Pnkp•Hen1 RNA repair system 
Biochemistry  2013;52(27):10.1021/bi400412x.
Clostridium thermocellum Pnkp is the end-healing and end-sealing subunit of a bacterial RNA repair system. CthPnkp is composed of three catalytic modules: an N-terminal 5′-OH polynucleotide kinase; a central 2′,3′ phosphatase; and a C-terminal ligase. The crystal structure of the kinase domain bound to ATP•Mg2+ revealed a rich network of ionic and hydrogen-bonding contacts to the α, β, and γ phosphates. By contrast, there are no enzymic contacts to the ribose and none with the adenine base other than a π-cation interaction with Arg116. Here we report that the enzyme uses ATP, GTP, CTP, UTP or dATP as a phosphate donor for the 5′-OH kinase reaction. The enzyme also catalyzes the reverse reaction, in which a polynucleotide 5′-PO4 group is transferred to ADP, GDP, CDP, UDP or dADP to form the corresponding NTP. We report new crystal structures of the kinase in complexes with GTP, CTP, UTP and dATP in which the respective nucleobases are stacked on Arg116 but make no other enzymic contacts. Mutating Arg116 to alanine elicits a 10-fold increase in Km for ATP, but has little effect on kcat. These findings illuminate the basis for non-specific donor nucleotide utilization by a P-loop phosphotransferase.
PMCID: PMC3855621  PMID: 23721485
21.  Discovery of Tetrahydropyrazolopyrimidine Carboxamide Derivatives As Potent and Orally Active Antitubercular Agents 
ACS Medicinal Chemistry Letters  2013;4(5):451-455.
Tetrahydropyrazolo[1,5-a]pyrimidine scaffold was identified as a hit series from a Mycobacterium tuberculosis (Mtb) whole cell high through-put screening (HTS) campaign. A series of derivatives of this class were synthesized to evaluate their structure–activity relationship (SAR) and structure–property relationship (SPR). Compound 9 had a promising in vivo DMPK profile in mouse and exhibited potent in vivo activity in a mouse efficacy model, achieving a reduction of 3.5 log CFU of Mtb after oral administration to infected mice once a day at 100 mg/kg for 28 days. Thus, compound 9 is a potential candidate for inclusion in combination therapies for both drug-sensitive and drug-resistant TB.
PMCID: PMC4027361  PMID: 24900693
Antituberculosis; tetrahydropyrazolo[1,5-a]pyrimidine; structure−activity relationship; structure−property relationship
22.  Local Fluctuations in Solution: Theory and Applications 
Advances in chemical physics  2013;153:311-372.
PMCID: PMC3967877  PMID: 24683278
23.  Longer ice-free seasons increase the risk of nest depredation by polar bears for colonial breeding birds in the Canadian Arctic 
Northern polar regions have warmed more than other parts of the globe potentially amplifying the effects of climate change on biological communities. Ice-free seasons are becoming longer in many areas, which has reduced the time available to polar bears (Ursus maritimus) to hunt for seals and hampered bears’ ability to meet their energetic demands. In this study, we examined polar bears’ use of an ancillary prey resource, eggs of colonial nesting birds, in relation to diminishing sea ice coverage in a low latitude region of the Canadian Arctic. Long-term monitoring reveals that bear incursions onto common eider (Somateria mollissima) and thick-billed murre (Uria lomvia) nesting colonies have increased greater than sevenfold since the 1980s and that there is an inverse correlation between ice season length and bear presence. In surveys encompassing more than 1000 km of coastline during years of record low ice coverage (2010–2012), we encountered bears or bear sign on 34% of eider colonies and estimated greater egg loss as a consequence of depredation by bears than by more customary nest predators, such as foxes and gulls. Our findings demonstrate how changes in abiotic conditions caused by climate change have altered predator–prey dynamics and are leading to cascading ecological impacts in Arctic ecosystems.
PMCID: PMC3924086  PMID: 24500172
arctic; bird; climate change; foraging; polar bear; predator–prey dynamics
24.  Unraveling Protein-Protein Interactions in Clathrin Assemblies via Atomic Force Spectroscopy 
Methods (San Diego, Calif.)  2012;59(3):316-327.
Atomic force microscopy (AFM), single molecule force spectroscopy (SMFS), and single particle force spectroscopy (SPFS) are used to characterize intermolecular interactions and domain structures of clathrin triskelia and clathrin-coated vesicles (CCVs). The latter are involved in receptor-mediated endocytosis (RME) and other trafficking pathways. Here, we subject individual triskelia, bovine-brain CCVs, and reconstituted clathrin-AP180 coats to AFM-SMFS and AFM-SPFS pulling experiments and apply novel analytics to extract force-extension relations from very large data sets. The spectroscopic fingerprints of these samples differ markedly, providing important new information about the mechanism of CCV uncoating. For individual triskelia, SMFS reveals a series of events associated with heavy chain alpha-helix hairpin unfolding, as well as cooperative unraveling of several hairpin domains. SPFS of clathrin assemblies exposes weaker clathrin-clathrin interactions that are indicative of inter-leg association essential for RME and intracellular trafficking. Clathrin-AP180 coats are energetically easier to unravel than the coats of CCVs, with a non-trivial dependence on force-loading rate.
PMCID: PMC3608793  PMID: 23270814
Clathrin Triskelion and Clathrin-coated Vesicles; Single Molecular Force Spectroscopy (SMFS); Single Particle Force Spectroscopy (SPFS); Atomic force microscopy (AFM); Macromolecular Assembly; Protein Interaction and Protein Folding
25.  A Kirkwood-Buff Force Field for the Aromatic Amino Acids 
In a continuation of our efforts to develop a united atom non-polarizable protein force field based upon the solution theory of Kirkwood and Buff i.e., the Kirkwood-Buff Force Field (KBFF) approach, we present KBFF models for the side chains of phenylalanine, tyrosine, tryptophan, and histidine, including both tautomers of neutral histidine and doubly-protonated histidine. The force fields were specifically designed to reproduce the thermodynamic properties of mixtures over the full composition range in an attempt to provide an improved description of intermolecular interactions. The models were developed by careful parameterization of the solution phase partial charges to reproduce the experimental Kirkwood-Buff integrals for mixtures of solutes representative of the amino acid sidechains in solution. The KBFF parameters and simulated thermodynamic and structural properties are presented for the following eleven binary mixtures: benzene + methanol, benzene + toluene, toluene + methanol, toluene + phenol, toluene + p-cresol, pyrrole + methanol, indole + methanol, pyridine + methanol, pyridine + water, histidine + water, and histidine hydrochloride + water. It is argued that the present approach and models provide a reasonable description of intermolecular interactions which ensures that the required balance between solute-solute, solute-solvent, and solvent-solvent distributions is obtained.
PMCID: PMC3910502  PMID: 21931889

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