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1.  Understanding the hepatitis C virus life cycle paves the way for highly effective therapies 
Nature medicine  2013;19(7):837-849.
More than two decades of intense research has provided a detailed understanding of hepatitis C virus (HCV), which chronically infects 2% of the world's population. This effort has paved the way for the development of antiviral compounds to spare patients from life-threatening liver disease. An exciting new era in HCV therapy dawned with the recent approval of two viral protease inhibitors, used in combination with pegylated interferon-α and ribavirin; however, this is just the beginning. Multiple classes of antivirals with distinct targets promise highly efficient combinations, and interferon-free regimens with short treatment duration and fewer side effects are the future of HCV therapy. Ongoing and future trials will determine the best antiviral combinations and whether the current seemingly rich pipeline is sufficient for successful treatment of all patients in the face of major challenges, such as HCV diversity, viral resistance, the influence of host genetics, advanced liver disease and other co-morbidities.
doi:10.1038/nm.3248
PMCID: PMC3984536  PMID: 23836234
2.  Maximum Running Speed of Captive Bar-Headed Geese Is Unaffected by Severe Hypoxia 
PLoS ONE  2014;9(4):e94015.
While bar-headed geese are renowned for migration at high altitude over the Himalayas, previous work on captive birds suggested that these geese are unable to maintain rates of oxygen consumption while running in severely hypoxic conditions. To investigate this paradox, we re-examined the running performance and heart rates of bar-headed geese and barnacle geese (a low altitude species) during exercise in hypoxia. Bar-headed geese (n = 7) were able to run at maximum speeds (determined in normoxia) for 15 minutes in severe hypoxia (7% O2; simulating the hypoxia at 8500 m) with mean heart rates of 466±8 beats min−1. Barnacle geese (n = 10), on the other hand, were unable to complete similar trials in severe hypoxia and their mean heart rate (316 beats.min−1) was significantly lower than bar-headed geese. In bar-headed geese, partial pressures of oxygen and carbon dioxide in both arterial and mixed venous blood were significantly lower during hypoxia than normoxia, both at rest and while running. However, measurements of blood lactate in bar-headed geese suggested that anaerobic metabolism was not a major energy source during running in hypoxia. We combined these data with values taken from the literature to estimate (i) oxygen supply, using the Fick equation and (ii) oxygen demand using aerodynamic theory for bar-headed geese flying aerobically, and under their own power, at altitude. This analysis predicts that the maximum altitude at which geese can transport enough oxygen to fly without environmental assistance ranges from 6,800 m to 8,900 m altitude, depending on the parameters used in the model but that such flights should be rare.
doi:10.1371/journal.pone.0094015
PMCID: PMC3977980  PMID: 24710001
3.  PhoB Activates Escherichia coli O157:H7 Virulence Factors in Response to Inorganic Phosphate Limitation 
PLoS ONE  2014;9(4):e94285.
Enterohemorrhagic Escherichia coli (EHEC), an emerging food- and water-borne hazard, is highly pathogenic to humans. In the environment, EHEC must survive phosphate (Pi) limitation. The response to such Pi starvation is an induction of the Pho regulon including the Pst system that senses Pi variation. The interplay between the virulence of EHEC, Pho-Pst system and environmental Pi remains unknown. To understand the effects of Pi deprivation on the molecular mechanisms involved in EHEC survival and virulence under Pho regulon control, we undertook transcriptome profiling of the EDL933 wild-type strain grown under high Pi and low Pi conditions and its isogenic ΔphoB mutant grown in low Pi conditions. The differentially expressed genes included 1067 Pi-dependent genes and 603 PhoB-dependent genes. Of these 131 genes were both Pi and PhoB-dependent. Differentially expressed genes that were selected included those involved in Pi homeostasis, cellular metabolism, acid stress, oxidative stress and RpoS-dependent stress responses. Differentially expressed virulence systems included the locus of enterocyte effacement (LEE) encoding the type-3 secretion system (T3SS) and its effectors, as well as BP-933W prophage encoded Shiga toxin 2 genes. Moreover, PhoB directly regulated LEE and stx2 gene expression through binding to specific Pho boxes. However, in Pi-rich medium, constitutive activation of the Pho regulon decreased LEE gene expression and reduced adherence to HeLa cells. Together, these findings reveal that EHEC has evolved a sophisticated response to Pi limitation involving multiple biochemical strategies that contribute to its ability to respond to variations in environmental Pi and to coordinating the virulence response.
doi:10.1371/journal.pone.0094285
PMCID: PMC3978041  PMID: 24710330
4.  Poly(beta-amino ester) nanoparticle-delivery of p53 has activity against small cell lung cancer in vitro and in vivo 
Molecular cancer therapeutics  2013;12(4):405-415.
Small cell lung cancer (SCLC) is an aggressive disease with one of the highest case-fatality rates among cancer. The recommended therapy for SCLC has not changed significantly over the past 30 years; new therapeutic approaches are a critical need. TP53 is mutated in the majority of SCLC cases and its loss is required in transgenic mouse models of the disease. We synthesized an array of biodegradable poly(beta-amino ester) (PBAE) polymers which self-assemble with DNA and assayed for transfection efficiency in the p53-mutant H446 SCLC cell line using high-throughput methodologies. Two of the top candidates were selected for further characterization and TP53 delivery in vitro and in vivo. Nanoparticle delivery of TP53 resulted in expression of exogenous p53, induction of p21, induction of apoptosis and accumulation of cells in sub-G1 consistent with functional p53 activity. Intratumoral injection of subcutaneous H446 xenografts with polymers carrying TP53 caused marked tumor growth inhibition. This is the first demonstration of TP53 gene therapy in SCLC using non-viral polymeric nanoparticles. This technology may have general applicability as a novel anti-cancer strategy based on restoration of tumor suppressor gene function.
doi:10.1158/1535-7163.MCT-12-0956
PMCID: PMC3624031  PMID: 23364678
p53; PBAE; nanoparticles; gene therapy; SCLC
5.  Inhibition of TWIST1 Leads to Activation of Oncogene-Induced Senescence in Oncogene Driven Non-Small Cell Lung Cancer 
Molecular cancer research : MCR  2013;11(4):329-338.
A large fraction of non-small cell lung cancers (NSCLC) are dependent on defined oncogenic driver mutations. Although targeted agents exist for EGFR- and EML4-ALK-driven NSCLC, no therapies target the most frequently found driver mutation, KRAS. Furthermore, acquired resistance to the currently targetable driver mutations is nearly universally observed. Clearly a novel therapeutic approach is needed to target oncogene driven NSCLC. We recently demonstrated that the basic helix-loop-helix transcription factor Twist1 cooperates with mutant Kras to induce lung adenocarcinoma in transgenic mouse models and that inhibition of Twist1 in these models led to Kras-induced senescence. In the current study, we examine the role of TWIST1 in oncogene driven human NSCLC. Silencing of TWIST1 in KRAS mutant human NSCLC cell lines resulted in dramatic growth inhibition and either activation of a latent oncogene-induced senescence program or in some cases, apoptosis. Similar effects were observed in EGFR mutation driven and c-Met amplified NSCLC cell lines. Growth inhibition by silencing of TWIST1 was independent of p53 or p16 mutational status and did not require previously defined mediators of senescence, p21 and p27, nor could this phenotype be rescued by overexpression of SKP2. In xenograft models, silencing of TWIST1 resulted in significant growth inhibition of KRAS mutant, EGFR mutant and c-Met amplified NSCLC. Remarkably, inducible silencing of TWIST1 resulted in significant growth inhibition of established KRAS mutant tumors. Together these findings suggest that silencing of TWIST1 in oncogene driver dependent NSCLC represents a novel and promising therapeutic strategy.
doi:10.1158/1541-7786.MCR-12-0456
PMCID: PMC3631276  PMID: 23364532
TWIST1; OIS; KRAS; NSCLC; EGFR
6.  Synthesis and Anti-Acetylcholinesterase Properties of Novel β- and γ-Substituted Alkoxy Organophosphonates 
Activated organophosphate (OP) insecticides and chemical agents inhibit acetylcholinesterase (AChE) to form OP-AChE adducts. Whereas the structure of the OP correlates with the rate of inhibition, the structure of the OP-AChE adduct influences the rate at which post-inhibitory reactivation or aging phenomena occurs. In this report, we prepared a panel of β-substituted ethoxy and γ-substituted propoxy phosphonoesters of the type p-NO2PhO-P(X)(R)[(O(CH2)nZ] (R = Me, Et; X = O, S; n = 2, 3; Z = halogen, OTs) and examined the inhibition of three AChEs by select structures in the panel. The β-fluoroethoxy methylphosphonate analog (R = Me, Z = F, n = 2) was the most potent anti-AChE compound comparable (ki ~ 6 ×106 M−1min−1) to paraoxon against EEAChE. Analogs with Z = Br, I, or OTs were weak inhibitors of the AChEs, and methyl phosphonates (R = Me) were more potent than the corresponding ethyl phosphonates (R =Et). As expected, analogs with a thionate linkage (P=S) were poor inhibitors of the AChEs.
doi:10.1016/j.bmcl.2013.02.010
PMCID: PMC3640285  PMID: 23453838
Organophosphates; Inhibition; Electric Eel AChE; Recombinant human AChE; Rat brain AChE
7.  The Health of HIV-exposed Children after Early Weaning 
Maternal & child nutrition  2011;9(2):217-232.
There are potential health risks associated with the use of early weaning to prevent mother-to-child transmission of HIV in resource-poor settings. Our objective was to examine growth and nutrient inadequacies among a cohort of children weaned early. Children participating in the Breastfeeding Antiretrovirals and Nutrition (BAN) Study in Lilongwe, Malawi, had HIV-infected mothers, were weaned at 6 months and fed LNS until 12 months. 40 HIV-negative, BAN-exited children were compared to 40 HIV-negative, community children matched on age, gender and local health clinic. Nutrient intake was calculated from 24-hour dietary recalls collected from BAN-exited children. Anthropometric measurements were collected from BAN-exited and matched community children at 15-16 months, and 2 months later. Longitudinal random effects sex-stratified models were used to evaluate anthropometric differences between the 2 groups. BAN-exited children consumed adequate energy, protein, and carbohydrates but inadequate amounts of fat. The prevalence of inadequate micronutrient intakes were: 46% for vitamin A; 20% for vitamin B6; 69% for folate; 13% for vitamin C; 19% for iron; 23% for zinc. Regarding growth, BAN-exited girls gained weight at a significantly lower rate (0.02g/kg/day [95%CI: 0.01, 0.03] than their matched comparison (0.05g/kg/day [95%CI: 0.03, 0.07]); BAN girls grew significantly slower (0.73cm/month [95%CI: 0.40,1.06]) than their matched comparison (1.55cm/month [95%CI: 0.98, 2.12]). Among this sample of BAN-exited children, early weaning was associated with dietary deficiencies and girls experienced reduced growth velocity. In resource-poor settings, HIV prevention programs must ensure that breastfeeding stop only once a nutritionally adequate and safe diet without breastmilk can be provided.
doi:10.1111/j.1740-8709.2011.00369.x
PMCID: PMC3787136  PMID: 22099216
LNS; early breastfeeding cessation; HIV; Malawi; child growth
8.  ExbB Cytoplasmic Loop Deletions Cause Immediate, Proton Motive Force-Independent Growth Arrest 
Journal of Bacteriology  2013;195(20):4580-4591.
The Escherichia coli TonB system consists of the cytoplasmic membrane proteins TonB, ExbB, and ExbD and multiple outer membrane active transporters for diverse iron siderophores and vitamin B12. The cytoplasmic membrane proteins harvest and transmit the proton motive force (PMF) to outer membrane transporters. This system, which spans the cell envelope, has only one component with a significant cytoplasmic presence, ExbB. Characterization of sequential 10-residue deletions in the ExbB cytoplasmic loop (residues 40 to 129; referred to as Δ10 proteins) revealed that it was required for all TonB-dependent activities, including interaction between the periplasmic domains of TonB and ExbD. Expression of eight out of nine of the Δ10 proteins at chromosomal levels led to immediate, but reversible, growth arrest. Arrest was not due to collapse of the PMF and did not require the presence of ExbD or TonB. All Δ10 proteins that caused growth arrest were dominant for that phenotype. However, several were not dominant for iron transport, indicating that growth arrest was an intrinsic property of the Δ10 variants, whether or not they could associate with wild-type ExbB proteins. The lack of dominance in iron transport also ruled out trivial explanations for growth arrest, such as high-level induction. Taken together, the data suggest that growth arrest reflected a changed interaction between the ExbB cytoplasmic loop and one or more unknown growth-regulatory proteins. Consistent with that, a large proportion of the ExbB cytoplasmic loop between transmembrane domain 1 (TMD1) and TMD2 is predicted to be disordered, suggesting the need for interaction with one or more cytoplasmic proteins to induce a final structure.
doi:10.1128/JB.00334-13
PMCID: PMC3807443  PMID: 23913327
9.  The ins and outs of hepatitis C virus entry and assembly 
Nature reviews. Microbiology  2013;11(10):688-700.
Preface
Hepatitis C virus, a major human pathogen, produces infectious virus particles with several unique features, such as an ability to interact with serum lipoproteins, a dizzyingly complicated process of virus entry, and a pathway of virus assembly and release that is closely linked to lipoprotein secretion. Here we review these unique features, with an emphasis on recent discoveries in virus particle structure, virus entry and virus particle assembly and release.
doi:10.1038/nrmicro3098
PMCID: PMC3897199  PMID: 24018384
10.  Oncogenic mutations in cervical cancer: genomic differences between adenocarcinomas and squamous cell carcinomas of the cervix 
Cancer  2013;119(21):3776-3783.
Background
Cervical cancer is the second leading cause of cancer deaths among women worldwide. We sought to describe the most common oncogenic mutations in cervical cancers, and to explore genomic differences between the two most common histological subtypes: adenocarcinoma and squamous cell carcinoma.
Methods
A high-throughput genotyping platform, termed Oncomap, was used to interrogate 80 cervical tumors for 1250 known mutations in 139 cancer genes. Samples were analyzed using a mass spectrometry-based genotyping platform (Sequenom), and validated with an orthogonal chemistry. EGFR mutations were further validated by massively parallel sequencing (Illumina). Human papilloma virus (HPV) genotyping was also performed.
Results
Validated mutations were detected in 60.0% (48/80) of tumors examined. The highest mutation rates were PIK3CA (31.3%), KRAS (8.8%), and EGFR (3.8%). PIK3CA mutation rates were not significantly different in adenocarcinoma and squamous cell carcinomas (25.0% vs. 37.5%, respectively, p=0.33). In contrast, KRAS mutations were identified only in adenocarcinoma (17.5% vs. 0%, p=0.01), and a novel EGFR mutation was detected only in squamous cell carcinomas (0% vs. 7.5%, p=0.24). There were no associations between HPV-16 or HPV-18 and somatic mutations or overall survival. In adjusted analyses, PIK3CA mutations were associated with shorter survival—67.1 vs. 90.3 months (HR=9.1, 95% CI 2.8–29.5, p<0.001).
Conclusions
Cervical cancers harbor high rates of potentially targetable oncogenic mutations. In addition, cervical squamous cell carcinoma and adenocarcinoma have distinct molecular profiles, suggesting that clinical outcomes may be improved with the use of more tailored treatment strategies, including PI3-kinase and MEK inhibitors.
doi:10.1002/cncr.28288
PMCID: PMC3972000  PMID: 24037752
cervical cancer; adenocarcinoma; squamous cell carcinoma; somatic mutations; PI3K; PIK3CA; EGFR; KRAS; DNA mutational analysis; human papilloma virus (HPV); neoplasm; mutation
11.  Reduced Inflammation and Lymphoid Tissue Immunopathology in Rhesus Macaques Receiving Anti–Tumor Necrosis Factor Treatment During Primary Simian Immunodeficiency Virus Infection 
The Journal of Infectious Diseases  2012;207(6):880-892.
Background. Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections induce robust, generalized inflammatory responses that begin during acute infection and lead to pathological systemic immune activation, fibrotic damage of lymphoid tissues, and CD4+ T-cell loss, pathogenic processes that contribute to disease progression.
Methods. To better understand the contribution of tumor necrosis factor (TNF), a key regulator of acute inflammation, to lentiviral pathogenesis, rhesus macaques newly infected with SIVmac239 were treated for 12 weeks in a pilot study with adalimumab (Humira), a human anti-TNF monoclonal antibody.
Results. Adalimumab did not affect plasma SIV RNA levels or measures of T-cell immune activation (CD38 or Ki67) in peripheral blood or lymph node T cells. However, compared with untreated rhesus macaques, adalimumab-treated rhesus macaques showed attenuated expression of proinflammatory genes, decreased infiltration of polymorphonuclear cells into the T-cell zone of lymphoid tissues, and weaker antiinflammatory regulatory responses to SIV infection (ie, fewer presumed alternatively activated [ie, CD163+] macrophages, interleukin 10–producing cells, and transforming growth factor β–producing cells), along with reduced lymphoid tissue fibrosis and better preservation of CD4+ T cells.
Conclusions. While HIV/SIV replication drives pathogenesis, these data emphasize the contribution of the inflammatory response to lentiviral infection to overall pathogenesis, and they suggest that early modulation of the inflammatory response may help attenuate disease progression.
doi:10.1093/infdis/jis643
PMCID: PMC3571439  PMID: 23087435
SIV; rhesus macaque; Sooty mangabey; lymph node; inflammation; adalimumab; TNF; macrophage; fibrosis; collagen; TGFb
12.  Murine microenvironment metaprofiles associate with human cancer etiology and intrinsic subtypes 
Purpose
Ionizing radiation is a well established carcinogen in rodent models and a risk factor associated with human cancer. We developed a mouse model that captures radiation effects on host biology by transplanting unirradiated Trp53 null mammary tissue to sham or irradiated hosts. Gene expression profiles of tumors that arose in irradiated mice are distinct from those that arose in naïve hosts. We asked whether expression metaprofiles could discern radiation-preceded human cancer or be informative in sporadic breast cancers.
Experimental Design
Affymetrix microarray gene expression data from 56 Trp53 null mammary tumors were used to define gene profiles and a centroid that discriminate tumors arising in irradiated hosts. These were applied to publicly available human cancer data sets.
Results
Host irradiation induces a metaprofile consisting of gene modules representing stem cells, cell motility, macrophages and autophagy. Human orthologs of the host irradiation metaprofile discriminated between radiation-preceded and sporadic human thyroid cancers. An irradiated host centroid was strongly associated with estrogen receptor negative breast cancer. When applied to sporadic human breast cancers, the irradiated host metaprofile strongly associated with basal-like and claudin-low breast cancer intrinsic subtypes. Comparing host irradiation in the context of TGFβ levels showed that inflammation was robustly associated with claudin-low tumors.
Conclusions
Detection of radiation-preceded human cancer by the irradiated host metaprofile raises possibilities of assessing human cancer etiology. Moreover, the association of the irradiated host metaprofiles with estrogen receptor negative status and claudin-low subtype suggests that host processes similar to those induced by radiation underlie sporadic cancers.
doi:10.1158/1078-0432.CCR-12-3554
PMCID: PMC3732211  PMID: 23339125
ionizing radiation; breast cancer; intrinsic subtypes; etiology
13.  Completion of the entire hepatitis C virus life-cycle in genetically humanized mice 
Nature  2013;501(7466):10.1038/nature12427.
More than 130 million people world-wide chronically infected with hepatitis C virus (HCV) are at risk of developing severe liver disease. Antiviral treatments are only partially effective and a vaccine is not available. Development of more efficient therapies has been hampered by the lack of a small animal model. Building on the observation that CD81 and occludin (OCLN) comprise the minimal set of human factors required to render mouse cells permissive to HCV entry1 we previously showed that transient expression of these two human genes is sufficient to allow viral uptake into fully immunocompetent inbred mice2. Here, we demonstrate that transgenic mice stably expressing human CD81 and OCLN also support HCV entry but innate and adaptive immune responses restrict HCV infection in vivo. Blunting antiviral immunity in genetically humanized mice infected with HCV results in measurable viremia over several weeks. In mice lacking the essential cellular co-factor cyclophilin A (CypA), HCV RNA replication is markedly diminished, providing genetic evidence that this process is faithfully recapitulated. Using a cell-based fluorescent reporter activated by the NS3-4A protease we visualize HCV infection in single hepatocytes in vivo. Persistently infected mice produce de novo infectious particles, which can be inhibited with directly acting antiviral drug treatment, thereby providing for the first time evidence for the completion of the entire HCV life-cycle in inbred mice. This genetically humanized mouse model opens new opportunities to genetically dissect HCV infection in vivo and provides an important preclinical platform for testing and prioritizing drug and vaccine candidates.
doi:10.1038/nature12427
PMCID: PMC3858853  PMID: 23903655
14.  First use of 18F-labeled ML-10 PET to assess apoptosis change in a newly diagnosed glioblastoma multiforme patient before and early after therapy 
Brain and Behavior  2014;4(2):312-315.
Objectives
The authors present the first use of the novel positron emission tomography (PET) apoptosis tracer 18F-labeled 2-(5-fluoro-pentyl)-2-methyl-malonic acid (18F-ML-10) for early-therapy response assessment of a newly diagnosed glioblastoma multiforme (GBM) patient.
Case report
A 71-year-old male with a newly diagnosed GBM received 18F-ML-10 PET scans prior to therapy initiation (baseline) and after completing 3 weeks of whole-brain radiation therapy with concomitant temozolomide chemotherapy (early-therapy assessment, ETA). The baseline 18F-ML-10 PET scan showed increased tracer uptake at the site of the GBM, with highest activity toward the central portion of the tumor. At the ETA time point, a new distribution of tracer uptake was observed compared to baseline. Normalized pixel-by-pixel subtraction of baseline from ETA was used to quantify change in tracer distribution between 18F-ML-10 PET imaging time points. Results of this analysis showed reduction in 18F-ML-10 uptake at the site of greatest baseline uptake, but increased uptake around the periphery of the tumor at the early-therapy time point.
Conclusion
The changing patterns of 18F-ML-10 uptake between baseline and ETA are suggestive for therapy-induced tumor cellular apoptosis.
doi:10.1002/brb3.217
PMCID: PMC3967545
18F-ML-10; early-therapy response assessment; glioblastoma multiforme; positron emission tomography
15.  Synthetic Nanoelectronic Probes for Biological Cells and Tissue 
Research at the interface between nanoscience and biology has the potential to produce breakthroughs in fundamental science and lead to revolutionary technologies. In this review, we focus on nanoelectronic/biological interfaces. First, we discuss nanoscale field effect transistors (nanoFETs) as probes to study cellular systems, including the realization of nanoFET comparable in size to biological nanostructures involved in communication using synthesized nanowires. Second, we overview current progress in multiplexed extracellular sensing using planar nanoFET arrays. Third, we describe the design and implementation of three distinct nanoFETs used to realize the first intracellular electrical recording from single cells. Fourth, we present recent progress in merging electronic and biological systems at the 3D tissue level by using macroporous nanoelectronic scaffolds. Finally, we discuss future development in this research area, the unique challenges and opportunities, and the tremendous impact these nanoFET based technologies might have in advancing biology and medical sciences.
doi:10.1146/annurev-anchem-062012-092623
PMCID: PMC3771379  PMID: 23451719
Nanowire; field effect transistor; intracellular; extracellular; synthetic tissue
16.  Synthesis of Long-T1 Silicon Nanoparticles for Hyperpolarized 29Si Magnetic Resonance Imaging 
ACS nano  2013;7(2):1609-1617.
We describe the synthesis, materials characterization and dynamic nuclear polarization (DNP) of amorphous and crystalline silicon nanoparticles for use as hyperpolarized magnetic resonance imaging (MRI) agents. The particles were synthesized by means of a metathesis reaction between sodium silicide (Na4Si4) and silicon tetrachloride (SiCl4) and were surface functionalized with a variety of passivating ligands. The synthesis scheme results in particles of diameter ~10 nm with long size-adjusted 29Si spin lattice relaxation (T1) times (> 600 s), which are retained after hyperpolarization by low temperature DNP.
doi:10.1021/nn305462y
PMCID: PMC3612549  PMID: 23350651
Silicon; nanoparticle; dynamic nuclear polarization; hyperpolarization; nanomedicine; magnetic resonance imaging
17.  Design and Synthesis of Diverse Functional Kinked Nanowire Structures for Nanoelectronic Bioprobes 
Nano letters  2013;13(2):746-751.
Functional kinked nanowires (KNWs) represent a new class of nanowire building blocks, in which functional devices, for example, nanoscale field-effect transistors (nanoFETs), are encoded in geometrically controlled nanowire superstructures during synthesis. The bottom-up control of both structure and function of KNWs enables construction of spatially isolated point-like nanoelectronic probes that are especially useful for monitoring biological systems where finely tuned feature size and structure are highly desired. Here we present three new types of functional KNWs including (1) the zero-degree KNW structures with two parallel heavily-doped arms of U-shaped structures with a nanoFET at the tip of the “U”, (2) series multiplexed functional KNW integrating multi-nanoFETs along the arm and at the tips of V-shaped structures, and (3) parallel multiplexed KNWs integrating nanoFETs at the two tips of W-shaped structures. First, U-shaped KNWs were synthesized with separations as small as 650 nm between the parallel arms, and used to fabricate three-dimensional nanoFET probes at least 3 times smaller than previous V-shaped designs. In addition, multiple nanoFETs were encoded during synthesis in one of arms/tip of V-shaped and distinct arms/tips of W-shaped KNWs. These new multiplexed KNW structures were structurally-verified by optical and electron microscopy of dopant-selective etched samples, and electrically-characterized using scanning gate microscopy and transport measurements. The facile design and bottom-up synthesis of these diverse functional KNWs provides a growing toolbox of building blocks for fabricating highly compact and multiplexed three-dimensional nanoprobes for applications in life sciences, including intra-cellular and deep tissue/cell recordings.
doi:10.1021/nl304435z
PMCID: PMC3572243  PMID: 23273386
silicon nanowire; nanoprobe; nanosensor; field-effect transistor
18.  Improving Participant Understanding of Informed Consent in an HIV-Prevention Clinical Trial: A Comparison of Methods 
AIDS and behavior  2012;16(2):412-421.
Empirical research on informed consent has shown that study participants often do not fully understand consent information. This study assessed participant understanding of three mock consent approaches describing an HIV-prevention clinical trial in Lilongwe, Malawi prior to trial implementation. Pregnant women (n = 297) were systematically selected from antenatal-care waiting lines and sequentially allocated to receive an enhanced standard consent form (group 1), a context-specific consent form (group 2), or context-specific counseling cards (group 3). Understanding of research concepts and study procedures was assessed immediately postintervention and at 1-week follow-up. At postintervention, participants in groups 2 and 3 understood more about research concepts and study procedures compared with group 1. Group 3 participants also understood more about study procedures compared with group 2. At follow-up, participants in groups 2 and 3 continued to understand more about research concepts and study procedures. Context-specific approaches improved understanding of consent information in this study.
doi:10.1007/s10461-011-9977-z
PMCID: PMC3923514  PMID: 21656146
Informed consent; Evaluation; Comprehension; Africa
19.  Laboratory Colonisation and Genetic Bottlenecks in the Tsetse Fly Glossina pallidipes 
Background
The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT) programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations.
Methodology/Principal Findings
We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC). There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population.
Conclusions/Significance
All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology.
Author Summary
There is only one mass reared laboratory colony of Glossina pallidipes, a vector of human African trypanosomiasis and arguably the main vector of animal African trypanosomiasis in eastern Africa. This colony is the main one used for basic research on this species and is intended to be used for Sterile Insect Technique (SIT) programs for control of field populations. The origins of this colony are not clear and the extent to which it is genetically representative of the species is unknown. Using population genetics analyses to compare the current colony with two potential source populations we have shown that the colony is from the Kenya/Uganda border and that its foundation and establishment in the laboratory were associated with a genetic bottleneck, i.e. reduction of genetic variation due to increased genetic drift in a population of reduced size. As a consequence, the genetic diversity of the colony is lower than that of G. pallidipes field populations.
doi:10.1371/journal.pntd.0002697
PMCID: PMC3923722  PMID: 24551260
20.  Inflammatory Flt3L is essential to mobilize dendritic cells and for T cell responses during Plasmodium infection 
Nature medicine  2013;19(6):730-738.
Summary
Innate sensing mechanisms trigger a variety of humoral and cellular events that are essential to adaptive immune responses. Here we describe an innate sensing pathway triggered by Plasmodium infection that regulates dendritic cell (DC) homeostasis and adaptive immunity via Flt3L release. Plasmodium-induced Flt3L release requires toll-like receptor activation and type I interferon production. We find that type I interferon supports the up-regulation of xanthine dehydrogenase, which metabolizes the xanthine accumulating in infected erythrocytes to uric acid. Uric acid crystals trigger mast cells to release soluble Flt3L from a pre-synthesized membrane-associated precursor. During infection Flt3L preferentially stimulates expansion of the CD8α+/CD103+ DC subset or its BDCA3+ human DC equivalent and has a significant impact on the magnitude of T cell activation, mostly in the CD8+ compartment. Our findings highlight a new mechanism that regulates DC homeostasis and T cell responses to infection.
doi:10.1038/nm.3197
PMCID: PMC3914008  PMID: 23685841
21.  Molecular Characterization of Basal-Like and Non-Basal-Like Triple-Negative Breast Cancer 
The Oncologist  2013;18(2):123-133.
Triple-negative breast cancer is a broad and diverse category for which additional subclassifications are needed. Therefore, future clinical trials should stratify patients based on a tumor′s basal-like versus non-basal-like gene expression profile, which appears to be the main biological difference seen within triple-negative breast cancer.
Learning Objectives
Contrast the definitions of TN and basal-like.Describe the undistinguishable global gene expression patterns of non-basal-like TN tumors versus non-TN tumors that are non-basal-like.Describe the relationship between TN heterogeneity and tumor heterogeneity plus microenvironmental heterogeneity.
Triple-negative (TN) and basal-like (BL) breast cancer definitions have been used interchangeably to identify breast cancers that lack expression of the hormone receptors and overexpression and/or amplification of HER2. However, both classifications show substantial discordance rates when compared to each other. Here, we molecularly characterize TN tumors and BL tumors, comparing and contrasting the results in terms of common patterns and distinct patterns for each. In total, when testing 412 TN and 473 BL tumors, 21.4% and 31.5% were identified as non-BL and non-TN, respectively. TN tumors identified as luminal or HER2-enriched (HER2E) showed undistinguishable overall gene expression profiles when compared versus luminal or HER2E tumors that were not TN. Similar findings were observed within BL tumors regardless of their TN status, which suggests that molecular subtype is preserved regardless of individual marker results. Interestingly, most TN tumors identified as HER2E showed low HER2 expression and lacked HER2 amplification, despite the similar overall gene expression profiles to HER2E tumors that were clinically HER2-positive. Lastly, additional genomic classifications were examined within TN and BL cancers, most of which were highly concordant with tumor intrinsic subtype. These results suggest that future clinical trials focused on TN disease should consider stratifying patients based upon BL versus non-BL gene expression profiles, which appears to be the main biological difference seen in patients with TN breast cancer.
doi:10.1634/theoncologist.2012-0397
PMCID: PMC3579595  PMID: 23404817
Breast cancer; Subtype; Gene expression; Triple-negative; basal-like
22.  Impact of tumor and epithelial phenotypes on metabolism in breast cancer 
Purpose
Cancer cells have altered metabolism, with increased glucose uptake, glycolysis, and biomass production. This study performed genomic and metabolomic analyses to elucidate how tumor and stromal genomic characteristics influence tumor metabolism.
Experimental Design
Thirty-three breast tumors and six normal breast tissues were analyzed by gene expression microarray and by mass spectrometry for metabolites. Gene expression data and clinical characteristics were evaluated in association with metabolic phenotype. To evaluate the role of stromal interactions in altered metabolism, cocultures were performed using breast cancer cells and primary cancer-associated fibroblasts (CAFs).
Results
Across all metabolites, unsupervised clustering resulted in two main sample clusters. Normal breast tissue and a subset of tumors with less aggressive clinical characteristics had lower levels of nucleic and amino acids and glycolysis byproducts, while more aggressive tumors had higher levels of these Warburg-associated metabolites. While tumor intrinsic subtype did not predict metabolic phenotype, metabolic cluster was significantly associated with expression of a wound response signature. In cocultures, CAFs from basal-like breast cancers increased glucose up take and basal-like epithelial cells increased glucose oxidation and glycogen synthesis, suggesting interplay of stromal and epithelial phenotypes on metabolism. Cytokine arrays identified hepatocyte growth factor (HGF) as a potential mediator of stromal-epithelial interaction, and antibody neutralization of HGF resulted in reduced expression of glucose transporter 1 (GLUT1) and decreased glucose uptake by epithelium.
Conclusions
Both tumor/epithelial and stromal characteristics play important roles in metabolism. Warburg-like metabolism is influenced by changes in stromal-epithelial interactions, including altered expression of HGF/Met pathway and GLUT1 expression.
doi:10.1158/1078-0432.CCR-12-2123
PMCID: PMC3684709  PMID: 23236214
tumor-stromal cell interactions; metabolomics; breast cancer; genomics; microenvironment
23.  SWI/SNF Chromatin-Remodeling Factor Smarcd3/Baf60c Controls Epithelial-Mesenchymal Transition by Inducing Wnt5a Signaling 
Molecular and Cellular Biology  2013;33(15):3011-3025.
We previously identified a gene signature predicted to regulate the epithelial-mesenchymal transition (EMT) in both epithelial tissue stem cells and breast cancer cells. A phenotypic RNA interference (RNAi) screen identified the genes within this 140-gene signature that promoted the conversion of mesenchymal epithelial cell adhesion molecule-negative (EpCAM−) breast cancer cells to an epithelial EpCAM+/high phenotype. The screen identified 10 of the 140 genes whose individual knockdown was sufficient to promote EpCAM and E-cadherin expression. Among these 10 genes, RNAi silencing of the SWI/SNF chromatin-remodeling factor Smarcd3/Baf60c in EpCAM− breast cancer cells gave the most robust transition from the mesenchymal to epithelial phenotype. Conversely, expression of Smarcd3/Baf60c in immortalized human mammary epithelial cells induced an EMT. The mesenchymal-like phenotype promoted by Smarcd3/Baf60c expression resulted in gene expression changes in human mammary epithelial cells similar to that of claudin-low triple-negative breast cancer cells. These mammary epithelial cells expressing Smarcd3/Baf60c had upregulated Wnt5a expression. Inhibition of Wnt5a by either RNAi knockdown or blocking antibody reversed Smarcd3/Baf60c-induced EMT. Thus, Smarcd3/Baf60c epigenetically regulates EMT by activating WNT signaling pathways.
doi:10.1128/MCB.01443-12
PMCID: PMC3719671  PMID: 23716599
24.  Different Requirements for Scavenger Receptor Class B Type I in Hepatitis C Virus Cell-Free versus Cell-to-Cell Transmission 
Journal of Virology  2013;87(15):8282-8293.
Hepatitis C virus (HCV) is believed to initially infect the liver through the basolateral side of hepatocytes, where it engages attachment factors and the coreceptors CD81 and scavenger receptor class B type I (SR-BI). Active transport toward the apical side brings the virus in close proximity of additional entry factors, the tight junction molecules claudin-1 and occludin. HCV is also thought to propagate via cell-to-cell spread, which allows highly efficient virion delivery to neighboring cells. In this study, we compared an adapted HCV genome, clone 2, characterized by superior cell-to cell spread, to its parental genome, J6/JFH-1, with the goal of elucidating the molecular mechanisms of HCV cell-to-cell transmission. We show that CD81 levels on the donor cells influence the efficiency of cell-to-cell spread and CD81 transfer between neighboring cells correlates with the capacity of target cells to become infected. Spread of J6/JFH-1 was blocked by anti-SR-BI antibody or in cells knocked down for SR-BI, suggesting a direct role for this receptor in HCV cell-to-cell transmission. In contrast, clone 2 displayed a significantly reduced dependence on SR-BI for lateral spread. Mutations in E1 and E2 responsible for the enhanced cell-to-cell spread phenotype of clone 2 rendered cell-free virus more susceptible to antibody-mediated neutralization. Our results indicate that although HCV can lose SR-BI dependence for cell-to-cell spread, vulnerability to neutralizing antibodies may limit this evolutionary option in vivo. Combination therapies targeting both the HCV glycoproteins and SR-BI may therefore hold promise for effective control of HCV dissemination.
doi:10.1128/JVI.01102-13
PMCID: PMC3719822  PMID: 23698298
25.  Anomaly Detection and Artifact Recovery in PET Attenuation-Correction Images Using the Likelihood Function 
IEEE journal of selected topics in signal processing  2013;7(1):10.1109/JSTSP.2012.2237380.
In dual modality PET/CT, CT data are used to generate the attenuation correction applied in the reconstruction of the PET emission image. This requires converting the CT image into a 511-keV attenuation map. Algorithms for making this transformation require assumptions about the makeup of material within the patient. Anomalous material such as contrast agent administered to enhance the CT scan confounds conversion algorithms and has been observed to result in inaccuracies, i.e., inconsistencies with the true 511-keV attenuation present at the time of the PET emission scan. These attenuation artifacts carry through to the final attenuation-corrected PET emission image and can resemble diseased tissue. We propose an approach to correcting this problem that employs the attenuation information carried by the PET emission data. A likelihood-based algorithm for identifying and correcting of contrast is presented and tested. The algorithm exploits the fact that contrast artifacts manifest as too-high attenuation values in an otherwise high quality attenuation image. In a separate study, the performance of the loglikelihood as an objective-function component of a detection/correction algorithm, independent of any particular algorithm was mapped out for several imaging scenarios as a function of statistical noise. Both the full algorithm and the loglikelihood performed well in studies with simulated data. Additional studies including those with patient data are required to fully understand their capabilities.
doi:10.1109/JSTSP.2012.2237380
PMCID: PMC3815546  PMID: 24198866

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