Characterization of retroviral infectivity and superinfection resistance during retrovirus-mediated transduction of mammalian cells

Retroviral vectors including lentiviral vectors are commonly used tools to stably express transgenes or RNA molecules in mammalian cells. Their utilities are roughly divided into two categories, stable overexpression of transgenes and RNA molecules, which requires maximal transduction efficiency, or functional selection with retrovirus (RV)-based libraries, which takes advantage of retroviral superinfection resistance. However, the dynamic features of RV-mediated transduction are not well characterized. Here, we engineered two murine stem cell virus-based retroviral vectors expressing dual fluorescence proteins and antibiotic markers, and analyzed virion production efficiency and virion stability, dynamic infectivity and superinfection resistance in different cell types, and strategies to improve transduction efficiency. We found that the highest virion production occurred between 60 and 72 h after transfection. The stability of the collected virion supernatant decreased by >60% after 3 days in storage. We found that RV infectivity varied drastically in the tested human cancer lines, while low transduction efficiency was partially overcome with increased virus titer, prolonged infection duration and/or repeated infections. Furthermore, we demonstrated that RV receptors PIT1 and PIT2 were lowly expressed in the analyzed cells, and that PIT1 and/or PIT2 overexpression significantly improved transduction efficiency in certain cell lines. Thus, our findings provide resourceful information for the optimal conditions of retroviral-mediated gene delivery.

First Direct-Detection Constraints on eV-Scale Hidden-Photon Dark Matter with DAMIC at SNOLAB

We present direct detection constraints on the absorption of hidden-photon dark matter with particle masses in the range 1.2-30  eV c^{-2} with the DAMIC experiment at SNOLAB. Under the assumption that the local dark matter is entirely constituted of hidden photons, the sensitivity to the kinetic mixing parameter κ is competitive with constraints from solar emission, reaching a minimum value of 2.2×10^{-14} at 17  eV c^{-2}. These results are the most stringent direct detection constraints on hidden-photon dark matter in the galactic halo with masses 3-12  eV c^{-2} and the first demonstration of direct experimental sensitivity to ionization signals <12  eV from dark matter interactions.

Corrigendum: Transcriptome Analysis of Hamelia patens (Rubiaceae) Anthers Reveals Candidate Genes for Tapetum and Pollen Wall Development

[This corrects the article on p. 1991 in vol. 7, PMID: 28119704.].

Transcriptome Analysis of Hamelia patens (Rubiaceae) Anthers Reveals Candidate Genes for Tapetum and Pollen Wall Development

Studies of the anther transcriptome on non-model plants without a known genome are surprisingly scarce. RNA-Seq and digital gene expression (DGE) profiling provides a comprehensive approach to identify candidate genes contributing to developmental processes in non-model species. Here we built a transcriptome library of developing anthers of Hamelia patens and analyzed DGE profiles from each stage to identify genes that regulate tapetum and pollen development. In total 7,720 putative differentially expressed genes across four anther stages were identified. The number of putative stage-specific genes was: 776 at microspore mother cell stage, 807 at tetrad stage, 322 at uninucleate microspore stage, and the highest number (1,864) at bicellular pollen stage. GO enrichment analysis revealed 243 differentially expressed and 108 stage-specific genes that are potentially related to tapetum development, sporopollenin synthesis, and pollen wall. The number of expressed genes, their function and expression profiles were all significantly correlated with anther developmental processes. Overall comparisons of anther and pollen transcriptomes with those of rice and Arabidopsis together with the expression profiles of homologs of known anther-expressed genes, revealed conserved patterns and also divergence. The divergence may reflect taxon-specific differences in gene expression, the use RNA-seq as a more sensitive methodology, variation in tissue composition and sampling strategies. Given the lack of genomic sequence, this study succeeded in assigning putative identity to a significant proportion of anther-expressed genes and genes relevant to tapetum and pollen development in H. patens. The anther transcriptome revealed a molecular distinction between developmental stages, serving as a resource to unravel the functions of genes involved in anther development in H. patens and informing the analysis of other members of the Rubiaceae.

Corrigendum: Temporal-Spatial Transcriptome Analyses Provide Insights into the Development of Petaloid Androecium in Canna indica

[This corrects the article on p. 1194 in vol. 7, PMID: 27582744.].

Temporal-Spatial Transcriptome Analyses Provide Insights into the Development of Petaloid Androecium in Canna indica

Canna indica (Zingiberales) is one of the most important ornamental species characterized with beautiful petaloid staminodes, which are considered to evolve from stamens. However, the genetic basis for the development of petaloid staminodes remains unclear largely because the genomic sequences are not available. By using RNA-Seq, we sequenced the transcripts in the flower of C. indica, and quantified the temporal gene expressions in flower primordium and differentiated flower, as well as the spatial gene expressions in petal and petaloid staminode. In total, 118,869 unigenes were assembled, among which 67,299 unigenes were annotated. Quantification analysis identified the differentially expressed genes in the temporal and spatial two comparisons, based on which, Gene Ontology enrichment analysis highlighted the representative terms in each sample, such as specification of organ number in flower primordium, growth in differentiated flower, secondary cell wall biogenesis in petal and cell division in petaloid staminode. Among the 51 analyzed MADS-box unigenes, 37 were up-regulated in differentiated flower compared with those in flower primordium. A-class unigenes were expressed higher in petal than in petaloid staminode, and C-class unigenes were expressed oppositely, whereas B-class unigenes demonstrated close expression levels in these two organs, indicating that petaloid staminode retains stamen identity to some degree. In situ hybridization provided more detailed expression patterns of these unigenes, and revealed the extended expression of B-class to the carpel at later stages when the style turned flat. These results constitute a preliminary basis for the study of flower development in C. indica and can be applied in further study of the evolution of Zingiberales.

The efficacy and safety of intensified enteric-coated mycophenolate sodium with low exposure of calcineurin inhibitors in Chinese de novo kidney transplant recipients: a prospective study

AIMS

The aim of this study was to investigate the efficacy and safety of a transient intensified enteric-coated mycophenolate sodium (EC-MPS) dosing regimen with low exposure of calcineurin inhibitors (CNIs) in Chinese de novo kidney transplantation.

METHODS

In a 6-month prospective study, a total of 97 recipients were enrolled and assigned to either an intensified EC-MPS dosing (IS) regimen or a standard EC-MPS dosing (SD) regimen. The area under the curve (AUC) of MPA was assessed at week 1 post transplant. The incidences of acute rejection, patient and graft survival, renal allograft function and adverse events were analysed.

RESULTS

The IS regimen displayed a trend of acute rejection risk reduction (IS 2.7% vs. SD 13.3%, p = 0.061) and allograft function improvement (IS 62.8 ± 14.0 ml/min per 1.73 m(2) vs. SD 56.6 ± 18.3 ml/min per 1.73 m(2) , p = 0.084) after 6-month follow-up. MPA-AUC0-12 h was substantially higher in the intensified EC-MPS group than the standard EC-MPS group, though without a significant difference (71.4 ± 41.7 vs. 53.0 ± 27.0 mg·h/l, p = 0.107). The IS regimen did not increase the incidence of adverse effects (IS 54.1% vs. 45.0%, p = 0.39), including diarrhoea or leucopenia.

CONCLUSIONS

The intensified EC-MPS dosing regimen maintaining low-dose CNIs in this study may be beneficial for Chinese adult de novo kidney transplant recipients in terms of acute rejection and allograft function and is safe within 6 months post transplant.

eEF-2 kinase is a critical regulator of Warburg effect through controlling PP2A-A synthesis

Cancer cells predominantly metabolize glucose by glycolysis to produce energy in order to meet their metabolic requirement, a phenomenon known as Warburg effect. Although Warburg effect is considered a peculiarity critical for survival and proliferation of cancer cells, the regulatory mechanisms behind this phenomenon remain incompletely understood. We report here that eukaryotic elongation factor-2 kinase (eEF-2K), a negative regulator of protein synthesis, has a critical role in promoting glycolysis in cancer cells. We showed that deficiency in eEF-2K significantly reduced the uptake of glucose and decreased the productions of lactate and adenosine triphosphate in tumor cells and in the Ras-transformed mouse embryonic fibroblasts. We further demonstrated that the promotive effect of eEF-2K on glycolysis resulted from the kinase-mediated restriction of synthesis of the protein phosphatase 2A-A (PP2A-A), a key factor that facilitates the ubiquitin-proteasomal degradation of c-Myc protein, as knockdown of eEF-2K expression led to a significant increase in PP2A-A protein synthesis and remarkable downregulation of c-Myc and pyruvate kinase M2 isoform, the key glycolytic enzyme transcriptionally activated by c-Myc. In addition, depletion of eEF-2K reduced the ability of the transformed cells to proliferate and enhanced the sensitivity of tumor cells to chemotherapy both in vitro and in vivo. These results, which uncover a role of the eEF-2K-mediated control of PP2A-A in tumor cell glycolysis, provide new insights into the regulation of the Warburg effect.

Recipient C6 rs9200 genotype is associated with hepatocellular carcinoma recurrence after orthotopic liver transplantation in a Han Chinese population

Hepatocellular carcinoma (HCC) recurrence is one of the leading causes of death after orthotopic liver transplantation (OLT). The sixth complement component (C6) is a late-acting complement protein that participates in the assembly of the membrane attack complex, which has an indispensable role in innate and acquired immune responses, as well as cancer immune surveillance. However, studies assessing the association between C6 and HCC recurrence after OLT are scarce. This study aimed to evaluate the association of donor and recipient C6 single-nucleotide polymorphisms with the risk for HCC recurrence after OLT. A total of 71 adult patients who underwent primary LT for HCC were enrolled. HCC recurrence was observed in 26 (36.6%) patients. Ten single-nucleotide polymorphisms were genotyped and analyzed in both donor and recipient groups. Patients with the rs9200 heterozygous GA variant presented significantly higher HCC recurrence rates (54.17 vs 27.66%, P=0.028), and lower cumulative tumor-free survival and overall survival (P=0.006 and P=0.013, respectively) compared with those harboring the GG/AA genotype, in multivariate logistic regression and Cox regression analyses. The rs9200 heterozygous GA variant in C6 persisted as a statistically independent prognostic factor (P<0.05) for predicting HCC recurrence after OLT. In conclusion, recipient C6 rs9200 polymorphism is associated with HCC recurrence after OLT, and improves the predictive value of clinical models.

Abstract P2-11-03: Phase I/II randomized study of combination immunotherapy with or without polysaccharide krestin (PSK) concurrently with a HER2 ICD peptide-based vaccine in patients with stage IV breast cancer receiving HER2-targeted monoclonal antibody therapy

Natural killer (NK) cell defects, commonly seen in metastatic breast cancer (MBC) lead to decrease in dendritic cell (DC) maturation, proinflammatory cytokine production, and tumor infiltrating T-cells (TILs). This results in a protumorigenic Th2 immune microenvironment with low response rates to immunotherapy (i.e., immune checkpoint blockade) and standard chemotherapy. PSK, a potent TLR-2 agonist, activates NK cells to produce IFN-γ and IL-12 and promote DC maturation/differentiation toward a Th1 profile in the tumor microenvironment which results in antigen specific TIL that can eradicate tumor. The combination immunotherapy of PSK and HER2 directed therapy described here, aims at inducing Th1 immunity and tumor specific T-cells. This proposed regimen could eradicate microscopic residual disease and prevent recurrence in optimally treated HER2+ MBC patients. Moreover, the regimen could result in enhanced trafficking of TILs to the site of tumor and improve the efficacy of checkpoint inhibitors and other therapies. A phase I/II randomized 2 arm study of combination immunotherapy with oral PSK (or placebo) given with a HER2 peptide vaccine and HER2 mAb therapy (trastuzumab (TZ) +/- pertuzumab (PZ)) was initiated to assess the safety of the approach and evaluate the effect of PSK on NK cell activity, pro-inflammatory cytokine/chemokine profile; and HER2 vaccine-induced T cell immunity.

Methods: Up to 30 patients with HER2+ MBC who are without evidence of disease after definitive therapy and currently on maintenance TZ +/- PZ are enrolled and randomly assigned in equal numbers to 1 of 2 arms (15 patients/arm): Arm 1: HER2 ICD vaccine + placebo or Arm 2: HER2 ICD vaccine + PSK. All patients receive concomitant treatment with 4 months of daily oral PSK or placebo, 3 monthly intradermal HER2 ICD vaccinations and continued TZ +/- PZ. Toxicity is evaluated per CTEP CTCAE 4.0, during and post vaccination. Serial blood draws for immunologic evaluation of NK cell activity and antigen-specific T cell immunity via flow cytometry and IFN-γ ELISPOT, respectively; and pro-inflammatory cytokines/chemokines.

Results: 24 subjects have been enrolled and 60 vaccines have been given. 16 subjects have completed all 3 vaccines and PSK/placebo; and 6 subjects are currently in progress. 2 subjects received &lt; 3 vaccines and were taken off study. Of 144 reported adverse events (AEs), 97% were Grade 1-2; 66 (46%) were possibly, probably, or definitely related to study treatment. Most common AEs are injection site reaction and flu-like symptoms. There have been a total of four Grade 3 AEs, 1 episode of self-limited nausea/vomiting attributed to study treatment; and cognitive disturbance, fatigue, and lymphopenia all in 1 subject and attributed to disease progression. There have been no Grade 4 AEs. Immunologic analyses are ongoing and will be presented along with completed clinical data on all patients.

Conclusion: Combination immunotherapy with PSK/placebo and concurrent HER2 directed therapy is safe and well-tolerated. Further ongoing immunologic studies will help define the immunogenicity of the approach.

Citation Format: Salazar LG, Higgins D, Childs J, Coveler AL, Liao J, Stanton S, Gooley T, Standish LJ, Sasagawa M, DISIS ML. Phase I/II randomized study of combination immunotherapy with or without polysaccharide krestin (PSK) concurrently with a HER2 ICD peptide-based vaccine in patients with stage IV breast cancer receiving HER2-targeted monoclonal antibody therapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-11-03.

Abstract P3-11-02: Weight maintenance initiated at midlife reduces mammary tumor incidence but metformin treatment does not mimic the effect

Weight gain and/or obesity are now considered to be risk factors for the development of postmenopausal breast cancer. Thus, weight loss and/or maintenance resulting from calorie restriction (CR) is recommended however success rates are infrequent. Metformin (MET) is a safe and effective treatment for type 2 diabetes mellitus and its use has been linked to reduced breast cancer incidence and mortality in comparison to other forms of diabetes treatments. Interestingly, MET's mechanism of action is considered to be similar to CR. The goal of the present investigation was to directly compare the effect of CR implemented at midlife with the administration of metformin on the development of mammary tumors (MT) in a relevant mouse model. Further, since these interventions would likely be used by obese women we studied both lean and obese mice. Female MMTV-TGF-α mice which develop MTs in the second year of life were fed ad libitum (AL) either a low fat (LF) (10.2% by calories) diet or a moderately high fat (HF) (33.5% by calories) diet from 10 until 30 weeks of age. At 30 weeks the mice on each diet were divided into AL, MET (250 mg/kg/bw/day) or CR (25% reduction in calories) subgroups and then followed until 90 weeks of age. HF-AL and HF-Met mice were significantly heavier that the other 4 groups whose weights were similar. The survival curves had an overall P value of P&lt;0.0001 with LF-CR having the best survival of 100% while the HF-AL and HF-Met had the poorest survival with rates of 68% and 63% respectively. HF-CR mice had a significantly better survival rate compared to HF-AL and HF-Met (P&lt;0.0001 for both). MT incidence (histologically confirmed) was significantly reduced in LF-CR (6%) compared to all other groups (45%-69%) (Chi-squared analysis). Tumor incidence in the HF-CR group (51%) was reduced compared to HF-AL (69%) and HF-Met (60%) mice but not significantly different due to adjustment for multiple comparisons, although the HF-CR vs HF-AL comparison was P&lt;0.02. However, when the incidence rate for tumors detected by palpation prior to euthanasia was examined LF-CR mice did not have any MTs although the palpable incidence rates were not significantly different due to the need for multiple comparisons (LF-CR vs LF-AL was P&lt;0.0097). The HF-CR group had significantly reduced palpable MT prior to euthanasia as compared to both HF-AL and the HF-Met (P&lt;0.0002 and P&lt;0.0001 respectively). Total tumor weight, grade and multiplicity were also examined for the effects of weight maintenance and MET. Presently the role of the AMPK pathway in these effects and serum measurements are being determined. In conclusion, the results to date indicate that weight maintenance during midlife can have a significant impact in delaying MT formation regardless of body weight status although the effects of MET are less dramatic.

Supported by NIH-NCI CA157012, The Hormel Foundation and Paint the Town Pink.

Citation Format: Cleary MP, Mizuno NK, Yang D-Q, Liao J, Grossmann ME. Weight maintenance initiated at midlife reduces mammary tumor incidence but metformin treatment does not mimic the effect. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-11-02.

Abstract P1-11-04: Long-term patient satisfaction with cosmetic outcome and psychosocial wellbeing after breast conserving therapy is affected only by lumpectomy volume

Introduction: Breast conserving therapy (BCT) is considered the treatment of choice for early stage breast cancer by National Cancer Institute guidelines. Little data exists on patient-reported satisfaction and quality of life outcomes after lumpectomy with radiation. This study aims to identify factors influencing satisfaction with cosmetic outcome and quality of life in patients receiving BCT using a validated instrument.

Methods: All patients treated with lumpectomy and radiation for breast cancer at our institution from 1997-2012 received a mailed questionnaire containing the BREAST-Q breast conservation module (graciously provided by Dr A. Pusic, Memorial Sloan Kettering Cancer Center), a validated quality of life survey instrument. A retrospective chart review was performed for survey responders for demographic, treatment, and staging information. Scores were calculated for satisfaction with appearance of the breast, adverse effects of radiation, sexual wellbeing, psychosocial wellbeing and physical wellbeing: upper body and arm. Pearson correlation coefficients were obtained. Wilcoxon rank-sum and one-way ANOVA were used to identify associations between patient variables and satisfaction scores. Multivariate regression was used to assess confounding variables.

Results: A total of 110 questionnaires (response rate of 29.5%) fit criteria for analysis. The mean age of respondents was 65.9±11.2 yrs, and mean time since diagnosis was 91.8±53.1 mos. We observed the strongest correlations between satisfaction with breast appearance and sexual wellbeing (r=0.66, p&lt;0.01), breast appearance and psychosocial wellbeing (r=0.62, p&lt;0.01), and fewer effects of radiation and physical wellbeing (r=0.65, p&lt;0.01). Lumpectomy volume was associated with decreased satisfaction with breast appearance (r=-0.32, p &lt;0.01) and psychosocial wellbeing (r=-0.19, p&lt;0.05). There was no correlation between satisfaction with breast appearance and patient age, time since surgery, history of re-excision, stage or localization technique. Patients with older age at diagnosis reported significantly fewer effects of radiation and better psychosocial, physical, and sexual wellbeing (all p&lt;0.05) (Table 1). The incidence of recurrence was 2.7% and did not impact satisfaction scores.

Distribution of Satisfaction/Quality of Life Outcomes by Age at Diagnosis  Satisfaction/Quality of Life*AgeNBreastAdverse Effects of RadiationPsychosocialSexualPhysical&lt;451458±2282±1973±1945±2074±1645-553264±2683±1980±2054±2579±1756-602667±1794±983±2370±1885±1361-651267±2989±2383±2053±2983±17&gt;652670±2391±1288±1663±2588±25All11065±2388±1682±2058±2482±19P 0.1590.0190.0140.0300.002*Rasch scores range from 0-100 where 100 indicates highest satisfaction

Conclusions: In women undergoing BCT, patient satisfaction with appearance of the breast and psychosocial wellbeing at 7.6 years of follow-up correlated with the volume of tissue removed but no other patient or tumor characteristics. Increasing age at diagnosis was associated with greater satisfaction in multiple domains. These results emphasize the importance of precise surgical technique and patient selection in order to achieve long-term patient satisfaction with BCT.

Citation Format: Welsh JL, Fu S, Liao J, Sugg SL, Scott-Conner CE, Weigel RJ, Erdahl LM, Lizarraga IM. Long-term patient satisfaction with cosmetic outcome and psychosocial wellbeing after breast conserving therapy is affected only by lumpectomy volume. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-11-04.

Abstract P3-01-11: Sentinel lymph node (SLN) localization is highly successful after neoadjuvant chemotherapy (NCT) for breast cancer

Background: Recent multi-center trial results are concerning for the ability to identify SLNs after NCT. SLN localization was shown to be less successful (80%) after NCT when compared with no NCT (99%) (SENTINA), and the SLN identification rate in Z1071 in which all patients received NCT was 93%.

Purpose: To examine the effect of NCT, patient and disease characteristics, imaging and surgical technique on SLN localization rates in breast cancer patients undergoing chemotherapy.

Methods: Retrospective, single institution study was performed on patients who underwent surgery for breast cancer from January 2008 to December 2013. All patients who underwent SLN biopsy and either adjuvant chemotherapy (ACT) or NCT, were included. All patients underwent lymphoscintigraphy, and SLN biopsy was performed with the definitive breast surgery.

Results: 68 patients underwent NCT, and 133 underwent ACT. Our SLN localization rate was 198/201 (98.5%) overall; 98.6% (67 of 68) with NCT and 97.7% (130/133) with ACT (p=1.0). Compared with the NCT group, the ACT patients were significantly older, white, with more ER/PR positive tumors. The NCT group had more positive nodes on preop imaging (64% v. 20%, p&lt;0.001), FNA (82% v. 22%, p&lt;0.001), and a lower use of blue dye (37% v. 61%, p=0.05) but there were no differences in the number of SLN removed (1.43 v. 1.33 p=0.32), or nodes that were positive on intraoperative evaluation (30 v. 33%, p=0.75). Comparing the patients who had successful and failed SLN localization, there were no differences in demographics, tumor type, Stage, prior breast surgery, preoperative node positivity on imaging or FNA or timing of chemotherapy.

Conclusion: In this single institution series, SLN non-localization was a rare event and not associated with NCT. We were unable to identify any patient or disease characteristics, imaging or surgical techniques associated with SLN non-localization. The etiology of the lower SLN identification rates with NCT in multi-institutional trials remains to be elucidated.

Citation Format: Sugg S, Hayes R, Gbenon A, Lizarraga I, Erdahl L, Weigel R, Liao J, Menda Y, Scott-Conner C. Sentinel lymph node (SLN) localization is highly successful after neoadjuvant chemotherapy (NCT) for breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-01-11.

Aqueous-phase mechanism for secondary organic aerosol formation from isoprene: application to the Southeast United States and co-benefit of SO2 emission controls

Isoprene emitted by vegetation is an important precursor of secondary organic aerosol (SOA), but the mechanism and yields are uncertain. Aerosol is prevailingly aqueous under the humid conditions typical of isoprene-emitting regions. Here we develop an aqueous-phase mechanism for isoprene SOA formation coupled to a detailed gas-phase isoprene oxidation scheme. The mechanism is based on aerosol reactive uptake coefficients (γ) for water-soluble isoprene oxidation products, including sensitivity to aerosol acidity and nucleophile concentrations. We apply this mechanism to simulation of aircraft (SEAC⁴RS) and ground-based (SOAS) observations over the Southeast US in summer 2013 using the GEOS-Chem chemical transport model. Emissions of nitrogen oxides (NO_x ≡ NO + NO₂) over the Southeast US are such that the peroxy radicals produced from isoprene oxidation (ISOPO₂) react significantly with both NO (high-NO_x pathway) and HO₂ (low-NO_x pathway), leading to different suites of isoprene SOA precursors. We find a mean SOA mass yield of 3.3 % from isoprene oxidation, consistent with the observed relationship of total fine organic aerosol (OA) and formaldehyde (a product of isoprene oxidation). Isoprene SOA production is mainly contributed by two immediate gas-phase precursors, isoprene epoxydiols (IEPOX, 58% of isoprene SOA) from the low-NO_x pathway and glyoxal (28%) from both low- and high-NO_x pathways. This speciation is consistent with observations of IEPOX SOA from SOAS and SEAC⁴RS. Observations show a strong relationship between IEPOX SOA and sulfate aerosol that we explain as due to the effect of sulfate on aerosol acidity and volume. Isoprene SOA concentrations increase as NO_x emissions decrease (favoring the low-NO_x pathway for isoprene oxidation), but decrease more strongly as SO₂ emissions decrease (due to the effect of sulfate on aerosol acidity and volume). The US EPA projects 2013-2025 decreases in anthropogenic emissions of 34% for NO_x (leading to 7% increase in isoprene SOA) and 48% for SO₂ (35% decrease in isoprene SOA). Reducing SO₂ emissions decreases sulfate and isoprene SOA by a similar magnitude, representing a factor of 2 co-benefit for PM_2.5 from SO₂ emission controls.

Aqueous-phase mechanism for secondary organic aerosol formation from isoprene: application to the Southeast United States and co-benefit of SO2 emission controls

Isoprene emitted by vegetation is an important precursor of secondary organic aerosol (SOA), but the mechanism and yields are uncertain. Aerosol is prevailingly aqueous under the humid conditions typical of isoprene-emitting regions. Here we develop an aqueous-phase mechanism for isoprene SOA formation coupled to a detailed gas-phase isoprene oxidation scheme. The mechanism is based on aerosol reactive uptake coefficients (γ) for water-soluble isoprene oxidation products, including sensitivity to aerosol acidity and nucleophile concentrations. We apply this mechanism to simulation of aircraft (SEAC⁴RS) and ground-based (SOAS) observations over the Southeast US in summer 2013 using the GEOS-Chem chemical transport model. Emissions of nitrogen oxides (NO_x ≡ NO + NO₂) over the Southeast US are such that the peroxy radicals produced from isoprene oxidation (ISOPO₂) react significantly with both NO (high-NO_x pathway) and HO₂ (low-NO_x pathway), leading to different suites of isoprene SOA precursors. We find a mean SOA mass yield of 3.3 % from isoprene oxidation, consistent with the observed relationship of total fine organic aerosol (OA) and formaldehyde (a product of isoprene oxidation). Isoprene SOA production is mainly contributed by two immediate gas-phase precursors, isoprene epoxydiols (IEPOX, 58% of isoprene SOA) from the low-NO_x pathway and glyoxal (28%) from both low- and high-NO_x pathways. This speciation is consistent with observations of IEPOX SOA from SOAS and SEAC⁴RS. Observations show a strong relationship between IEPOX SOA and sulfate aerosol that we explain as due to the effect of sulfate on aerosol acidity and volume. Isoprene SOA concentrations increase as NO_x emissions decrease (favoring the low-NO_x pathway for isoprene oxidation), but decrease more strongly as SO₂ emissions decrease (due to the effect of sulfate on aerosol acidity and volume). The US EPA projects 2013-2025 decreases in anthropogenic emissions of 34% for NO_x (leading to 7% increase in isoprene SOA) and 48% for SO₂ (35% decrease in isoprene SOA). Reducing SO₂ emissions decreases sulfate and isoprene SOA by a similar magnitude, representing a factor of 2 co-benefit for PM_2.5 from SO₂ emission controls.

Instrumentation and Measurement Strategy for the NOAA SENEX Aircraft Campaign as Part of the Southeast Atmosphere Study 2013

Natural emissions of ozone-and-aerosol-precursor gases such as isoprene and monoterpenes are high in the southeast of the US. In addition, anthropogenic emissions are significant in the Southeast US and summertime photochemistry is rapid. The NOAA-led SENEX (Southeast Nexus) aircraft campaign was one of the major components of the Southeast Atmosphere Study (SAS) and was focused on studying the interactions between biogenic and anthropogenic emissions to form secondary pollutants. During SENEX, the NOAA WP-3D aircraft conducted 20 research flights between 27 May and 10 July 2013 based out of Smyrna, TN. Here we describe the experimental approach, the science goals and early results of the NOAA SENEX campaign. The aircraft, its capabilities and standard measurements are described. The instrument payload is summarized including detection limits, accuracy, precision and time resolutions for all gas-and-aerosol phase instruments. The inter-comparisons of compounds measured with multiple instruments on the NOAA WP-3D are presented and were all within the stated uncertainties, except two of the three NO₂ measurements. The SENEX flights included day- and nighttime flights in the Southeast as well as flights over areas with intense shale gas extraction (Marcellus, Fayetteville and Haynesville shale). We present one example flight on 16 June 2013, which was a daytime flight over the Atlanta region, where several crosswind transects of plumes from the city and nearby point sources, such as power plants, paper mills and landfills, were flown. The area around Atlanta has large biogenic isoprene emissions, which provided an excellent case for studying the interactions between biogenic and anthropogenic emissions. In this example flight, chemistry in and outside the Atlanta plumes was observed for several hours after emission. The analysis of this flight showcases the strategies implemented to answer some of the main SENEX science questions.

Achievement of linear response for competitive bioaffinity assays of ligands: criteria of optimized interaction systems

For a linear response, an optimized competitive bioaffinity assay of a ligand requiresC_RT> 3 ×C_PT,C_PT> 50 ×K_dR, andK_dR> 260 ×K_dX(C_RTandC_PTare concentrations of the probe and protein whileK_dXandK_dRareK_dfor the ligand and probe, respectively).

Instrumentation and Measurement Strategy for the NOAA SENEX Aircraft Campaign as Part of the Southeast Atmosphere Study 2013

Natural emissions of ozone-and-aerosol-precursor gases such as isoprene and monoterpenes are high in the southeast of the US. In addition, anthropogenic emissions are significant in the Southeast US and summertime photochemistry is rapid. The NOAA-led SENEX (Southeast Nexus) aircraft campaign was one of the major components of the Southeast Atmosphere Study (SAS) and was focused on studying the interactions between biogenic and anthropogenic emissions to form secondary pollutants. During SENEX, the NOAA WP-3D aircraft conducted 20 research flights between 27 May and 10 July 2013 based out of Smyrna, TN. Here we describe the experimental approach, the science goals and early results of the NOAA SENEX campaign. The aircraft, its capabilities and standard measurements are described. The instrument payload is summarized including detection limits, accuracy, precision and time resolutions for all gas-and-aerosol phase instruments. The inter-comparisons of compounds measured with multiple instruments on the NOAA WP-3D are presented and were all within the stated uncertainties, except two of the three NO₂ measurements. The SENEX flights included day- and nighttime flights in the Southeast as well as flights over areas with intense shale gas extraction (Marcellus, Fayetteville and Haynesville shale). We present one example flight on 16 June 2013, which was a daytime flight over the Atlanta region, where several crosswind transects of plumes from the city and nearby point sources, such as power plants, paper mills and landfills, were flown. The area around Atlanta has large biogenic isoprene emissions, which provided an excellent case for studying the interactions between biogenic and anthropogenic emissions. In this example flight, chemistry in and outside the Atlanta plumes was observed for several hours after emission. The analysis of this flight showcases the strategies implemented to answer some of the main SENEX science questions.