Publications by authors named "Erin Doyle"

38 Publications

Digital imaging and vision analysis in science project improves the self-efficacy and skill of undergraduate students in computational work.

PLoS One 2021 5;16(5):e0241946. Epub 2021 May 5.

Department of Education, Doane University, Crete, Nebraska, United States of America.

In many areas of science, the ability to use computers to process, analyze, and visualize large data sets has become essential. The mismatch between the ability to generate large data sets and the computing skill to analyze them is arguably the most striking within the life sciences. The Digital Image and Vision Applications in Science (DIVAS) project describes a scaffolded series of interventions implemented over the span of a year to build the coding and computing skill of undergraduate students majoring primarily in the natural sciences. The program is designed as a community of practice, providing support within a network of learners. The program focus, images as data, provides a compelling 'hook' for participating scholars. Scholars begin the program with a one-credit spring semester seminar where they are exposed to image analysis. The program continues in the summer with a one-week, intensive Python and image processing workshop. From there, scholars tackle image analysis problems using a pair programming approach and can finish the summer with independent research. Finally, scholars participate in a follow-up seminar the subsequent spring and help onramp the next cohort of incoming scholars. We observed promising growth in participant self-efficacy in computing that was maintained throughout the project as well as significant growth in key computational skills. DIVAS program funding was able to support seventeen DIVAS over three years, with 76% of DIVAS scholars identifying as women and 14% of scholars identifying as members of an underrepresented minority group. Most scholars (82%) entered the program as first year students, with 94% of DIVAS scholars retained for the duration of the program and 100% of scholars remaining a STEM major one year after completing the program. The outcomes of the DIVAS project support the efficacy of building computational skill through repeated exposure of scholars to relevant applications over an extended period within a community of practice.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241946PLOS
May 2021

A subset of liver resident natural killer cells is expanded in hepatitis C-infected patients with better liver function.

Sci Rep 2021 Jan 15;11(1):1551. Epub 2021 Jan 15.

Division of Liver Diseases, Icahn School of Medicine at Mount Sinai School, 1425 Madison Ave., Icahn 11-23, New York, NY, 10029, USA.

Viral hepatitis leads to immune-mediated liver injury. The rate of disease progression varies between individuals. We aimed to phenotype immune cells associated with preservation of normal liver function during hepatitis C virus (HCV) infection. Clinical data and specimens were obtained from 19 HCV-infected patients undergoing liver transplantation. Liver and peripheral blood mononuclear cells were isolated and eight subsets of innate immune cells were delineated by multiparameter flow cytometry. Cytokine assays and microarrays were performed. Intrahepatic CD56/CD16 natural killer (NK) cells comprised the only subset correlating with better liver function, i.e., lower bilirubin (p = 0.0002) and lower model for end stage of liver disease scores (p = 0.03). The signature of liver NK cells from HCV-infected patients included genes expressed by NK cells in normal liver and by decidual NK cells. Portal vein blood had a higher concentration of interleukin (IL)-10 than peripheral blood (p = 0.03). LMCs were less responsive to toll-like receptor (TLR) stimulation than PBMCs, with fewer pro-inflammatory gene-expression pathways up-regulated after in vitro exposure to lipopolysaccharide and a TLR-7/8 agonist. Hepatic CD56/CD16 NK cells may be critical for maintaining liver homeostasis. Portal vein IL-10 may prime inhibitory pathways, attenuating TLR signaling and reducing responsiveness to pro-inflammatory stimuli.
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http://dx.doi.org/10.1038/s41598-020-80819-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7810844PMC
January 2021

Pre-mortem risk factors for mortality in kittens less than 8 weeks old at a dedicated kitten nursery.

J Feline Med Surg 2020 Nov 30:1098612X20974960. Epub 2020 Nov 30.

Strategy and Research, American Society for the Prevention of Cruelty to Animals, New York, NY, USA.

Objectives: Kittens have unique requirements for care in a shelter setting given their higher susceptibility to infectious disease and socialization needs. Significant time and resources are necessary to care for this vulnerable population and dedicated kitten nurseries are one way to meet the requirements of kittens too young for neutering and rehoming. However, young kittens remain at a higher risk of dying relative to adult cats, even in specialized settings. Efforts to investigate kitten mortality have focused on post-mortem findings and little is known about pre-mortem clinical signs that may be associated with death. The purpose of this study was to elucidate predictors of mortality in underage kittens.

Methods: The medical records of kittens aged <8 weeks reared in a kitten nursery in New York City during 2017 were examined. The data collected included signalment (estimated age and weight at intake, sex), physical findings (body condition score [BCS]), clinical signs (weight loss, anorexia, diarrhea, upper respiratory tract infection [URI]), diagnoses (panleukopenia, trauma), how early in the feline breeding season the kitten entered (April-November), and whether the kitten had died or was euthanized. The data were analyzed using Cox proportional hazard modeling with 1353 kittens to identify factors associated with any death or euthanasia.

Results: Elevated risk of dying was found for kittens in the lightest weight group (13 times greater), diagnosed with panleukopenia (13 times greater), exhibiting weight loss (>9 times greater), diagnosed with URI (almost four times greater), exhibiting anorexia (three times greater), identified with a low BCS at intake (two times greater) and experiencing diarrhea (almost two times greater).

Conclusions And Relevance: These findings identify clinical signs and diagnoses that can serve as prognostic indicators for underage kitten survival in a shelter/rescue setting and can aid in enhancing protocols for monitoring, intervention and euthanasia decision-making.
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http://dx.doi.org/10.1177/1098612X20974960DOI Listing
November 2020

Sequencing and Annotation of Duggie and Hocus, Two Subcluster B1 Mycobacteriophages.

Microbiol Resour Announc 2020 Jul 9;9(28). Epub 2020 Jul 9.

Department of Biology, Doane University, Crete, Nebraska, USA

Two mycobacteriophage genomes were newly sequenced and annotated. Duggie and Hocus were discovered, enriched, and isolated from soil using mc155. The bacteriophages are lytic Siphoviridae and belong to the B1 subcluster. The Hocus and Duggie genomes are highly similar to one another in both nucleotide sequence and gene content.
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http://dx.doi.org/10.1128/MRA.00432-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7348018PMC
July 2020

Impact of the Timing of Spay-Neuter Related to Transport on Disease Rates in Relocated Dogs.

Animals (Basel) 2020 Apr 6;10(4). Epub 2020 Apr 6.

Shelter Medicine Services, American Society for the Prevention of Cruelty to Animals (ASPCA®), New York, NY 10128, USA.

Companion animal relocation programs are an important method to address geographic and resource disparities in pet overpopulation through transport from areas with high homeless pet populations to areas with high adopter demand. Despite mitigation by following best practices, a potential risk of animal relocation is increased disease incidence related to infectious disease spread and the effects of stress during transport. Surgical sterilization may compound disease risk due to the impact of surgical stress on disease susceptibility and the potential for disease exposure from other patients. Our study aimed to provide information about disease and surgical complication incidence as relates to the timing of surgical sterilization in relocated dogs. A population of 431 dogs relocated to a shelter in Washington State was monitored for disease while at the destination shelter and immediately post-adoption. No increased disease incidence was identified for dogs altered within two weeks of transport at the destination shelter compared with those altered within two weeks prior to transport at the source shelter. Because of disparities addressed by relocation programs, surgical sterilization of relocated companion animals is typically best performed at the destination shelter. Our study indicates that disease incidence is not increased by spay-neuter at the destination shelter.
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http://dx.doi.org/10.3390/ani10040630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222758PMC
April 2020

Opioid Prescribing Behaviors - Prescription Behavior Surveillance System, 11 States, 2010-2016.

MMWR Surveill Summ 2020 01 31;69(1):1-14. Epub 2020 Jan 31.

Certified Technical Experts, Inc., Montgomery, AL.

Problem/condition: In 2017, a total of 70,237 persons in the United States died from a drug overdose, and 67.8% of these deaths involved an opioid. Historically, the opioid overdose epidemic in the United States has been closely associated with a parallel increase in opioid prescribing and with widespread misuse of these medications. National and state policy makers have introduced multiple measures to attempt to assess and control the opioid overdose epidemic since 2010, including improvements in surveillance systems.

Period Covered: 2010-2016 DESCRIPTION OF SYSTEM: The Prescription Behavior Surveillance System (PBSS) was created in 2011. Its goal was to track rates of prescribing of controlled substances and possible misuse of such drugs using data from selected state prescription drug monitoring programs (PDMP). PBSS data measure prescribing behaviors for prescription opioids using multiple measures calculated from PDMP data including 1) opioid prescribing, 2) average daily opioid dosage, 3) proportion of patients with daily opioid dosages ≥90 morphine milligram equivalents, 4) overlapping opioid prescriptions, 5) overlapping opioid and benzodiazepine prescriptions, and 6) multiple-provider episodes. For this analysis, PBSS data were available for 2010-2016 from 11 states representing approximately 38.0% of the U.S.

Population: Average quarterly percent changes (AQPC) in the rates of opioid prescribing and possible opioid misuse measures were calculated for each state.

Results And Interpretation: Opioid prescribing rates declined in all 11 states during 2010-2016 (range: 14.9% to 33.0%). Daily dosage declined least (AQPC: -0.4%) in Idaho and Maine, and most (AQPC: -1.6%) in Florida. The percentage of patients with high daily dosage had AQPCs ranging from -0.4% in Idaho to -2.3% in Louisiana. Multiple-provider episode rates declined by at least 62% in the seven states with available data. Variations in trends across the 11 states might reflect differences in state policies and possible differential effects of similar policies.

Public Health Actions: Use of PDMP data from individual states enables a more detailed examination of trends in opioid prescribing behaviors and indicators of possible misuse than is feasible with national commercially available prescription data. Comparison of opioid prescribing trends among states can be used to monitor the temporal association of national or state policy interventions and might help public health policymakers recognize changes in the use or possible misuse of controlled prescription drugs over time and allow for prompt intervention through amended or new opioid-related policies.
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http://dx.doi.org/10.15585/mmwr.ss6901a1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7011442PMC
January 2020

Individual liver plasmacytoid dendritic cells are capable of producing IFNα and multiple additional cytokines during chronic HCV infection.

PLoS Pathog 2019 07 29;15(7):e1007935. Epub 2019 Jul 29.

Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.

Plasmacytoid dendritic cells (pDCs) are "natural" interferon α (IFNα)-producing cells. Despite their importance to antiviral defense, autoimmunity, and ischemic liver graft injury, because DC subsets are rare and heterogeneous, basic questions about liver pDC function and capacity to make cytokines remain unanswered. Previous investigations failed to consistently detect IFNα mRNA in HCV-infected livers, suggesting that pDCs may be incapable of producing IFNα. We used a combination of molecular, biochemical, cytometric, and high-dimensional techniques to analyze DC frequencies/functions in liver and peripheral blood mononuclear cells (PBMCs) of hepatitis C virus (HCV)-infected patients, to examine correlations between DC function and gene expression of matched whole liver tissue and liver mononuclear cells (LMCs), and to determine if pDCs can produce multiple cytokines. T cells often produce multiple cytokines/chemokines but until recently technical limitations have precluded tests of polyfunctionality in individual pDCs. Mass cytometry (CyTOF) revealed that liver pDCs are the only LMC that produces detectable amounts of IFNα in response TLR-7/8 stimulation. Liver pDCs secreted large quantities of IFNα (~2 million molecules of IFNα/cell/hour) and produced more IFNα than PBMCs after stimulation, p = 0.0001. LMCs secreted >14-fold more IFNα than IFNλ in 4 hours. Liver pDC frequency positively correlated with whole liver expression of "IFNα-response" pathway (R2 = 0.58, p = 0.007) and "monocyte surface" signature (R2 = 0.54, p = 0.01). Mass cytometry revealed that IFNα-producing pDCs were highly polyfunctional; >90% also made 2-4 additional cytokines/chemokines of our test set of 10. Liver BDCA1 DCs, but not BDCA3 DCs, were similarly polyfunctional. pDCs from a healthy liver were also polyfunctional. Our data show that liver pDCs retain the ability to make abundant IFNα during chronic HCV infection and produce many other immune modulators. Polyfunctional liver pDCs are likely to be key drivers of inflammation and immune activation during chronic HCV infection.
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http://dx.doi.org/10.1371/journal.ppat.1007935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687199PMC
July 2019

Genome Sequences of Three Cluster C Mycobacteriophages, Bipolarisk, Bread, and FudgeTart.

Microbiol Resour Announc 2019 Jul 11;8(28). Epub 2019 Jul 11.

Department of Biology, Doane University, Crete, Nebraska, USA

Three mycobacteriophages, Bipolarisk, Bread, and FudgeTart, were isolated from enriched soil samples found in Crete, NE. All three phages are lytic, belong to subcluster C1, and infect mc155. The structures of the three genomes are similar, with slight variations in gene number and content.
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http://dx.doi.org/10.1128/MRA.00290-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624755PMC
July 2019

Finding Some Good in an Invasive Species: Introduction and Assessment of a Novel CURE to Improve Experimental Design in Undergraduate Biology Classrooms.

J Microbiol Biol Educ 2018 29;19(2). Epub 2018 Jun 29.

Biology Department, Doane University, Crete, NE 68333.

Reports such as call for integration of course-based undergraduate research experiences (CUREs) into biology curricula and less emphasis on "cookbook" laboratories. CUREs, often characterized by a single open-ended research question, allow students to develop hypotheses, design experiments, and collaborate with peers. Conversely, "cookbook" labs incentivize task completion and have pre-determined experimental outcomes. While research comparing CUREs and "cookbook" labs is growing, there are fewer comparisons among CUREs. Here, we present a novel CURE built around an invasive grass, . We evaluated this CURE's effectiveness in improving students' understanding of the competency relating to the application of the scientific process through development and testing of hypotheses. We did so by comparing changes in pre- and posttest scores on the Experimental Design Ability Test (EDAT) between Brome CURE students and students in a concurrent CURE, SEA-PHAGES. While students in both CUREs showed improvements at the end of the semester, Brome CURE students showed a greater increase in EDAT scores than did SEA-PHAGES CURE students. Additionally, Brome CURE students had significantly higher gains in 6 of the 10 EDAT criteria. We conclude that the Brome CURE is an effective ecological parallel to the SEA-PHAGES CURE and can help students gain a meaningful understanding of competencies. Journal of Microbiology & Biology Education.
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http://dx.doi.org/10.1128/jmbe.v19i2.1517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022745PMC
June 2018

Two ancestral genes shaped the Xanthomonas campestris TAL effector gene repertoire.

New Phytol 2018 07 20;219(1):391-407. Epub 2018 Apr 20.

LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France.

Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome). The 53 sequenced tal genes encode 21 distinct DNA binding domains that sort into seven major DNA binding specificities. In silico analysis of the Brassica rapa promoterome identified a repertoire of predicted TALE targets, five of which were experimentally validated using quantitative reverse transcription polymerase chain reaction. The Xc TALome shows multiple signs of DNA rearrangements that probably drove its evolution from two ancestral tal genes. We discovered that Tal12a and Tal15a of Xcc strain Xca5 contribute together in the development of disease symptoms on susceptible B. oleracea var. botrytis cv Clovis. This large and polymorphic repertoire of TALEs opens novel perspectives for elucidating TALE-mediated susceptibility of Brassicaceae to black rot disease and for understanding the molecular processes underlying TALE evolution.
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http://dx.doi.org/10.1111/nph.15148DOI Listing
July 2018

Newly discovered hepatitis C virus minicores circulate in human blood.

Hepatol Commun 2018 01 12;2(1):21-28. Epub 2017 Nov 12.

Division of Liver Diseases, Department of Medicine Icahn School of Medicine at Mount Sinai New York NY.

Hepatitis C virus (HCV) is one of the most prevalent causes of chronic blood-borne infections worldwide. Despite developments of highly effective treatments, most infected individuals are unaware of their infection. Approximately 75% of infections are in low- and middle-income countries; therefore, continuing research in HCV molecular virology and the development of vaccines and affordable diagnostics is required to reduce the global burden. Various intracellular forms of the HCV nucleocapsid (core) protein are produced in cell culture; these comprise the conventional p21 core and the newly discovered shorter isoforms (minicores). Minicores lack the N-terminus of p21 core. This study was conducted to determine if minicores are secreted in cell culture and more importantly if they circulate in the blood of individuals infected with HCV. We also developed a new monoclonal antibody that detects minicores targeting a C-terminal region common to p21 core and minicores. Direct evidence of minicores requires western blot analysis to distinguish the detection of p21 core from minicores. However, the sensitivity for western blot detection of HCV proteins from blood is nil without their prior purification/enrichment from blood. Therefore, we developed a purification method based on a heparin/Mn precipitation of apolipoprotein B-containing lipoproteins because HCV is thought to circulate as a hybrid lipoviral particle. Minicores are secreted in culture when cells are grown in the presence of human serum. The heparin/Mn precipitate from HCV-infected cell culture supernatants and from the blood of 4 patients with high-titer genotype-1 HCV contained minicores. : Minicores are major newly discovered HCV proteins that are secreted and circulate in blood during natural infections. Minicore proteins have translational potential as targets in diagnostic assays and in vaccine development. ( 2018;2:21-28).
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http://dx.doi.org/10.1002/hep4.1125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776872PMC
January 2018

Genome Sequences of Four Cluster P Mycobacteriophages.

Genome Announc 2018 Jan 11;6(2). Epub 2018 Jan 11.

Biology Department, Doane University, Crete, Nebraska, USA.

Four bacteriophages infecting mc155 (three belonging to subcluster P1 and one belonging to subcluster P2) were isolated from soil and sequenced. All four phages are similar in the left arm of their genomes, but the P2 phage differs in the right arm. All four genomes contain features of temperate phages.
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http://dx.doi.org/10.1128/genomeA.01101-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764923PMC
January 2018

daTALbase: A Database for Genomic and Transcriptomic Data Related to TAL Effectors.

Mol Plant Microbe Interact 2018 04 14;31(4):471-480. Epub 2018 Feb 14.

1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France.

Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility genes (S genes), triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs amino acid sequences. New candidate S genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements. By contrasting differential expression data and binding site predictions across different datasets, patterns of TALE diversification or convergence may be unveiled, but this requires the seamless integration of different genomic and transcriptomic data. With this in mind, we present daTALbase, a curated relational database that integrates TALE-related data including bacterial TALE sequences, plant promoter sequences, predicted TALE binding sites, transcriptomic data of host plants in response to TALE-harboring bacteria, and other associated data. The database can be explored to uncover new candidate S genes as well as to study variation in TALE repertories and their corresponding targets. The first version of the database here presented includes data for Oryza sp.-Xanthomonas pv. oryzae interactions. Future versions of the database will incorporate information for other pathosystems involving TALEs.
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http://dx.doi.org/10.1094/MPMI-06-17-0153-FIDOI Listing
April 2018

Prescribing patterns of buprenorphine waivered physicians.

Drug Alcohol Depend 2017 12 18;181:213-218. Epub 2017 Oct 18.

RAND Corporation and University of Pittsburgh, United States. Electronic address:

Background: DATA 2000 enabled physicians with approved training to be waivered to prescribe buprenorphine for the treatment of opioid use disorders (OUD) for a limited number of patients. A rule change in 2016 increased the patient limit for certain buprenorphine waivered physicians from 100 to 275. This study examines the prescribing patterns of buprenorphine prescribers by waiver limit status (30- or 100-patient limit).

Methods: Prescription Monitoring Program (PMP) data from Ohio, California, and Maine were used to identify prescriptions for buprenorphine for OUD from January 2010 to April 2015. Analysis of prescribing patterns by prescriber waiver status included monthly patient censuses and treatment episode duration by state, year, and the frequency with which prescribers were near their respective patient limits.

Results: In the three states, 8638 physicians initiated 468,148 buprenorphine episodes. The adjusted mean monthly patient census was 42.9 for 100-patient waivered prescribers, 13.6 patients for 30-patient waivered prescribers, and 7.6 patients for prescribers unassociated with a waiver. Half (48.5%) of episodes were associated with 100-patient waivered prescribers, 26.9% with 30-patient waivered prescribers, and 24.4% with non-waivered prescribers. 30-patient waivered physicians were more likely to have no buprenorphine treatment episodes in a given month than 100-patient waivered prescribers.

Conclusions: Most buprenorphine prescribers practice well under their current patient limit and have numerous months with no patient episodes. For the few high prescribers, increasing the maximum patient limit beyond 100 has the potential to improve access but alone may not have widespread impact unless integrated into complementary approaches toward increasing prescriber capacity.
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http://dx.doi.org/10.1016/j.drugalcdep.2017.10.002DOI Listing
December 2017

A Low-Cost Imaging Method for the Temporal and Spatial Colorimetric Detection of Free Amines on Maize Root Surfaces.

Front Plant Sci 2017 30;8:1513. Epub 2017 Aug 30.

Department of Biology, Doane University, CreteNE, United States.

Plant root exudates are important mediators in the interactions that occur between plants and microorganisms in the soil, yet much remains to be learned about spatial and temporal variation in their production. This work outlines a method utilizing a novel colorimetric paper to detect spatial and temporal changes in the production of nitrogen-containing compounds on the root surface. While existing methods have made it possible to conduct detailed analysis of root exudate composition, relatively less is known about where in the root system exudates are produced and how this localization changes as the root grows. Furthermore, there is much to learn about how exudate localization and composition varies in response to stress. Root exudates are chemically diverse secretions composed of organic acids, amino acids, proteins, sugars, and other metabolites. The sensor utilized for the method, ninhydrin, is a colorless substance in solution that reacts with free amino groups to form a purple dye. A detection paper was developed by formulating ninhydrin into a print solution that was uniformly deposited onto paper with a commercial ink jet printer. This "ninhydrin paper" was used to analyze the chemical makeup of root surfaces from maize seedlings grown vertically on germination paper. Through contact between the ninhydrin paper and seedling root surfaces, combined with images of both the seedlings and dried ninhydrin papers captured using a standard flatbed scanner, nitrogen-containing substances on the root surface can be localized and concentration of signal estimated for over 2 weeks of development. The method was found to be non-inhibiting to plant growth over the analysis period although damage to root hairs was observed. The method is sensitive in the detection of free amines at concentrations as little as 140 μM. Furthermore, ninhydrin paper is stable, showing consistent color changes up to 2 weeks after printing. This relatively simple, low-cost method could contribute to a better understanding of root exudates and mechanisms used by plants to interact with the complex soil environment during growth and development.
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http://dx.doi.org/10.3389/fpls.2017.01513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582365PMC
August 2017

Multiple Sources of Prescription Payment and Risky Opioid Therapy Among Veterans.

Med Care 2017 07;55 Suppl 7 Suppl 1:S33-S36

*VA Connecticut Healthcare System West Haven †Yale University School of Medicine New Haven, CT ‡Brandeis University Waltham, MA §Office of Clinical Analytics and Reporting, Veterans Health Administration, Washington, DC.

Background: Opioid overdose and other related harms are a major source of morbidity and mortality among US Veterans, in part due to high-risk opioid prescribing.

Objectives: We sought to determine whether having multiple sources of payment for opioids-as a marker for out-of-system access-is associated with risky opioid therapy among veterans.

Research Design: Cross-sectional study examining the association between multiple sources of payment and risky opioid therapy among all individuals with Veterans Health Administration (VHA) payment for opioid analgesic prescriptions in Kentucky during fiscal year 2014-2015.

Measures: Source of payment categories: (1) VHA only source of payment (sole source); (2) sources of payment were VHA and at least 1 cash payment [VHA+cash payment(s)] whether or not there was a third source of payment; and (3) at least one other noncash source: Medicare, Medicaid, or private insurance [VHA+noncash source(s)]. Our outcomes were 2 risky opioid therapies: combination opioid/benzodiazepine therapy and high-dose opioid therapy, defined as morphine equivalent daily dose ≥90 mg.

Results: Of the 14,795 individuals in the analytic sample, there were 81.9% in the sole source category, 6.6% in the VHA+cash payment(s) category, and 11.5% in the VHA+noncash source(s) category. In logistic regression, controlling for age and sex, persons with multiple payment sources had significantly higher odds of each risky opioid therapy, with those in the VHA+cash having significantly higher odds than those in the VHA+noncash source(s) group.

Conclusions: Prescribers should examine the prescription monitoring program as multiple payment sources increase the odds of risky opioid therapy.
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http://dx.doi.org/10.1097/MLR.0000000000000722DOI Listing
July 2017

TAL Effectors Drive Transcription Bidirectionally in Plants.

Mol Plant 2017 02 10;10(2):285-296. Epub 2016 Dec 10.

Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA. Electronic address:

TAL effectors delivered by phytopathogenic Xanthomonas species are DNA-sequence-specific transcriptional activators of host susceptibility genes and sometimes resistance genes. The modularity of DNA recognition by TAL effectors makes them important also as tools for gene targeting and genome editing. Effector binding elements (EBEs) recognized by native TAL effectors in plants have been identified only on the forward strand of target promoters. Here, we demonstrate that TAL effectors can drive plant transcription from EBEs on either strand and in both directions. Furthermore, we show that a native TAL effector from Xanthomonas oryzae pv. oryzicola drives expression of a target with an EBE on each strand of its promoter. By inserting that promoter and derivatives between two reporter genes oriented head to head, we show that the TAL effector drives expression from either EBE in the respective orientations, and that activity at the reverse-strand EBE also potentiates forward transcription driven by activity at the forward-strand EBE. Our results reveal new modes of action for TAL effectors, suggesting the possibility of yet unrecognized targets important in plant disease, expanding the search space for off-targets of custom TAL effectors, and highlighting the potential of TAL effectors for probing fundamental aspects of plant transcription.
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http://dx.doi.org/10.1016/j.molp.2016.12.002DOI Listing
February 2017

Hepatitis C virus double-stranded RNA is the predominant form in human liver and in interferon-treated cells.

Hepatology 2017 08 10;66(2):357-370. Epub 2016 Nov 10.

Icahn School of Medicine at Mount Sinai, New York, NY.

Hepatitis C virus (HCV) is unique among RNA viruses in its ability to establish chronic infection in the majority of exposed adults. HCV persists in the liver despite interferon (IFN)-stimulated gene (ISG) induction; robust induction actually predicts treatment failure and viral persistence. It is unclear which forms of HCV RNA are associated with ISG induction and IFN resistance during natural infections. To thoroughly delineate HCV RNA populations, we developed conditions that fully separate the strands of long double-stranded RNA (dsRNA) and allow the released RNAs to be quantified in reverse transcription/polymerase chain reaction assays. These methods revealed that dsRNA, a pathogen-associated molecular pattern (PAMP), comprised 52% (standard deviation, 28%) of the HCV RNA in the livers of patients with chronic infection. HCV dsRNA was proportionally higher in patients with the unfavorable IL28B TT (rs12979860) genotype. Higher ratios of HCV double-stranded to single-stranded RNA (ssRNA) correlated positively with ISG induction. In Huh-7.5 cells, IFN treatment increased the total amount of HCV dsRNA through a process that required de novo viral RNA synthesis and shifted the ratio of viral dsRNA/ssRNA in favor of dsRNA. This shift was blocked by ribavirin (RBV), an antiviral drug that reduces relapse in HCV patients. Northern blotting established that HCV dsRNA contained genome-length minus strands.

Conclusion: HCV dsRNA is the predominant form in the HCV-infected liver and has features of both a PAMP and a genomic reservoir. Interferon treatment increased rather than decreased HCV dsRNA. This unexpected finding suggests that HCV produces dsRNA in response to IFN, potentially to antagonize antiviral defenses. (Hepatology 2017;66:357-370).
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http://dx.doi.org/10.1002/hep.28846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573989PMC
August 2017

Impact of HCV core gene quasispecies on hepatocellular carcinoma risk among HALT-C trial patients.

Sci Rep 2016 06 1;6:27025. Epub 2016 Jun 1.

Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Mutations at positions 70 and/or 91 in the core protein of genotype-1b, hepatitis C virus (HCV) are associated with hepatocellular carcinoma (HCC) risk in Asian patients. To evaluate this in a US population, the relationship between the percentage of 70 and/or 91 mutant HCV quasispecies in baseline serum samples of chronic HCV patients from the HALT-C trial and the incidence of HCC was determined by deep sequencing. Quasispecies percentage cut-points, ≥42% of non-arginine at 70 (non-R(70)) or ≥98.5% of non-leucine at 91 (non-L(91)) had optimal sensitivity at discerning higher or lower HCC risk. In baseline samples, 88.5% of chronic HCV patients who later developed HCC and 68.8% of matched HCC-free control patients had ≥42% non-R(70) quasispecies (P = 0.06). Furthermore, 30.8% of patients who developed HCC and 54.7% of matched HCC-free patients had quasispecies with ≥98.5% non-L(91) (P = 0.06). By Kaplan-Meier analysis, HCC incidence was higher, but not statistically significant, among patients with quasispecies ≥42% non-R(70) (P = 0.08), while HCC incidence was significantly reduced among patients with quasispecies ≥98.5% non-L(91) (P = 0.01). In a Cox regression model, non-R(70) ≥42% was associated with increased HCC risk. This study of US patients indicates the potential utility of HCV quasispecies analysis as a non-invasive biomarker of HCC risk.
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http://dx.doi.org/10.1038/srep27025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4887904PMC
June 2016

Real-World Sustained Virologic Response Rates of Sofosbuvir-Containing Regimens in Patients Coinfected With Hepatitis C and HIV.

Clin Infect Dis 2016 06 1;62(12):1497-1504. Epub 2016 Mar 1.

Division of Liver Diseases.

Background: Patients with hepatitis C virus (HCV) with or without human immunodeficiency virus (HIV) achieve high sustained virological response (SVR) rates on sofosbuvir (SOF)-containing regimens in clinical trials. Real world data on patients coinfected with HCV and HIV treated with SOF-based regimens are lacking.

Methods: This observational cohort study included HIV/HCV-coinfected adults with genotype 1 HCV who initiated treatment with a SOF-containing regimen between December 2013 and December 2014 (n = 89) at the Mount Sinai Hospital or the Brooklyn Hospital Center. The primary outcome was SVR at 12 weeks after the end of treatment. The secondary outcomes were risk factors for treatment failure, serious adverse events, and side effects. A post hoc per protocol analysis of SVR was performed on patients who completed treatment and follow-up.

Results: In an intention-to-treat analysis, SVR rates were 76% (31/41) for simeprevir (SMV)/SOF, 94% (16/17) for SMV/SOF/ribavirin (RBV), and 52% (16/31) for SOF/RBV. The SVR rates of SMV/SOF/RBV and SMV/SOF did not differ significantly in this small study (P = .15). However the SVR rate of SMV/SOF/RBV was higher than that of SOF/RBV (P < .01). In a per protocol analysis, SMV/SOF/RBV had a higher SVR rate than SOF/RBV: 100% (16/16) vs 57% (16/28) (P < .01). The most commonly reported adverse effects were rash, pruritus, fatigue, and insomnia. One patient who had decompensated cirrhosis prior to treatment initiation died after receiving SMV/SOF.

Conclusions: SMV/SOF ± RBV is an effective option with minimal adverse effects for most HIV-positive patients with genotype 1 HCV. SMV should be used with caution in patients with decompensated cirrhosis.
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http://dx.doi.org/10.1093/cid/ciw119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4885645PMC
June 2016

Bisphosphonates as potential adjuvants for patients with cancers of the digestive system.

World J Gastroenterol 2016 Jan;22(3):906-16

Celina Ang, Department of Medicine, Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.

Best known for their anti-resorptive activity in bone, bisphosphonates (BPs) have generated interest as potential antineoplastic agents given their pleiotropic biological effects which include antiproliferative, antiangiogenic and immune-modulating properties. Clinical studies in multiple malignancies suggest that BPs may be active in the prevention or treatment of cancer. Digestive tract malignancies represent a large and heterogeneous disease group, and the activity of BPs in these cancers has not been extensively studied. Recent data showing that some BPs inhibit human epidermal growth factor receptor (HER) signaling highlight a potential therapeutic opportunity in digestive cancers, many of which have alterations in the HER axis. Herein, we review the available evidence providing a rationale for the repurposing of BPs as a therapeutic adjunct in the treatment of digestive malignancies, especially in HER-driven subgroups.
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http://dx.doi.org/10.3748/wjg.v22.i3.906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716044PMC
January 2016

A cell culture system for distinguishing hepatitis C viruses with and without liver cancer-related mutations in the viral core gene.

J Hepatol 2015 Dec 26;63(6):1323-33. Epub 2015 Jul 26.

Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Electronic address:

Background & Aims: Although patients infected by genotype 1b hepatitis C virus (HCV) with Q(70) and/or M(91)core gene mutations have an almost five-fold increased risk of developing hepatocellular carcinoma (HCC) and increased insulin resistance, the absence of a suitable experimental system has precluded direct experimentation on the effects of these mutations on cellular gene expression.

Methods: HuH7 cells were treated long-term with human serum to induce differentiation and to produce a model system for testing high-risk and control HCV. For clinical validation, profiles of infected cells were compared to each other and to those of liver biopsies of patients with early-stage HCV-related cirrhosis followed prospectively for up to 23 years (n=216).

Results: Long-term culture in human serum produced growth-arrested, hepatocyte-like cells whose gene profile overlapped significantly with that of primary human hepatocytes. High-risk (Q(70)/M(91)) and control (R(70)/L(91)) viruses had dramatically different effects on gene expression of these cells. The high-risk virus enhanced expression of pathways associated with cancer and type II diabetes, while the control virus enhanced pathways associated with oxidative phosphorylation. Of special clinical relevance, the transcriptome of cells replicating the high-risk virus correlated significantly with an HCC high-risk profile in patients (Bonferroni-corrected p=0.03), whereas no such association was observed for non-HCC-related clinical outcomes.

Conclusions: The cell-based system allowed direct head-to-head comparison of HCV variants, and provided experimental support for previous clinical data indicating an oncogenic effect of core gene mutations. This simple experimental system distinguished HCV variants and will enable future mechanistic analysis and exploration of interventional approaches.
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http://dx.doi.org/10.1016/j.jhep.2015.07.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654634PMC
December 2015

The effect of locally delivered recombinant human bone morphogenetic protein-2 with hydroxyapatite/tri-calcium phosphate on the biomechanical properties of bone in diabetes-related osteoporosis.

J Orthop Traumatol 2015 Jun 25;16(2):151-9. Epub 2014 Nov 25.

Division of Orthopaedic Trauma, Department of Orthopaedic Surgery, NYU Hospital for Joint Diseases, 301 E 17th Street, Suite 1402, New York, NY, 10003, USA,

Background: Recombinant human bone morphogenetic protein-2 (rhBMP-2) is particularly effective in improving osteogenesis in patients with diminished bone healing capabilities, such as individuals with type 1 diabetes mellitus (T1DM) who have impaired bone healing capabilities and increased risk of developing osteoporosis. This study measured the effects of rhBMP-2 treatment on osteogenesis by observing the dose-dependent effect of localized delivery of rhBMP-2 on biomechanical parameters of bone using a hydroxyapatite/tri-calcium phosphate (HA/TCP) carrier in a T1DM-related osteoporosis animal model.

Materials And Methods: Two different doses of rhBMP-2 (LD low dose, HD high dose) with a HA/TCP carrier were injected into the femoral intramedullary canal of rats with T1DM-related osteoporosis. Two more diabetic rat groups were injected with saline alone and with HA/TCP carrier alone. Radiographs and micro-computed tomography were utilized for qualitative assessment of bone mineral density (BMD). Biomechanical testing occurred at 4- and 8-week time points; parameters tested included torque to failure, torsional rigidity, shear stress, and shear modulus.

Results: At the 4-week time point, the LD and HD groups both exhibited significantly higher BMD than controls; at the 8-week time point, the HD group exhibited significantly higher BMD than controls. Biomechanical testing revealed dose-dependent, higher trends in all parameters tested at the 4- and 8-week time points, with minimal significant differences.

Conclusions: Groups treated with rhBMP-2 demonstrated improved bone mineral density at both 4 and 8 weeks compared to control saline groups, in addition to strong trends towards improvement of intrinsic and extrinsic biomechanical properties when compared to control groups. Data revealed trends toward dose-dependent increases in peak torque, torsional rigidity, shear stress, and shear modulus 4 weeks after rhBMP-2 treatment.

Level Of Evidence: Not applicable.
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http://dx.doi.org/10.1007/s10195-014-0327-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441641PMC
June 2015

Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene.

PLoS Pathog 2014 Feb 27;10(2):e1003972. Epub 2014 Feb 27.

Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America ; Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.

Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo), which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. A TAL effector finds its target(s) via a partially degenerate code whereby the modular effector amino acid sequence identifies nucleotide sequences to which the protein binds. Virulence contributions of some Xoo TAL effectors have been shown, and their relevant targets, susceptibility (S) genes, identified, but the role of TAL effectors in leaf streak is uncharacterized. We used host transcript profiling to compare leaf streak to blight and to probe functions of Xoc TAL effectors. We found that Xoc and Xoo induce almost completely different host transcriptional changes. Roughly one in three genes upregulated by the pathogens is preceded by a candidate TAL effector binding element. Experimental analysis of the 44 such genes predicted to be Xoc TAL effector targets verified nearly half, and identified most others as false predictions. None of the Xoc targets is a known bacterial blight S gene. Mutational analysis revealed that Tal2g, which activates two genes, contributes to lesion expansion and bacterial exudation. Use of designer TAL effectors discriminated a sulfate transporter gene as the S gene. Across all targets, basal expression tended to be higher than genome-average, and induction moderate. Finally, machine learning applied to real vs. falsely predicted targets yielded a classifier that recalled 92% of the real targets with 88% precision, providing a tool for better target prediction in the future. Our study expands the number of known TAL effector targets, identifies a new class of S gene, and improves our ability to predict functional targeting.
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http://dx.doi.org/10.1371/journal.ppat.1003972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937315PMC
February 2014

TAL effector specificity for base 0 of the DNA target is altered in a complex, effector- and assay-dependent manner by substitutions for the tryptophan in cryptic repeat -1.

PLoS One 2013 3;8(12):e82120. Epub 2013 Dec 3.

Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America.

TAL effectors are re-targetable transcription factors used for tailored gene regulation and, as TAL effector-nuclease fusions (TALENs), for genome engineering. Their hallmark feature is a customizable central string of polymorphic amino acid repeats that interact one-to-one with individual DNA bases to specify the target. Sequences targeted by TAL effector repeats in nature are nearly all directly preceded by a thymine (T) that is required for maximal activity, and target sites for custom TAL effector constructs have typically been selected with this constraint. Multiple crystal structures suggest that this requirement for T at base 0 is encoded by a tryptophan residue (W232) in a cryptic repeat N-terminal to the central repeats that exhibits energetically favorable van der Waals contacts with the T. We generated variants based on TAL effector PthXo1 with all single amino acid substitutions for W232. In a transcriptional activation assay, many substitutions altered or relaxed the specificity for T and a few were as active as wild type. Some showed higher activity. However, when replicated in a different TAL effector, the effects of the substitutions differed. Further, the effects differed when tested in the context of a TALEN in a DNA cleavage assay, and in a TAL effector-DNA binding assay. Substitution of the N-terminal region of the PthXo1 construct with that of one of the TAL effector-like proteins of Ralstonia solanacearum, which have arginine in place of the tryptophan, resulted in specificity for guanine as the 5' base but low activity, and several substitutions for the arginine, including tryptophan, destroyed activity altogether. Thus, the effects on specificity and activity generated by substitutions at the W232 (or equivalent) position are complex and context dependent. Generating TAL effector scaffolds with high activity that robustly accommodate sites without a T at position 0 may require larger scale re-engineering.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082120PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849474PMC
September 2014

Higher expression of several interferon-stimulated genes in HIV-1-infected females after adjusting for the level of viral replication.

J Infect Dis 2013 Sep 10;208(5):830-8. Epub 2013 Jun 10.

Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA 02139, USA.

Background: Clinical studies have shown faster disease progression and stronger immune activation in human immunodeficiency virus (HIV)-1-infected females when compared with males for the same level of HIV-1 replication. Here we determine whether the elevated levels of HIV-1-induced interferon-alpha (IFN-α) production observed in females are associated with higher interferon-stimulated gene (ISG) expression levels in T cells, hence suggesting type-I IFN as a mechanism for the higher HIV-1-associated immune activation observed.

Methods: T-cell and dendritic cell populations were isolated from treatment-naive chronically HIV-1-infected individuals enrolled in the Adult Clinical Trials Group 384 by fluorescence-activated cell sorting. The expression of 98 genes involved in Toll-like receptor and type I IFN signaling pathways were quantified using Nanostring technology.

Results: Several ISGs were significantly correlated with HIV-1 viral load and/or CD4(+) T-cell count. Higher expression levels of a subset of these ISGs were observed in cells derived from females as compared to males after adjusting for viral load and were correlated to higher levels of T-cell activation.

Conclusion: These data show that higher IFN-α production is associated with higher ex vivo expression of several ISGs in females. This might contribute to higher levels of immune activation and the observed faster HIV-1 disease progression in females for a given level of viral replication.
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http://dx.doi.org/10.1093/infdis/jit262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733517PMC
September 2013

TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins.

Trends Cell Biol 2013 Aug 23;23(8):390-8. Epub 2013 May 23.

Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011, USA.

Transcription activator-like (TAL) effectors are transcription factors injected into plant cells by pathogenic bacteria of the genus Xanthomonas. They function as virulence factors by activating host genes important for disease, or as avirulence factors by turning on genes that provide resistance. DNA-binding specificity is encoded by polymorphic repeats in each protein that correspond one-to-one with different nucleotides. This code has facilitated target identification and opened new avenues for engineering disease resistance. It has also enabled TAL effector customization for targeted gene control, genome editing, and other applications. This article reviews the structural basis for TAL effector-DNA specificity, the impact of the TAL effector-DNA code on plant pathology and engineered resistance, and recent accomplishments and future challenges in TAL effector-based DNA targeting.
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http://dx.doi.org/10.1016/j.tcb.2013.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3729746PMC
August 2013

Neuroplasticity, axonal guidance and micro-RNA genes are associated with morphine self-administration behavior.

Addict Biol 2013 May 15;18(3):480-95. Epub 2012 Jul 15.

Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA.

Neuroadaptations in the ventral striatum (VS) and ventral midbrain (VMB) following chronic opioid administration are thought to contribute to the pathogenesis and persistence of opiate addiction. In order to identify candidate genes involved in these neuroadaptations, we utilized a behavior-genetics strategy designed to associate contingent intravenous drug self-administration with specific patterns of gene expression in inbred mice differentially predisposed to the rewarding effects of morphine. In a Yoked-control paradigm, C57BL/6J mice showed clear morphine-reinforced behavior, whereas DBA/2J mice did not. Moreover, the Yoked-control paradigm revealed the powerful consequences of self-administration versus passive administration at the level of gene expression. Morphine self-administration in the C57BL/6J mice uniquely up- or down-regulated 237 genes in the VS and 131 genes in the VMB. Interestingly, only a handful of the C57BL/6J self-administration genes (<3%) exhibited a similar expression pattern in the DBA/2J mice. Hence, specific sets of genes could be confidently assigned to regional effects of morphine in a contingent- and genotype-dependent manner. Bioinformatics analysis revealed that neuroplasticity, axonal guidance and micro-RNAs (miRNAs) were among the key themes associated with drug self-administration. Noteworthy were the primary miRNA genes H19 and micro-RNA containing gene (Mirg), processed, respectively, to mature miRNAs miR-675 and miR-154, because they are prime candidates to mediate network-like changes in responses to chronic drug administration. These miRNAs have postulated roles in dopaminergic neuron differentiation and mu-opioid receptor regulation. The strategic approach designed to focus on reinforcement-associated genes provides new insight into the role of neuroplasticity pathways and miRNAs in drug addiction.
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http://dx.doi.org/10.1111/j.1369-1600.2012.00470.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477247PMC
May 2013

Addition of transcription activator-like effector binding sites to a pathogen strain-specific rice bacterial blight resistance gene makes it effective against additional strains and against bacterial leaf streak.

New Phytol 2012 Sep 2;195(4):883-893. Epub 2012 Jul 2.

Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.

Xanthomonas transcription activator-like (TAL) effectors promote disease in plants by binding to and activating host susceptibility genes. Plants counter with TAL effector-activated executor resistance genes, which cause host cell death and block disease progression. We asked whether the functional specificity of an executor gene could be broadened by adding different TAL effector binding elements (EBEs) to it. We added six EBEs to the rice Xa27 gene, which confers resistance to strains of the bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) that deliver the TAL effector AvrXa27. The EBEs correspond to three other effectors from Xoo strain PXO99(A) and three from strain BLS256 of the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc). Stable integration into rice produced healthy lines exhibiting gene activation by each TAL effector, and resistance to PXO99(A) , a PXO99(A) derivative lacking AvrXa27, and BLS256, as well as two other Xoo and 10 Xoc strains virulent toward wildtype Xa27 plants. Transcripts initiated primarily at a common site. Sequences in the EBEs were found to occur nonrandomly in rice promoters, suggesting an overlap with endogenous regulatory sequences. Thus, executor gene specificity can be broadened by adding EBEs, but caution is warranted because of the possible coincident introduction of endogenous regulatory elements.
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http://dx.doi.org/10.1111/j.1469-8137.2012.04216.xDOI Listing
September 2012