Insertion of a FLAG-tag sequence at the end of exon 9 of the TBX5 gene in three induced pluripotent stem cell lines (DHMi004-A-4, DHMi004-A-5, DHMi004-A-6) by CRISPR/Cas9 technology.

The identification of TBX5-related regulatory sequences in genes essential for heart development is hampered by the absence of antibodies which allow precipitation of TBX5:DNA complexes. Employing CRISPR/Cas9 technology, we have inserted a FLAG-tag sequence at the end of exon 9 of the TBX5 gene prior to the stop codon by homologous recombination. The translated TBX5-FLAG fusion protein of the three iPSC lines can effectively be precipitated by anti-FLAG antibodies and, thus, allow the detection of specific TBX5-binding sites and their associated genes.

Glutaryl-CoA Dehydrogenase Misfolding in Glutaric Acidemia Type 1.

Glutaric acidemia type 1 (GA1) is a neurotoxic metabolic disorder due to glutaryl-CoA dehydrogenase (GCDH) deficiency. The high number of missense variants associated with the disease and their impact on GCDH activity suggest that disturbed protein conformation can affect the biochemical phenotype. We aimed to elucidate the molecular basis of protein loss of function in GA1 by performing a parallel analysis in a large panel of missense variants using different biochemical and biophysical methodologies.

Effects of postfire climate and seed availability on postfire conifer regeneration.

Large, severe fires are becoming more frequent in many forest types across the western United States and have resulted in tree mortality across tens of thousands of hectares. Conifer regeneration in these areas is limited because seeds must travel long distances to reach the interior of large burned patches and establishment is jeopardized by increasingly hot and dry conditions. To better inform postfire management in low elevation forests of California, USA, we collected 5-yr postfire recovery data from 1,234 study plots in 19 wildfires that burned from 2004-2012 and 18 yrs of seed production data from 216 seed fall traps (1999-2017).

From the stand scale to the landscape scale: predicting the spatial patterns of forest regeneration after disturbance.

Shifting disturbance regimes can have cascading effects on many ecosystems processes. This is particularly true when the scale of the disturbance no longer matches the regeneration strategy of the dominant vegetation. In the yellow pine and mixed conifer forests of California, over a century of fire exclusion and the warming climate are increasing the incidence and extent of stand-replacing wildfire; such changes in severity patterns are altering regeneration dynamics by dramatically increasing the distance from live tree seed sources.

Network analysis of wildfire transmission and implications for risk governance.

We characterized wildfire transmission and exposure within a matrix of large land tenures (federal, state, and private) surrounding 56 communities within a 3.3 million ha fire prone region of central Oregon US. Wildfire simulation and network analysis were used to quantify the exchange of fire among land tenures and communities and analyze the relative contributions of human versus natural ignitions to wildfire exposure.

Climate influences on whitebark pine mortality from mountain pine beetle in the Greater Yellowstone Ecosystem.

Extensive mortality of whitebark pine, beginning in the early to mid-2000s, occurred in the Greater Yellowstone Ecosystem (GYE) of the western USA, primarily from mountain pine beetle but also from other threats such as white pine blister rust. The climatic drivers of this recent mortality and the potential for future whitebark pine mortality from mountain pine beetle are not well understood, yet are important considerations in whether to list whitebark pine as a threatened or endangered species. We sought to increase the understanding of climate influences on mountain pine beetle outbreaks in whitebark pine forests, which are less well understood than in lodgepole pine, by quantifying climate-beetle relationships, analyzing climate influences during the recent outbreak, and estimating the suitability of future climate for beetle outbreaks.

A statistical model for determining impact of wildland fires on Particulate Matter (PM₂.₅) in Central California aided by satellite imagery of smoke.

As the climate in California warms and wildfires become larger and more severe, satellite-based observational tools are frequently used for studying impact of those fires on air quality. However little objective work has been done to quantify the skill these satellite observations of smoke plumes have in predicting impacts to PM2.5 concentrations at ground level monitors, especially those monitors used to determine attainment values for air quality under the Clean Air Act.

Climate and weather influences on spatial temporal patterns of mountain pine beetle populations in Washington and Oregon.

Widespread outbreaks of mountain pine beetle in North America have drawn the attention of scientists, forest managers, and the public. There is strong evidence that climate change has contributed to the extent and severity of recent outbreaks. Scientists are interested in quantifying relationships between bark beetle population dynamics and trends in climate.

Estimating contribution of wildland fires to ambient ozone levels in National Parks in the Sierra Nevada, California.

Data from four continuous ozone and weather monitoring sites operated by the National Park Service in Sierra Nevada, California, are used to develop an ozone forecasting model and to estimate the contribution of wildland fires on ambient ozone levels. The analyses of weather and ozone data pointed to the transport of ozone precursors from the Central Valley as an important source of pollution in these National Parks. Comparisons of forecasted and observed values demonstrated that accurate forecasts of next-day hourly ozone levels may be achieved by using a time series model with historic averages, expected local weather and modeled PM values as explanatory variables.

Development of a statistical model for estimating spatial and temporal ambient ozone patterns in the Sierra Nevada, California.

Statistical approaches for modeling spatially and temporally explicit data are discussed for 79 passive sampler sites and 9 active monitors distributed across the Sierra Nevada, California. A generalized additive regression model was used to estimate spatial patterns and relationships between predicted ozone exposure and explanatory variables, and to predict exposure at nonmonitored sites. The fitted model was also used to estimate probability maps for season average ozone levels exceeding critical (or subcritical) levels in the Sierra Nevada region.

The effects of the farnesyl transferase inhibitor FTI L-778,123 on normal, myelodysplastic, and myeloid leukemia bone marrow progenitor proliferation in vitro.

The effects of the farnesyl transferase inhibitor FTI-778,123 on the proliferation of normal, MDS, AML, and CML hemopoietic progenitor cells was studied. MDS myeloid and erythroid progenitors are significantly more sensitive to FTI than normal progenitors while AML myeloid progenitors may be somewhat more sensitive than normal progenitors. In contrast, no difference between CML and normal progenitors are detectable.

A novel method for single cell detection of in situ telomerase or histone H3 in combination with clonal analysis by FISH.

A novel method for simultaneously detecting clonality by FISH, and presence of telomerase activity (telo+ cells) or histone H3 mRNA (H3+) in single cells from a mixed leukemic population is reported. The methods were validated using K562 cells mixed with peripheral blood granulocytes and bone marrow aspirate cells from newly diagnosed AML patients. Fifty patients with AML were analyzed for telo+ cells, while eight AML patients were analyzed for FISH-Telomerase and FISH-H3+ during remission induction therapy.

A statistical approach to estimate O3 uptake of ponderosa pine in a mediterranean climate.

In highly polluted sites, stomatal behavior is sluggish with respect to light, vapor pressure deficit, and internal CO2 concentration (Ci) and poorly described by existing models. Statistical models were developed to estimate stomatal conductance (gs) of 40-year-old ponderosa pine at three sites differing in pollutant exposure for the purpose of calculating O3 uptake. Gs was estimated using julian day, hour of day, pre-dawn xylem potential and photosynthetic photon flux density (PPFD).

O uptake and drought stress effects on carbon acquisition of ponderosa pine in natural stands.

• The effect of O exposure or uptake on carbon acquisition (net assimilation (A) or gross photosynthesis (P )), with and without drought stress, is reported here in 40-yr-old-ponderosa pine (Pinus ponderosa) trees. • Maximum daily gas exchange was measured monthly for 12 trees at four sites differing in pollutant exposure over two growing seasons with above- and below-average annual precipitation. Gas exchange measures were estimated between sampling periods using a generalized additive regression model.

Amplification and overexpression of topoisomerase IIalpha predict response to anthracycline-based therapy in locally advanced breast cancer.

Purpose: The putative association between erbB-2 overexpression and favorable response to anthracyline-based therapy in breast cancer is controversial, and the mechanism unclear. We sought to determine whether coamplification and overexpression of the topoisomerase IIalpha gene, near erbB-2 on chromosome 17, and a known anthracycline target, may underlie the association.

Experimental Design: Thirty-five patients who had locally advanced breast cancer (LABC) and who had received neoadjuvant, anthracycline-based therapy were studied.

Abnormalities of molecular regulators of proliferation and apoptosis in carcinoma of the oral cavity and oropharynx.

Objective: Abnormalities in genes regulating cell proliferation and death may affect disease outcome in squamous cell carcinoma (SCC) of the head and neck.

Methods: Proliferative activity (Histone H3 in-situ-hybridization (HISH) labeling index (LI)) and the genes and/or gene products of Cyclin D-1, c-erbB-2, Bcl-2, p21, and p53, were investigated in 35 patients with SCC of the oral cavity and oropharynx, previously studied for p27 expression.

Results: Overexpression or very low expression of Cyclin D-1 was associated with unfavorable disease outcome and shorter time-to-recurrence.

P15INK4B gene methylation and expression in normal, myelodysplastic, and acute myelogenous leukemia cells and in the marrow cells of cured lymphoma patients.

P15INK4B methylation and expression was studied in bone marrow cells obtained from normal individuals, from patients who had been cured of lymphoma, and from patients with either MDS or AML. The level of p15 methylation was very low in normal BM cells and in CD34+ and CD34- subpopulations (0-6.5%; med, = 2.

Alterations in IRF1/IRF2 expression in acute myelogenous leukemia.

The interferon response genes 1 and 2 have been shown to be involved in the regulation of differentiation and proliferation of cells of the myeloid series, with the former functioning as an anti-oncogene and the latter as an oncogene. In the study described here, the levels of expression of these two genes and the ratio of their expression were compared in AML and normal marrow. The ratio of gene expression was significantly less in AML marrow cells as compared to normal marrow cells [med ratio = 1.

Preparation of autologous leukemia and lymphoma vaccines expressing alpha-gal epitopes.

This study describes a novel method for increasing the immunogenicity of autologous tumor vaccines in leukemia and lymphoma patients by exploiting the natural anti-Gal antibody for in situ targeting of the vaccinating cells to antigen-presenting cells (APCs). Incubation of leukemia or lymphoma cells with neuraminidase and recombinant alpha 1,3-galactosyltransferase results in the synthesis of many alpha-gal epitopes (Gal alpha 1-3Gal beta 1-4GlcNAc-R) on their cell membranes. Vaccination with such processed tumor cells results in the binding of the natural anti-Gal immunoglobulin G (IgG) antibody to these epitopes and opsonization of these cells for effective phagocytosis by APCs, such as dendritic cells and macrophages.

Poor prognosis acute myelogenous leukemia: 3--biological and molecular biological changes during remission induction therapy.

This is the third paper in a series which describes a new remission induction regimen for patients with 'poor prognosis' acute myelogenous leukemia (AML). Twenty-four patients were treated with two one day pulses of chemotherapy separated by 96 h. Each pulse consisted of two doses of cytarabine and a single dose of mitoxantrone.

Effectiveness of interferon-alfa and mid-cycle chemotherapy added to an anthracycline-based regimen in the treatment of aggressive non-Hodgkin's lymphoma.

Interferon-alfa in combination with cytotoxic chemotherapy has been shown to be effective in treating certain types of non-Hodgkin's lymphoma (NHL) (1). However, there is no published data on upfront induction treatment of aggressive NHL with IFN-alfa containing regimens. Studies have also shown that one can overcome regrowth resistance by administering mid-cycle agents which slow tumor proliferation between courses of cytotoxic therapy (2).

Quantitation of interferon regulatory factor transcripts in patients with acute myeloid leukemia.

Interferon regulatory factors IRF-1 and IRF-2, the two mutually antagonistic factors, fluctuate during the cell cycle and play an important role in normal and neoplastic growth processes. The relative levels of these two transcripts were analyzed in 5 normal and 43 acute myeloid leukemia (AML) bone marrow (BM) specimens by a semiquantitative RT-PCR method. IRF-1 and IRF-2 cDNA sequences were coamplified using primers that were designed to span regions of high homology between the genes.

High remission rate in acute myeloblastic leukemia with only two days of chemotherapy.

Twenty five patients with AML who had neither a history of toxic exposure or myelodysplasia were treated with a remission induction regimen consisting of two pulses of chemotherapy separated by 96 hrs. Each pulse consisted of cytarabine 2gm/m(2) (at t=0 and t=12 hrs) with mitoxantrone [30mg/m(2) ] administered immediately after the second cytarabine administration. Amifostine was administered three times a week [on Monday, Wednesday, and Friday] until the outcome of therapy was known.