Whole-exome sequencing reveals a C-terminal germline variant in CEBPA-associated acute myeloid leukemia: 45-year follow-up of a large family.

Familial acute myeloid leukemia is rare and linked to germline mutations in RUNX1, GATA2 or CCAAT/enhancer binding protein-α (CEBPA). We re-evaluated a large family with acute myeloid leukemia originally seen at NIH in 1969. We utilized whole-exome sequencing to study this family, and conducted in silico bioinformatics analysis, protein structural modeling and laboratory experiments to assess the impact of the identified CEBPA Q311P mutation. Unlike most previously identified germline mutations in CEBPA, which were N-terminal frameshift mutations, we identified a novel Q311P variant that was located in the C-terminal bZip domain of C/EBPα. Protein structural modeling suggested that the Q311P mutation alters the ability of the CEBPA dimer to bind DNA. Electrophoretic mobility shift assays showed that the Q311P mutant had attenuated binding to DNA, as predicted by the protein modeling. Consistent with these findings, we found that the Q311P mutation has reduced transactivation, consistent with a loss-of-function mutation. From 45 years of follow-up, we observed incomplete penetrance (46%) of CEBPA Q311P. This study of a large multi-generational pedigree reveals that a germline mutation in the C-terminal bZip domain can alter the ability of C/EBP-α to bind DNA and reduces transactivation, leading to acute myeloid leukemia.

Comparison of whole carcass condemnation and partial carcass condemnation data for integration in a national syndromic surveillance system: The Swiss experience

We obtained partial carcass condemnation (PCC) data for cattle (2009-2010) from a Swiss slaughterhouse. Data on whole carcass condemnations (WCC) carried out at the same slaughterhouse over those years were extracted from the national database for meat inspection. We found that given the differences observed in the WCC and PCC time series, it is likely that both indicators respond to different health events in the population and that one cannot be substituted by the other. Because PCC recordings are promising for syndromic surveillance, the meat inspection database should be capable to record both WCC and PCC data in the future. However, a standardised list of reasons for PCC needs to be defined and used nationwide in all slaughterhouses.

Risk Factors for Whole Carcass Condemnations in the Swiss Slaughter Cattle Population

We used meat-inspection data collected over a period of three years in Switzerland to evaluate slaughterhouse-level, farm-level and animal-level factors that may be associated with whole carcass condemnation (WCC) in cattle after slaughter. The objective of this study was to identify WCC risk factors so they can be communicated to, and managed by, the slaughter industry and veterinary services. During meat inspection, there were three main important predictors of the risk of WCC; the slaughtered animal's sex, age, and the size of the slaughterhouse it was processed in. WCC for injuries and significant weight loss (visible welfare indicators) were almost exclusive to smaller slaughterhouses. Cattle exhibiting clinical syndromes that were not externally visible (e.g. pneumonia lesions) and that are associated with fattening of cattle, end up in larger slaughterhouses. For this reason, it is important for animal health surveillance to collect data from both types of slaughterhouses. Other important risk factors for WCC were on-farm mortality rate and the number of cattle on the farm of origin. This study highlights the fact that the many risk factors for WCC are as complex as the production system itself, with risk factors interacting with one another in ways which are sometimes difficult to interpret biologically. Risk-based surveillance aimed at farms with reoccurring health problems (e.g. a history of above average condemnation rates) may be more appropriate than the selection, of higher-risk animals arriving at slaughter. In Switzerland, the introduction of a benchmarking system that would provide feedback to the farmer with information on condemnation reasons, and his/her performance compared to the national/regional average could be a first step towards improving herd-management and financial returns for producers.

Supporting Whole-Class Collaborative Inquiry in a Secondary Mathematics Classroom

Recent mathematics education reform efforts call for the instantiation of mathematics classroom environments where students have opportunities to reason and construct their understandings as part of a community of learners. Despite some successes, traditional models of instruction still dominate the educational landscape. This limited success can be attributed, in part, to an underdeveloped understanding of the roles teachers must enact to successfully organize and participate in collaborative classroom practices. Towards this end, an in-depth longitudinal case study of a collaborative high school mathematics classroom was undertaken guided by the following two questions: What roles do these collaborative practices require of teacher and students? How does the community’s capacity to engage in collaborative practices develop over time? The analyses produced two conceptual models: one of the teacher’s role, along with specific instructional strategies the teacher used to organize a collaborative learning environment, and the second of the process by which the class’s capacity to participate in collaborative inquiry practices developed over time.

Orchestrating Whole Group Discourse to Mediate Mathematical Meaning

The most common pattern of classroom discourse follows a three-part exchange of teacher initiation, student response, and teacher evaluation or follow-up (IRE/IRF) (Cazden, 2001). Although sometimes described as encouraging illusory understanding (Lemke, 1990), triadic exchanges can mediate meaning (Nassaji & Wells, 2000). This paper focuses on one case from a study of discursive practices of seven middle grades teachers identified for their expertise in mathematics instruction. The central result of the study was the development of a model to explain how teachers use discourse to mediate mathematical meaning in whole group instruction. Drawing on the model for analysis, thick descriptions of one teacher’s skillful orchestration of triadic exchanges that enhance student understanding of mathematics are presented.

Whole genome analysis of Fusobacterium nucleatum, Rickettsia typhi and Francisella tularensis

The genomes of Fusobacterium nucleatum subspecies polymorphum strain ATCC 10953, Rickettsia typhi strain Wilmington, and Francisella tularensis subspecies holarctica strain OSU18 were sequenced, annotated, and analyzed. Each genome was then compared to the sequenced genomes of closely related bacteria. The genome of F. nucleatum ATCC 10953 was compared to two additional F. nucleatum subspecies, subspecies nucleatum and subspecies vincentii. This analysis revealed substantial evidence of horizontal gene transfer along with considerable genetic diversity within the species of F. nucleatum. R. typhi was compared to R. prowazekii and R. conorii. This analysis uncovered a hotspot for chromosomal rearrangements in the Spotted Fever Group but not the Typhus Group Rickettsia and revealed the close genetic relationship between the Typhus Group rickettsial species. F. tularensis OSU18 was compared to two additional F. tularensis strains. These comparisons uncovered significant chromosomal rearrangements between F. tularensis subspecies due to recombination between insertion sequence elements. ^

Weed Management Programs in Soybeans

The purpose of this study was to evaluate various herbicides and application timings in soybean for crop injury and weed control.

Water Infiltration following Land Rolling of Soybeans

Land rolling of soybean fields has become a popular practice in north central and northwest Iowa during the past five years. Although this technique was first utilized to push rocks into the ground to avoid combine damage and aid in harvesting lodged crops in Canada, producers in Iowa quickly learned that pushing corn root-balls flat at the time of planting and pushing small rocks into the ground can increase harvest efficiency. Typically fields are rolled shortly after planting. One disturbing trend that was noticed, however, was that rolled fields tended to have more water standing between the rows after moderate or heavy rain events. This would imply that water infiltration was slower in fields that had been rolled compared with fields that had not been rolled. Infiltration measurements were taken on a few plots in 2010 at the ISU Northern Research Farm. It seemed that water infiltration was less on the rolled plots. However, we wanted more measurements before publishing any results. In 2011 infiltration measurements were taken on the research farm and on neighboring farms where soybeans had been rolled. The goal was to determine if water infiltration had been reduced by land rolling.

Soil and Plant Fertility Management for Soybeans

Producers utilizing a two year rotation of corn and soybean often apply fertilizer on a biannual basis, spreading recommended amounts of phosphorus and potassium for both crops prior to corn establishment. This approach minimizes application costs and is in accordance with university fertility recommendations that have found a low probability of fertilizer yield response when soils tested at the medium/optimum level or above. However, the field trials on which these state recommendations were developed are often several decades old. Increases in average corn and soybean yields and associated increases in crop nutrient removal rates have called into question the validity of these recommendations for current production environments. This study investigated the response of soil test levels and grain yield to annual and biannual fertilizer applications made at 1x and 2x rates of current university fertilizer recommendations.

Yields of Corn, Soybeans, and Alfalfa in Western Iowa: 1990 to 2011

The ISU Western Research Farm, Castana, Iowa is one of the oldest in Iowa dating to 1946. It also has a unique location in the loess hills of western Iowa. The research farm was set up to study the deep loess soils, particularly crop production and soil conservation methods. Although the work at the research farm has transitioned away from traditional plot work, yields of major crops grown at the farm, and climate data are collected each year. Crop yields are a reflection of current technologies and weather. In western Iowa, rainfall is especially critical and is often the limiting factor.

Evaluation of Narrow Row Soybeans

Producers continue to look at different management practices to increase corn and soybean yields. One area of interest is planting corn and soybeans in narrow rows. Traditionally, these crops have been planted in row widths of 30 to 38 in. Planters on the market today have the capability to plant corn and soybeans in 15- and 20-in. rows, as well as in twin rows that are spaced eight inches apart. This study was set up to evaluate the yield impact of planting soybeans in 15-in. rows versus the traditional 30-in. row spacing.

Whole Genome Analysis of Pinkeye Scores in Angus Cattle

Infectious Bovine Keratoconjunctivitis (IBK), known as pinkeye, is a common infectious disease affecting the eyes of cattle. It is characterized by excessive tearing, inflammation of the conjunctiva, and ulceration of the cornea. Although pinkeye is non-fatal, it has a marked economic impact on the cattle industry, due to the decreased performance of infected individuals. Genetic effects on the susceptibility of IBK have been studied and Hereford, Jersey, and Holstein breeds were found to be more susceptible to IBK than Bos Indicus breeds. The objectives of our study were: 1) to estimate genetic parameters of IBK scored in different categories by using genomic threshold model, and 2) to detect markers in linkage disequilibrium with quantitative tract loci (QTL) associated with IBK.

Evaluation of Foliar Fungicides and Insecticides on Soybeans

Use of foliar fungicides and insecticides are an effective strategy for managing foliar diseases of soybean. There are many different fungicides and insecticides available for use currently in Iowa. Iowa State University personnel assessed the success of fungicides and insecticides across Iowa. This study was conducted at six locations: Sutherland (NW), Kanawha (NC), Nashua (NE), Ames (central), Crawfordsville (SE), and Lewis (SW) research farms (Figure 1).

High Yield of Soybeans Study

The research project was designed to study soybean plant and yield responses to certain products. Soybean producers generally look to maximize profit, and with increased soybean prices, financial returns have been obtained from even smaller yield responses. The project began in 2011 as a two-year study designed to look at the effects of both seed and foliar treatments applied to soybeans.

Evaluation of Foliar Fungicides and Insecticides on Soybeans

Use of foliar fungicides and insecticides are an effective strategy for managing foliar diseases of soybean. There are many different fungicides and insecticides available for use currently in Iowa. Iowa State University personnel assessed the success of fungicides and insecticides across Iowa. This study was conducted at six locations: Sutherland (NW), Kanawha (NC), Nashua (NE), Ames (central), Crawfordsville (SE), and Lewis (SW) research farms (Figure 1).