Financial Exigency: Need It Affect the Quality of Biology Curricula?

Declining enrollments and financial restraints require that science departments seek ways to meet academic commitments within the framework of reduced budgets and faculty resources without sacrificing quality programs. The following describes our evaluation of the role of the laboratory in the undergraduate biology curriculum and the positive effects achieved on our academic, financial, and faculty resources by separating labs from lecture courses and reducing the number of labs required for majors and nonmajors. Several years ago we experienced increased enrollments coupled with only modest increases in funds to deliver our undergraduate instructional programs. To resolve this problem we developed a new approach to the role of lecture and laboratory courses for our biology majors, the nonmajor, and the students in the allied health programs serviced by our department. The changes effected by us then would appear to be equally appropriate in today\u27s economy when inflationary pressures and a decline in students make it imperative that departments look to ways to meet their academic commitments within the framework of declining budgets and faculty resources

An automated high-content screening image analysis pipeline for the identification of selective autophagic inducers in human cancer cell lines.

Automated image processing is a critical and often rate-limiting step in high-content screening (HCS) workflows. The authors describe an open-source imaging-statistical framework with emphasis on segmentation to identify novel selective pharmacological inducers of autophagy. They screened a human alveolar cancer cell line and evaluated images by both local adaptive and global segmentation. At an individual cell level, region-growing segmentation was compared with histogram-derived segmentation. The histogram approach allowed segmentation of a sporadic-pattern foreground and hence the attainment of pixel-level precision. Single-cell phenotypic features were measured and reduced after assessing assay quality control. Hit compounds selected by machine learning corresponded well to the subjective threshold-based hits determined by expert analysis. Histogram-derived segmentation displayed robustness against image noise, a factor adversely affecting region growing segmentation

Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study

Background: Tissue MicroArray technology aims to perform immunohistochemical staining on hundreds of different tissue samples simultaneously. It allows faster analysis, considerably reducing costs incurred in staining. A time consuming phase of the methodology is the selection of tissue areas within paraffin blocks: no utilities have been developed for the identification of areas to be punched from the donor block and assembled in the recipient block.Results: The presented work supports, in the specific case of a primary subtype of breast cancer (tubular breast cancer), the semi-automatic discrimination and localization between normal and pathological regions within the tissues. The diagnosis is performed by analysing specific morphological features of the sample such as the absence of a double layer of cells around the lumen and the decay of a regular glands-and-lobules structure. These features are analysed using an algorithm which performs the extraction of morphological parameters from images and compares them to experimentally validated threshold values. Results are satisfactory since in most of the cases the automatic diagnosis matches the response of the pathologists. In particular, on a total of 1296 sub-images showing normal and pathological areas of breast specimens, algorithm accuracy, sensitivity and specificity are respectively 89%, 84% and 94%.Conclusions: The proposed work is a first attempt to demonstrate that automation in the Tissue MicroArray field is feasible and it can represent an important tool for scientists to cope with this high-throughput technique

How does management affect soil C sequestration and greenhouse gas fluxes in boreal and temperate forests? : A review

Acknowledgements This review has been supported by the grant Holistic management practices, modelling and monitoring for European forest soils – HoliSoils (EU Horizon 2020 Grant Agreement No 101000289) and the Academy of Finland Fellow project (330136, B. Adamczyk). In addition to the HoliSoils consortium partners, Dr. Abramoff contributed on this study and her work was supported by the United States Department of Energy, Office of Science, Office of Biological and Environmental Research. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the United States Department of Energy under contract DE-AC05-00OR22725.Peer reviewedPublisher PD

A functional analysis of the pyrimidine catabolic pathway in Arabidopsis

Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to β-alanine, CO2 and NH3 through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and β-ureidopropionase (EC 3.5.1.6, PYD3).A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism. PYD expression and catabolism of [2-14C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source.PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-14C]-uracil or to grow on uracil as the sole nitrogen source. By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source. These results confirm PYD1 function and suggest the possible existence of another, as yet unknown, activity for uracil degradation to dihydrouracil in this plant.The localization of PYD-green fluorescent protein fusions in the plastid (PYD1), secretory system (PYD2) and cytosol (PYD3) suggests potentially complex metabolic regulation