David R. Howard

Impact of DNA–Surface Interactions on the Stability of DNA Hybrids

The structure and stability of single- and double-stranded DNA hybrids immobilized on gold are strongly affected by nucleotide-surface interactions. To systematically analyze the effects of these interactions, a set of model DNA hybrids was prepared in conformations that ranged from end-tethered double-stranded to directly adsorbed single-stranded (hairpins) and characterized by surface plasmon resonance (SPR) imaging, X-ray photoelectron spectroscopy (XPS), fluorescence microscopy, and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The stabilities of these hybrids were evaluated by exposure to a series of stringency rinses in solutions of successively lower ionic strength and by competitive hybridization experiments. In all cases, directly adsorbed DNA hybrids are found to be significantly less stable than either free or end-tethered hybrids. The surface-induced weakening and the associated asymmetry in hybridization responses of the two strands forming hairpin stems are most pronounced for single-stranded hairpins containing blocks of m adenine (A) nucleotides and n thymine (T) nucleotides, which have high and low affinity for gold surfaces, respectively. The results allow a qualitative scale of relative stabilities to be developed for DNA hybrids on surfaces. Additionally, the results suggest a route for selectively weakening portions of immobilized DNA hybrids and for introducing asymmetric hybridization responses by using sequence design to control nucleotide-surface interactions--a strategy that may be used in advanced biosensors and in switches or other active elements in DNA-based nanotechnology.

Assessment of a bioinformatics across life science curricula initiative

At the University of Wisconsin‐La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within those departments. Here, we assess student confidence in solving and ability to solve bioinformatics‐related problems. Assessment data show increases in student performance on bioinformatics‐related problems and more confidence in solving such problems with increased exposure to the field of bioinformatics. Additionally, the faculty perceive an increased awareness of the applications of bioinformatics among the students in their courses. The combination of three different assessment tools, a student self‐assessment of learning, a content exam, and faculty survey, was an effective and efficient approach for evaluating this multi‐departmental program.

Design and Implementation of an Interdepartmental Bioinformatics Program across Life Science Curricula

Over the past 10 years, there has been a technical revolution in the life sciences leading to the emergence of a new discipline called bioinformatics. In response, bioinformatics‐related topics have been incorporated into various undergraduate courses along with the development of new courses solely focused on bioinformatics. This report describes the design and implementation of an interdepartmental bioinformatics program throughout several life science programs. Using elements of the backward curricular design process, nine faculty members from the Biology, Microbiology, and Chemistry Departments at the University of Wisconsin – La Crosse incorporated bioinformatics in a coordinated manner into 10 courses. Key molecular biology concepts were first identified followed by development of bioinformatics exercises that centered on these concepts. An overview of how the program was constructed and implemented and a summary of the exercises that were designed will be presented.

The hibernating 13-lined ground squirrel as a model organism for potential cold storage of platelets

Hibernating mammals have developed many physiological adaptations to extreme environments. During hibernation, 13-lined ground squirrels (Ictidomys tridecemlineatus) must suppress hemostasis to survive prolonged body temperatures of 4-8°C and 3-5 heartbeats per minute without forming lethal clots. Upon arousal in the spring, these ground squirrels must be able to quickly restore normal clotting activity to avoid bleeding. Here we show that ground squirrel platelets stored in vivo at 4-8°C were released back into the blood within 2 h of arousal in the spring with a body temperature of 37°C but were not rapidly cleared from circulation. These released platelets were capable of forming stable clots and remained in circulation for at least 2 days before newly synthesized platelets were detected. Transfusion of autologous platelets stored at 4°C or 37°C showed the same clearance rates in ground squirrels, whereas rat platelets stored in the cold had a 140-fold increase in clearance rate. Our results demonstrate that ground squirrel platelets appear to be resistant to the platelet cold storage lesions observed in other mammals, allowing prolonged storage in cold stasis and preventing rapid clearance upon spring arousal. Elucidating these adaptations could lead to the development of methods to store human platelets in the cold, extending their shelf life.

Juvenile exposure to vinclozolin shifts sex ratios and impairs reproductive capacity of zebrafish

Exposure to endocrine disruptors during critical periods of development can impact the sustainability of wild fish populations. Anti-androgenic compounds have received less attention, but are capable of modulating gonad differentiation and maturation, and impairing reproduction in fish. The fungicide vinclozolin (VZ) has been shown to impair reproduction in adult fish, but less is known about its effects following exposure earlier in development. Here we show that waterborne exposure to 400μg VZ/L during critical periods of sex differentiation (21-35 days post fertilization) permanently shifts sex ratios towards females, and alters the maturation of the gonad. Both fecundity and fertility were reduced, even when oogenesis and spermatogenesis recover and sperm motility is not altered. These results demonstrate the need to better understand the impacts of early exposure to anti-androgenic compounds on fish.

Effects of hibernation on bone marrow transcriptome in thirteen-lined ground squirrels.

Mammalian hibernators adapt to prolonged periods of immobility, hypometabolism, hypothermia, and oxidative stress, each capable of reducing bone marrow activity. In this study bone marrow transcriptomes were compared among thirteen-lined ground squirrels collected in July, winter torpor, and winter interbout arousal (IBA). The results were consistent with a suppression of acquired immune responses, and a shift to innate immune responses during hibernation through higher complement expression. Consistent with the increase in adipocytes found in bone marrow of hibernators, expression of genes associated with white adipose tissue are higher during hibernation. Genes that should strengthen the bone by increasing extracellular matrix were higher during hibernation, especially the collagen genes. Finally, expression of heat shock proteins were lower, and cold-response genes were higher, during hibernation. No differential expression of hematopoietic genes involved in erythrocyte or megakaryocyte production was observed. This global view of the changes in the bone marrow transcriptome over both short term (torpor vs. IBA) and long term (torpor vs. July) hypothermia can explain several observations made about circulating blood cells and the structure and strength of the bone during hibernation.

Confocal microscopy as a useful approach to describe gill rakers of Asian species of carp and native filter-feeding fishes of the upper Mississippi River system

To better understand potential diet overlap among exotic Asian species of carp and native species of filter-feeding fishes of the upper Mississippi River system, microscopy was used to document morphological differences in the gill rakers. Analysing samples first with light microscopy and subsequently with confocal microscopy, the three-dimensional structure of gill rakers in Hypophthalmichthys molitrix, Hypophthalmichthys nobilis and Dorosoma cepedianum was more thoroughly described and illustrated than previous work with traditional microscopy techniques. The three-dimensional structure of gill rakers in Ictiobus cyprinellus was described and illustrated for the first time.