Bird Feeding, Bird Watching

A year ago at Christmas time, I became seriously fascinated with watching birds at feeders while we were visiting our daughter in Shenandoah, Iowa. She had put out a small hanging feeder, and I spread some loose seed in the garden plot behind the house. With my binoculars, I watched for hours by the window, seeing the birds in minute detail, and I considered trying this when we got back home

Visualization

In pockets of deep prehistory, humans made the first marks on their world. Those marks were completely new images, images that had not existed before. The painting and tooling on stone walls recorded and attempted to explain human interaction with the world. Languages, alphabets, systems of numbers and physical structures came much later. Each new tool eventually became interconnected with the others to produce more complex means of studying, recording and building the human-world relationship. These pockets of activity moved, merged, divided or died. The accumulations of perceptions, knowledge and technology continued to mix and reconnect

Reading and Understanding the Scientific Literature: ACE 10 Course: Biochemistry 435 Advanced Topics

ACE 10 Question Learning Objectives Writing: Students will generally be writing in a scientific format for the first time. This may be very different from prior writing in the university. This will come from discussions in the classroom sessions and from feedback on the course paper chapters that are submitted during the progress of the course. Oral Communication: This is reinforced by the presentation of relevant papers from the scientific literature during most of the class periods. Students need to learn to master the content of such papers, prioritize the important elements, and present them in a coherent fashion. The student effort receives intrinsic feedback during the process by questions and comments from the instructor and from the other students. Critical Thinking: Critical thinking can only be done once a student has mastered a significant amount of foundational literature. Students at the start of the topic will have little ability to carry out critical thinking about the course theme. As students read more of the primary literature and seek out other references to flesh out certain aspects and to reconcile contradictory reports, they will be encouraged to reflect on the epistemology of the conclusions. Ethics: Each section of the class involves one class session related to an ethical issue. This usually involves a case study that is read prior to the class and a group discussion. In some cases, it is productive to have students attempt to present differing viewpoints, but in for other topics, students seem able to grasp the diverse social impacts. Student Work Rubric for evaluating student work Broad range of topics for each section of BIOC435 Method of Analysis Findings Improving ACE 10 Learnin

Branching

For many years I have observed and photographed visual patterns. Sometimes I stumble upon them, and other times I search to find them, record them and perhaps make some sense of the relationships I see in the many variations. In the early \u2770s I began to put these observations together and to classify the many patterns into branching and layering. These two systems I see as primal information from which the human can better understand an underlying structure in the universe. These universal patterns act as building blocks to many diverse and complex forms and phenomena. The images and ideas continue to excite me as an artist-teacher and science student. My slide collection continues to grow and my notes reflect the ever changing relationships I see

Chloroquine and cytosolic galectins affect endosomal escape of antisense oligonucleotides after Stabilin-mediated endocytosis

Non-DNA-binding Stabilin-2/HARE receptors expressed on liver sinusoidal endothelial cells specifically bind to and internalize several classes of phosphorothioate antisense oligonucleotides (PS-ASOs). After Stabilin-mediated uptake, PS-ASOs are trafficked within endosomes (\u3e97%–99%), ultimately resulting in destruction in the lysosome. The ASO entrapment in endosomes lowers therapeutic efficacy, thereby increasing the overall dose for patients. Here, we use confocal microscopy to characterize the intracellular route transverse by PS-ASOs after Stabilin receptor-mediated uptake in stable recombinant Stabilin-1 and -2 cell lines. We found that PS-ASOs as well as the Stabilin-2 receptor transverse the classic path: clathrincoated vesicle-early endosome-late endosome-lysosome. Chloroquine exposure facilitated endosomal escape of PS-ASOs leading to target knockdown by more than 50% as compared to untreated cells, resulting in increased PS-ASO efficacy. We also characterize cytosolic galectins as novel contributor for PS-ASO escape. Galectins knockdown enhances ASO efficacy by more than 60% by modulating EEA1, Rab5C, and Rab7A mRNA expression, leading to a delay in the endosomal vesicle maturation process. Collectively, our results provide additional insight for increasing PS-ASO efficacy by enhancing endosomal escape, which can further be utilized for other nucleic acid-based modalities

The ligand-binding profile of HARE: Hyaluronan and chondroitin sulfates A, C, and D bind to overlapping sites distinct from the sites for heparin, acetylated low-density lipoprotein, dermatan sulfate, and CS-E

Abstract The hyaluronic acid receptor for endocytosis (HARE)/ Stabilin-2 is the primary systemic scavenger receptor for hyaluronan (HA), the chondroitin sulfates (CS), dermatan sulfate (DS), and nonglycosaminoglycan (GAG) ligands such as acetylated low-density lipoprotein (AcLDL), pro-collagen propeptides, and advanced glycation end products. We recently discovered that HARE is also a systemic scavenger receptor for heparin (Hep) (Harris EN, Weigel JA, Weigel PH. 2008. The human hyaluronan receptor for endocytosis [HARE/Stabilin-2] is a systemic clearance receptor for heparin. J Biol Chem. 283:17341–17350). Our goal was to map the binding sites of eight different ligands within HARE. We used biotinylated GAGs and radio-iodinated streptavidin or AcLDL to assess the binding activities of ligands directly or indirectly (by competition with unlabeled ligands) in endocytosis assays using stable cell lines expressing the 315 or 190 kDa HA receptor for endocytosis (315- or 190-HARE) isoforms, and ELISA-like assays, with purified recombinant soluble 190-HARE ecto-domain. For example, Hep binding to HARE was competed by DS, CS-E, AcLDL, and dextran sulfate, but not by other CS types, HA, dextran, or heparosan. 125I-AcLDL binding to HARE was partially competed by Hep and dextran sulfate, but not competed by HA. Two ligands, DS and CS-E, competed with both Hep and HA to some degree. Hep and HA binding or endocytosis is mutually inclusive; binding of these two GAGs occurs with functionally separate, noncompetitive, and apparently noninteracting domains. Thus, HARE binds to HA and Hep simultaneously. Although the domain(s) responsible for Hep binding remains unknown, the Link domain was required for HARE binding to HA, CS-A, CS-C, and CS-D. These results enable us to outline, for the first time, a binding activity map for multiple ligands of HARE

The ligand-binding profile of HARE: Hyaluronan and chondroitin sulfates A, C, and D bind to overlapping sites distinct from the sites for heparin, acetylated low-density lipoprotein, dermatan sulfate, and CS-E

Abstract The hyaluronic acid receptor for endocytosis (HARE)/ Stabilin-2 is the primary systemic scavenger receptor for hyaluronan (HA), the chondroitin sulfates (CS), dermatan sulfate (DS), and nonglycosaminoglycan (GAG) ligands such as acetylated low-density lipoprotein (AcLDL), pro-collagen propeptides, and advanced glycation end products. We recently discovered that HARE is also a systemic scavenger receptor for heparin (Hep) (Harris EN, Weigel JA, Weigel PH. 2008. The human hyaluronan receptor for endocytosis [HARE/Stabilin-2] is a systemic clearance receptor for heparin. J Biol Chem. 283:17341–17350). Our goal was to map the binding sites of eight different ligands within HARE. We used biotinylated GAGs and radio-iodinated streptavidin or AcLDL to assess the binding activities of ligands directly or indirectly (by competition with unlabeled ligands) in endocytosis assays using stable cell lines expressing the 315 or 190 kDa HA receptor for endocytosis (315- or 190-HARE) isoforms, and ELISA-like assays, with purified recombinant soluble 190-HARE ecto-domain. For example, Hep binding to HARE was competed by DS, CS-E, AcLDL, and dextran sulfate, but not by other CS types, HA, dextran, or heparosan. 125I-AcLDL binding to HARE was partially competed by Hep and dextran sulfate, but not competed by HA. Two ligands, DS and CS-E, competed with both Hep and HA to some degree. Hep and HA binding or endocytosis is mutually inclusive; binding of these two GAGs occurs with functionally separate, noncompetitive, and apparently noninteracting domains. Thus, HARE binds to HA and Hep simultaneously. Although the domain(s) responsible for Hep binding remains unknown, the Link domain was required for HARE binding to HA, CS-A, CS-C, and CS-D. These results enable us to outline, for the first time, a binding activity map for multiple ligands of HARE

Antisense oligonucleotides: treatment strategies and cellular internalization

The clinical application of antisense oligonucleotides (ASOs) is becoming more of a reality as several drugs have been approved for the treatment of human disorders and many others are in various phases in development and clinical trials. ASOs are short DNA/RNA oligos which are heavily modified to increase their stability in biological fluids and retain the properties of creating RNA-RNA and DNA-RNA duplexes that knock-down or correct genetic expression. This review outlines several strategies that ASOs utilize for the treatment of various congenital diseases and syndromes that develop with aging. In addition, we discuss some of the mechanisms for specific non-targeted ASO internalization within cells

Endocytic Function, Glycosaminoglycan Specificity, and Antibody Sensitivity of the Recombinant Human 190-kDa Hyaluronan Receptor for Endocytosis (HARE)

The human hyaluronan receptor for endocytosis (hHARE) mediates the endocytic clearance of hyaluronan (HA) and chondroitin sulfate from lymph fluid and blood. Two hHARE isoforms (190 and 315 kDa) are present in sinusoidal endothelial cells of liver, spleen, and lymph nodes (Zhou, B., McGary, C. T., Weigel, J. A., Saxena, A., and Weigel, P. H. (2003) Glycobiology 13, 339–349). Here we report the specificity and function of the 190-kDa HARE, expressed without the larger isoform, in Flp-In 293 cell lines (190hHARE cells). Like the native protein, recombinant hHARE contains ~25 kDa of N-linked oligosaccharides, binds HA in a ligand blot assay, cross-reacts with three anti-rat HARE monoclonal antibodies, and is inactivated by reduction. The 190hHARE cell lines mediated rapid, continuous 125I-HA endocytosis and degradation for \u3e1 day. About 30–50% of the total cellular receptors were on the cell surface, and their recycling time for reutilization was ~8.5 min. The average Kd for the binding of HA to the 190-kDa hHARE at 4 °C was 7 nm with 118,000 total HA binding sites per cell. Competition studies at 37 °C indicated that the 190- kDa hHARE binds HA and chondroitin better than dermatan sulfate and chondroitin sulfates A, C, D, and E, but it does not bind to heparin, heparan sulfate, or keratan sulfate. Although competition was observed at 37 °C, none of the glycosaminoglycans tested, except HA, competed for 125I-HA binding by 190hHARE cells at 4 °C. Anti-HARE monoclonal antibodies #30 and #154, which do not inhibit 125I-HA uptake mediated by the 175-kDa rat HARE, partially blocked HA endocytosis by the 190-kDa hHARE. We conclude that the 190-kDa hHARE can function independently of other hHARE isoforms to mediate the endocytosis of multiple glycosaminoglycans. Furthermore, the rat and human small HARE isoforms have different glycosaminoglycan specificities and sensitivities to inhibition by cross-reacting antibodies