Commentary on Robert Riley's article "A personal account of the discovery of hyperbolic structures on some knot complements"

We give some background and biographical commentary on the postumous article that appears in this [journal issue | ArXiv] by Robert Riley on his part of the early history of hyperbolic structures on some compact 3-manifolds. A complete list of Riley's publications appears at the end of the article.Comment: 5 page

Delineation of Yakutat foreland coho salmon (Oncorhynchus kisutch) stocks using otolith chemistry

Thesis (M.S.) University of Alaska Fairbanks, 2007Otolith chemistry was utilized to identify suspected coho salmon sub-stock populations on the Yakutat Foreland of southeast Alaska. In order to demonstrate that otolith chemistry might be successful in sub-stock differentiation, water samples were collected from four adjacent river systems and chemically segregated by collection site. Juvenile coho salmon and adult coho salmon were collected from the same four river systems and were subsequently analyzed for levels of select Ba, Ca, Mg, and Sr isotopes in all otolith edge and core regions using laser ablation-inductively coupled plasma-mass spectrometry. Otolith Sr⁸⁷/Ca⁴⁸ and Mg²⁴/Ca⁴⁸ were used to segregate collection sites, identify sub-stock populations, and infer straying rates for coho salmon on the Yakutat Foreland. Juvenile core and edge otolith chemistry returned moderate to high classification accuracy for three out of four collection' sites (60%-92%) in statistical discriminant analyses. Adult core otolith chemistry could not segregate samples according to collection site in three out of four sites (7%-50%). Yakutat Foreland otolith chemistry analysis results allowed for (1) differentiation of adjacent freshwater systems, (2) a significant amount of coho salmon stock delineation, and (3) a higher suggested rate of straying from natal sites than coho salmon in other locations.1. Delineation of coho salmon stocks of the Yakutat foreland in Southeast Alaska using otolith chemistry -- Conclusion

Structure-function analysis of phototropin receptor kinases

The ability of plants to convert energy provided by the sun into a form accessible by heterotrophic organisms ensures that they form a basal part of most ecosystems. However, in addition to being a vital energy source light can also serve as an environmental indicator. In order to maximise light perception, plants have evolved a suite of photosensors with differing sensitivities, which in combination provide detailed information regarding light availability and quality. The major photoreceptor families identified in plants include the phytochromes, which are most sensitive to red and far-red light, and the cryptochromes and phototropins, which are UV-A and blue light receptors. Additional photosensors, including the recently identified ZEITLUPE/ADAGIO family, have roles in modulating the action of these main components. Plants can also respond to UV-B and green light, although the photoreceptors responsible for their detection remain elusive. Phototropins are blue light sensors that are responsible for a range of responses (including phototropism, chloroplast movement and stomatal opening) that combine to increase the photosynthetic efficiency of plants. Initially identified in the model plant Arabidopsis thaliana, phototropins have since been characterised in the unicellular alga Chalmydomonas reinhardtii, pteridophytes and angiosperms. The light sensitivity of phototropins is derived from the action of two highly conserved regions known as LOV domains which subsequently induce activity of an integral serine/threonine kinase domain via movement of a conserved alpha-helix (Jalpha-helix). Although little is known regarding phototropin signal transduction an obvious biochemical consequence of phototropin light stimulation is autophosphorylation. Phototropin autophosphorylation has previously been studied using a baculovirus/insect cell expression system, with the consequences of phototropin mutation on phototropin kinase activity within this heterologous system having comparable effects to those when identically-mutated phototropins were introduced into transgenic Arabidopsis. Whilst the ability of phototropins to act as light-regulated kinases is well established, the mechanism by which this occurs remains unclear. In this study a baculovirus/insect cell expression system is used to further characterise the mode of phototropin autophosphorylation and the functionality of a mutated phototropin 1 which demonstrates increased autophosphorylation activity in this system is assessed in planta using transgenic Arabidopsis. It was initially of interest to further evaluate the mode of phototropin autophosphorylation. For example, it is unclear whether phototropin autophosphorylation occurs via an intramolecular mechanism or whether this process involves cross-phosphorylation between phototropin molecules. In Chapter 3 the mode of phototropin autophosphorylation activity was further examined using the baculovirus/insect cell expression system to assess the effect of protein truncations and specific point mutations on phototropin kinase activity. Such mutational analysis reveals that phototropin 1 is capable of intermolecular phosphorylation in vitro and also suggests that further phototropin autophosphorylation sites exist in addition to those previously mapped. Additionally, the importance of LOV2 and the Jalpha-helix as components of the phototropin receptor activation are confirmed. The implications of such findings for our understanding of phototropin autophosphorylation are discussed. LOV domains bind flavin mononucleotide as a chromophore. The light-induced formation of a covalent adduct between the LOV domain and the associated chromophore is thought to induce conformational changes culminating in phototropin kinase activation. In Chapter 4 the two leading hypotheses proposed to permit signal transmission between the light-sensitive LOV domains and the integral kinase domain are examined. Previous work has shown that photosensitivity within one of the two LOV domains (LOV2) is sufficient for light-regulated kinase activity, suggesting that light-induced kinase activation is primarily induced via LOV2. This allowed the effect of point mutations within LOV2 on the light-regulated kinase activation of the full-length phototropin protein to be assessed using the baculovirus/insect cell expression system. Work presented here suggests that a single point mutation within LOV2 (Gln575 to Leu; Q575L) is sufficient to reduce signal transmission between LOV2 and the phototropin kinase domain whilst not altering the photosensitivity of the LOV2 domain. In contrast, mutation of a highly conserved salt bridge at the surface of LOV2 does not alter LOV2 domain signal transmission. Interestingly, the reduced light-induced kinase activity of the phot1 Q575L mutant could be counteracted by an additional mutation within the Jalpha-helix (Ile608 to Glu; I608E) which has previously been shown to increase the autophosphorylation of mock-treated phot1 in vitro in comparison with a wild-type control. Such findings suggest that conformational changes may occur in sequence to induce phototropin kinase activation. The final component of this work involved transgenic Arabidopsis to examine the in planta functionality of phot1 I608E, which has been shown to have increased autophosphorylation in vitro when expressed using the baculovirus/insect cell system. However, rather than demonstrating phenotypes consistent with a constitutively-active form of phototropin, transgenic Arabidopsis expressing phot1 I608E appeared to have only partial functionality in planta and indeed appeared to inhibit phot-mediated phenotypes when expressed in a wild-type background. Possible explanations of the observed phenotypes are discussed. The studies presented here further advance our knowledge of the light-induced mechanism which results in activation of the phototropin photoreceptor and also provide insight into the potential differing roles of phototropin autophosphorylation in planta

Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1 Causes Circadian Clock Defects

The circadian clock plays a crucial role in coordinating plant metabolic and physiological functions with predictable environmental variables, such as dusk and dawn, while also modulating responses to biotic and abiotic challenges. Much of the initial characterization of the circadian system has focused on transcriptional initiation, but it is now apparent that considerable regulation is exerted after this key regulatory step. Transcript processing, protein stability, and cofactor availability have all been reported to influence circadian rhythms in a variety of species. We used a genetic screen to identify a mutation within a putative RNA binding protein (SPLICEOSOMAL TIMEKEEPER LOCUS1 [STIPL1]) that induces a long circadian period phenotype under constant conditions. STIPL1 is a homolog of the spliceosomal proteins TFP11 (Homo sapiens) and Ntr1p (Saccharomyces cerevisiae) involved in spliceosome disassembly. Analysis of general and alternative splicing using a high-resolution RT-PCR system revealed that mutation of this protein causes less efficient splicing of most but not all of the introns analyzed. In particular, the altered accumulation of circadian-associated transcripts may contribute to the observed mutant phenotype. Interestingly, mutation of a close homolog of STIPL1, STIP-LIKE2, does not cause a circadian phenotype, which suggests divergence in function between these family members. Our work highlights the importance of posttranscriptional control within the clock mechanism. © 2012 American Society of Plant Biologists. All rights reserved

Topological Signals of Singularities in Ricci Flow

We implement methods from computational homology to obtain a topological signal of singularity formation in a selection of geometries evolved numerically by Ricci flow. Our approach, based on persistent homology, produces precise, quantitative measures describing the behavior of an entire collection of data across a discrete sample of times. We analyze the topological signals of geometric criticality obtained numerically from the application of persistent homology to models manifesting singularities under Ricci flow. The results we obtain for these numerical models suggest that the topological signals distinguish global singularity formation (collapse to a round point) from local singularity formation (neckpinch). Finally, we discuss the interpretation and implication of these results and future applications.Comment: 24 pages, 14 figure

C1: How the C1 platform will change the production approach for therapeutic proteins

For over 30 years, Dyadic has proven itself, both commercially and scientifically, to be a high quality and highly productive producer of enzymes and proteins for specialty chemical applications using a proprietary and patented expression system based on the Myceliopthora thermophila fungus, nicknamed C1. The C1 platform technology, a hyper-productive fungal expression system, was used to develop & manufacture large quantities of desired proteins at industrial scale at significantly lower capital and operating expenditures. In this presentation we shall demonstrate how the benefits of C1 as a successful production host is now being harnessed by Dyadic to produce biological medicines and vaccines. Using new and improved C1 base strains along with better molecular genetics tools that have been developed over the past several years, we demonstrate the ability of C1 to express mAbs that are secreted, folded correctly and reach high yields. MAbs produced in C1 have almost identical binding kinetics to mAbs produced using CHO cells. In addition, our research program includes comprehensive approach to identify and knock-out proteases for further enhancing protein stability and improving yields. We have also achieved encouraging results, knowledge and experience in the rVaccine space from our prior research collaboration with Sanofi Pasteur to express rVaccines against Influenza virus. Results of a mice test that was conducted by Sanofi Pasteur, clearly demonstrated that HA produced by C1, generated high immunogenicity response against the virus without any adverse affects. Like other filamentous fungal strains, C1 has high mannose glycoform structures. However, unlike most fungi and yeasts, C1 does not have ‘high’ mannose (branched 30-50 mannose species), but rather has ‘oligo’ mannose structure (branched 5-9 mannose species). In addition, no O-glycosylation has been observed on C1 secreted proteins, in contrast to Pichia that O-glycosylates all secreted antibodies, necessitating deletion of the O-glycosylation machinery. Using the benefits of those advantages, we have started Glycoengineering program aiming to develop C1 strain that produces proteins with defined human-like glycan patterns. The progress we have already made in C1 glycoengineering will also be presented. Thus, Dyadic firmly believe that the C1 strains that we are developing with offer certain competitive advantages over other leading pharmaceutical expression systems, such as CHO cells, has the potential to become the production system of choice for therapeutic protein and vaccines manufacturing