Enhanced SUMOylation of proteins containing a SUMO-interacting motif by SUMO-Ubc9 fusion

Identifying new targets for SUMO and understanding the function of protein SUMOylation are largely limited by low level of SUMOylation. It was found recently that Ubc9, the SUMO E2 conjugating enzyme, is covalently modified by SUMO at a lysine 14 in the N-terminal alpha helix, and that SUMO-modified Ubc9 has enhanced conjugation activity for certain target proteins containing a SUMO-interacting motif (SIM). Here, we show that, compared to intact Ubc9, the SUMO-Ubc9 fusion protein has higher conjugating activity for SIM-containing targets such as Sp100 and human cytomegalovirus IE2. Assays using an IE2 SIM mutant revealed the requirement of SIM for the enhanced IE2 SUMOylation by SUMO-Ubc9. In pull-down assays with cell extracts, the SUMO-Ubc9 fusion protein bound to more diverse cellular proteins and interacted with some SIM-containing proteins with higher affinities than Ubc9. Therefore, the devised SUMO-Ubc9 fusion will be useful for identifying SIM-containing SUMO targets and producing SUMO-modified proteins.     

Genomic selection: prediction of accuracy and maximisation of long term response

Genomic selection refers to the use of dense markers covering the whole genome to estimate the breeding value of selection candidates for a quantitative trait. This paper considers prediction of breeding value based on a linear combination of the markers. In this case the best estimate of each marker’s effect is the expectation of the effect conditional on the data. To calculate this requires a prior distribution of marker effects. If the marker effects are normally distributed with constant variance, BLUP can be used to calculate the estimated effects of the markers and hence the estimated breeding value (EBV). In this case the model is equivalent to a conventional animal model in which the relationship matrix among the animals is estimated from the markers instead of the pedigree. The accuracy of the EBV can approach 1.0 but a very large amount of data is required. An alternative model was investigated in which only some markers have non-zero effects and these effects follow a reflected exponential distribution. In this case the expected effect of a marker is a non-linear function of the data such that apparently small effects are regressed back almost to zero and consequently these markers can be deleted from the model. The accuracy in this case is considerably higher than when marker effects are normally distributed. If genomic selection is practiced for several generations the response declines in a manner that can be predicted from the marker allele frequencies. Genomic selection is likely to lead to a more rapid decline in the selection response than phenotypic selection unless new markers are continually added to the prediction of breeding value. A method to find the optimum index to maximise long term selection response is derived. This index varies the weight given to a marker according to its frequency such that markers where the favourable allele has low frequency receive more weight in the index.     

The Clamp Loader Assembles the �� Clamp onto Either a 3�� or 5�� Primer Terminus: THE UNDERLYING BASIS FAVORING 3�� LOADING*

Clamp loaders assemble sliding clamps onto 3′ primed sites for DNA polymerases. Clamp loaders are thought to be specific for a 3′ primed site, and unable to bind a 5′ site. We demonstrate here that the Escherichia coli γ complex clamp loader can load the β clamp onto a 5′ primed site, although with at least 20-fold reduced efficiency relative to loading at a 3′ primed site. Preferential clamp loading at a 3′ site does not appear to be due to DNA binding, as the clamp loader forms an avid complex with β at a 5′ site. Preferential loading at a 3′ versus a 5′ site occurs at the ATP hydrolysis step, needed to close the ring around DNA. We also address DNA structural features that are recognized for preferential loading at a 3′ site. Although the single-stranded template strand extends in opposite directions from 3′ and 5′ primed sites, thus making it a favorite candidate for distinguishing between 3′ and 5′ sites, the single-strand polarity at a primed template junction does not determine 3′ site selection for clamp loading. Instead, we find that clamp loader recognition of a 3′ site lies in the duplex portion of the primed site, not the single-strand portion. We present evidence that the β clamp facilitates its own loading specificity for a 3′ primed site. Implications to eukaryotic clamp loader complexes are proposed.     

Discovery and Exploitation of Inhibitor-resistant Aurora and Polo Kinase Mutants for the Analysis of Mitotic Networks

The Aurora and Polo-like kinases are central components of mitotic signaling pathways, and recent evidence suggests that substantial cross-talk exists between Aurora A and Plk1. In addition to their validation as novel anticancer agents, small molecule kinase inhibitors are increasingly important tools to help dissect clinically relevant protein phosphorylation networks. However, one major problem associated with kinase inhibitors is their promiscuity toward “off-target” members of the kinome, which makes interpretation of data obtained from complex cellular systems challenging. Additionally, the emergence of inhibitor resistance in patients makes it clear that an understanding of resistance mechanisms is essential to inform drug design. In this study, we exploited structural knowledge of the binding modes of VX-680, an Aurora kinase inhibitor, and BI 2536, a Polo-like kinase inhibitor, to design and evaluate drug-resistant kinase mutants. Using inducible stable human cell lines, we authenticated mitotic targets for both compounds and demonstrated that Aurora A mutants exhibit differential cellular sensitivity toward the inhibitors VX-680 and MLN8054. In addition, we validated Aurora B as an important anti-proliferative target for VX-680 in model human cancer cells. Finally, this chemical genetic approach allowed us to prove that Aurora A activation loop phosphorylation is controlled by a Plk1-mediated pathway in human cells.Protein kinase inhibitors are prime examples of small molecules with the potential to revolutionize the treatment of chronic disease states such as inflammation and cancer (1, 2). For example, the discovery of inhibitors of the BCR-ABL kinase has transformed the survival rates of patients diagnosed with tyrosine kinase-driven leukemias (3). Moreover, inhibitors of many distinct protein kinases have emerged as indispensable biological tools, in part through their rapid and often reversible mode of action, but also because of their widespread availability and utility in a range of research settings. Remarkably, scientific conclusions drawn in many thousands of peer-reviewed research papers every year rely upon experiments conducted with kinase inhibitors, but in only a handful of studies is the important question of inhibitor specificity explicitly addressed (4–7). This is a vital issue because claims for specificity have rarely stood the test of time, yet a detailed knowledge of kinase inhibitor promiscuity would be beneficial in the clinic, where the simultaneous blockade of multiple signaling pathways can be exploited as an anticancer strategy (8).The vast majority of kinase inhibitors bind in the conserved ATP-binding site located between the N- and C-terminal lobes of the catalytic domain, where they prevent nucleotide binding or lock the kinase into a structurally inactive confirmation. Inhibitor structure-activity relationship trends, which are often gleaned from combined biochemical and structural analysis, can be mechanistically revealing, but often fail to adequately address the interconnected issues of specificity and chemical resistance. Indeed, the emergence of drug resistance in chronic myeloid leukemia patients is testament to the high mutagenic susceptibility of protein kinases either selected for, or induced by, inhibitor exposure in vivo, making the discovery of mechanistically distinct inhibitors as backup therapies vitally important (9, 10).In human cells, the key mitotic events of centrosome separation, bipolar spindle formation, and chromosome segregation are linked to the physical separation of the genomes during cytokinesis (11). These conserved signaling programs are controlled by dedicated mitotic protein kinases, which include two prominent human gene families, the Aurora kinases (comprising Aurora A, B, and C) and the Polo-like kinases (comprising Plk1–4), whose overexpression in a spectrum of cancers make them outstanding drug candidates (12). A more detailed knowledge of the substrates and physiological events regulated by Aurora and Polo signaling pathways has been facilitated by the development of potent inhibitors of both enzyme families (13, 14). These include clinical candidates such as the dual Aurora/tyrosine kinase inhibitors VX-680 (15, 16) and AT9283 (17) and the Aurora inhibitors MLN8054 (18) and AZD1152 (19). In addition, the clinically advanced Plk1–3 inhibitor BI 2536 has been well characterized in human cells (20) and cancer models (21).One of the frustrations associated with interpreting cellular data obtained with compounds such as VX-680 and BI 2536 is their unknown cellular selectivity. No kinome-wide data are available in public data bases for any kinase inhibitors, and it is likely that these compounds have multiple kinase and non-kinase targets in human cells. For example, VX-680 inhibits both Aurora A and B in human cells and tyrosine kinases such as ABL, Src, and Flt3 in vitro (15, 22), raising the question as to which, if any, of these targets are critical for phenotypes and anti-proliferative effects observed after drug exposure. In addition, Plk1 and Aurora A signaling functions are mutually dependent in proliferating human cells (23–26). This makes interpretation of experiments in which Aurora A or Plk1 inhibitors are employed potentially confusing because phenotypes assigned to one inhibitor target might actually be due to indirect inhibition of the other kinase. To begin to address these issues, we have investigated the cellular plasticity of kinase inhibition by both VX-680 and BI 2536. By evaluating drug-resistant Aurora A and B proteins in vitro and exploiting these mutants in stable human cell lines, we demonstrate that drug-resistant forms of these kinases can be used to prove that phenotypes arising from VX-680 exposure are actually due to inhibition of the predicted mitotic targets. We demonstrate that a VX-680-resistant Aurora A mutant remains sensitive to the distinct anti-proliferative agent MLN8054 in human cells and that Aurora B is the critical target of VX-680 that promotes cell death in a cancer cell model. Furthermore, by analyzing a Plk1 mutant with decreased sensitivity to BI 2536, we establish that a mitotic phenotype arising from exposure to this drug is indeed due to Plk1 inhibition and that, during mitosis, Plk1 controls Aurora A phosphorylation at the critical activating residue Thr²⁸⁸.     

Population Structure of Humpback Whales from Their Breeding Grounds in the South Atlantic and Indian Oceans

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.     

Prospects for Developing Odour Baits To Control Glossina fuscipes spp., the Major Vector of Human African Trypanosomiasis

We are attempting to develop cost-effective control methods for the important vector of sleeping sickness, Glossina fuscipes spp. Responses of the tsetse flies Glossina fuscipes fuscipes (in Kenya) and G. f. quanzensis (in Democratic Republic of Congo) to natural host odours are reported. Arrangements of electric nets were used to assess the effect of cattle-, human- and pig-odour on (1) the numbers of tsetse attracted to the odour source and (2) the proportion of flies that landed on a black target (1×1 m). In addition responses to monitor lizard (Varanus niloticus) were assessed in Kenya. The effects of all four odours on the proportion of tsetse that entered a biconical trap were also determined. Sources of natural host odour were produced by placing live hosts in a tent or metal hut (volumes≈16 m³) from which the air was exhausted at ∼2000 L/min. Odours from cattle, pigs and humans had no significant effect on attraction of G. f. fuscipes but lizard odour doubled the catch (P<0.05). Similarly, mammalian odours had no significant effect on landing or trap entry whereas lizard odour increased these responses significantly: landing responses increased significantly by 22% for males and 10% for females; the increase in trap efficiency was relatively slight (5–10%) and not always significant. For G. f. quanzensis, only pig odour had a consistent effect, doubling the catch of females attracted to the source and increasing the landing response for females by ∼15%. Dispensing CO₂ at doses equivalent to natural hosts suggested that the response of G. f. fuscipes to lizard odour was not due to CO₂. For G. f. quanzensis, pig odour and CO₂ attracted similar numbers of tsetse, but CO₂ had no material effect on the landing response. The results suggest that identifying kairomones present in lizard odour for G. f. fuscipes and pig odour for G. f. quanzensis may improve the performance of targets for controlling these species.     

Human Pancreatic Islet Isolation: Part I: Digestion and Collection of Pancreatic Tissue

Management of Type 1 diabetes is burdensome, both to the individual and society, costing over 100 billion dollars annually. Despite the widespread use of glucose monitoring and new insulin formulations, many individuals still develop devastating secondary complications. Pancreatic islet transplantation can restore near normal glucose control in diabetic patients ¹, without the risk of serious hypoglycemic episodes that are associated with intensive insulin therapy. Providing sufficient islet mass is important for successful islet transplantation. However, donor characteristic, organ procurement and preservation affect the isolation outcome ². At University of Illinois at Chicago (UIC) we have developed a successful isolation protocol with an improved purification gradient ³. The program started in January 2004, and more than 300 isolations were performed up to November 2008. The pancreata were sent in cold preservation solutions (UW, University of Wisconsin or HTK, Histidine-Tryptophan Ketoglutarate) ^4-7 to the Cell Isolation Laboratory at UIC for islet isolation. Pancreatic islets were isolated using the UIC method, which is a modified version of the method originally described by Ricordi et al ⁸. Briefly, after cleaning the pancreas from the surrounding tissue, it was perfused with enzyme solution (Serva Collagenase + Neutral Protease or Sigma V enzyme). The distended pancreas was then transferred to the Ricordi digestion chamber, connected to a modified, closed circulation tubing system, and warmed up to 37°C. During the digestion, the chamber was shaken gently. Samples were taken continuously to monitor the digestion progress. Once free islets were detected under the microscope, the digestion was stopped by flushing cold (4°C) RPMI dilution solution (Mediatech, Herndon, VA) into the circulation system to dilute the enzyme. After being collected and washed in M199 media supplemented with human albumin, the tissue was sampled for pre-purification count and incubated with UW solution before purification. Purification process will be described in Part II: Purification and Culture of Human Islets.     

Actinomycetes scale‐up for the production of the antibacterial,nocathiacin

An Amycolatopsis fastidiosa culture, which produces the nocathiacin class of antibacterial compounds, was scaled up to the 15,000 L working volume. Lower volume pilot fermentations (600, 900, and 1,500 L scale) were conducted to determine process feasibility at the 15,000 L scale. The effects of inoculum volume, impeller tip speed, volumetric gas flow rate, superficial gas velocity, backpressure, and sterilization heat stress were examined to determine optimal scale‐up operating conditions. Inoculum volume (6 vs. 2 vol %) and medium sterilization (R_o of 68 vs. 92 min^?1) had no effect on productivity or titer, and higher impeller tip speeds (2.1 vs. 2.9 m/s) had a slight effect (20% decrease). In contrast, higher backpressure, incorporating increased head pressure at the 15,000 L scale (1.2 vs. 0.7 kg/cm²) and low gas flow rates (0.25 vs. 0.8 vvm), appeared to be problematic (40–50% decrease). High off‐gas CO₂ levels were likely reasons for observed lower productivity. Consequently, air flow rate for this 25‐fold scale‐up (600–15,000 L) was controlled to match off‐gas CO₂ profiles of acceptable smaller scale batches to maintain levels below 0.5%. The 15,000 L‐scale fermentation achieved an expected nocathiacin I titer of 310 mg/L after 7 days. Other on‐line data (i.e., pH, oxygen uptake rate, and CO₂ evolution rate) and off‐line data (i.e., analog production, glucose utilization, ammonium production, and dry cell weight) at the 15,000 L scale also tracked similarly to the smaller scale, demonstrating successful fermentation scale‐up. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Nuclear transport factors in neuronal function

Active nucleocytoplasmic transport of macromolecules requires soluble transport carriers of the importin/karyopherin superfamily. Although the nuclear transport machinery is essential in all eukaryotic cells, neurons must also mobilise importins and associated proteins to overcome unique spatiotemporal challenges. These include switches in importin α subtype expression during neuronal differentiation, localized axonal synthesis of importin β1 to coordinate a retrograde injury signaling complex on axonal dynein, and trafficking of regulatory and signaling molecules from synaptic terminals to cell bodies. Targeting of RNAs encoding critical components of the importins complex and the Ran system to axons allows sophisticated local regulation of the system for mobilization upon need. Finally, a number of importin family members have been associated with mental or neurodegenerative diseases. The extended roles recently discovered for importins in the nervous system might also be relevant in non-neuronal cells, and the localized modes of importin regulation in neurons offer new avenues to interrogate their cytoplasmic functions.