Patient Adipose Stem Cell-Derived Adipocytes Reveal Genetic Variation that Predicts Antidiabetic Drug Response

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Modifying the N-terminus of polyamides: PyImPyIm has improved sequence specificity over f-ImPyIm

Seven N-terminus modified derivatives of a previously published minor-groove binding polyamide (f-ImPyIm, 1) were synthesized and the biochemical and biophysical chemistry evaluated. These compounds were synthesized with the aim of attaining a higher level of sequence selectivity over f-ImPyIm (1), a previously published strong minor-groove binder. Two compounds possessing a furan or a benzofuran moiety at the N-terminus showed a footprint of 0.5 μM at the cognate ACGCGT site (determined by DNase I footprinting); however, the specificity of these compounds was not improved. In contrast, PyImPyIm (4) produced a footprint of 0.5 μM but showed a superior specificity using the same technique. When evaluated by thermal melting experiments and circular dichroism using ACGCGT and the non-cognate AAATTT sequence, all compounds were shown to bind in the minor-groove of DNA and stabilize the cognate sequence much better than the non-cognate (except for the non-amido-compound that did not bind either sequence, as expected). PyImPyIm (4) was interesting as the ΔT_m for this compound was only 4 °C but the footprint was very selective. No binding was observed for this compound with a third DNA (non-cognate, ACCGGT). ITC studies on compound 4 showed exothermic binding with ACGCGT and no heat change was observed for titrating the compound to the other two DNA sequences. The heat capacity (ΔC_p) of the PIPI/ACGCGT complex calculated from the hydrophobic interactions and SASA calculations was comparable to the experimental value obtained from ITC (−146 cal mol⁻¹ K⁻¹). SPR results provided confirmation of the sequence specificity of PyImPyIm (4), with a K_eq value determined to be 7.1 × 10⁶ M⁻¹ for the cognate sequence and no observable binding to AAATTT and ACCGGT. Molecular dynamic simulations affirmed that PyImPyIm (4) binds as a dimer in an overlapped conformation, and it fits snugly in the minor-groove of the ACGCGT oligonucleotide. PyImPyIm (4) is an especially interesting molecule, because although the binding affinity is slightly reduced, the specificity with respect to f-ImPyIm (1) is significantly improved.     

A pathway for multivariate analysis of ecological communities using copulas

We describe a new pathway for multivariate analysis of data consisting of counts of species abundances that includes two key components: copulas, to provide a flexible joint model of individual species, and dissimilarity‐based methods, to integrate information across species and provide a holistic view of the community. Individual species are characterized using suitable (marginal) statistical distributions, with the mean, the degree of over‐dispersion, and/or zero‐inflation being allowed to vary among a priori groups of sampling units. Associations among species are then modeled using copulas, which allow any pair of disparate types of variables to be coupled through their cumulative distribution function, while maintaining entirely the separate individual marginal distributions appropriate for each species. A Gaussian copula smoothly captures changes in an index of association that excludes joint absences in the space of the original species variables. A permutation‐based filter with exact family‐wise error can optionally be used a priori to reduce the dimensionality of the copula estimation problem. We describe in detail a Monte Carlo expectation maximization algorithm for efficient estimation of the copula correlation matrix with discrete marginal distributions (counts). The resulting fully parameterized copula models can be used to simulate realistic ecological community data under fully specified null or alternative hypotheses. Distributions of community centroids derived from simulated data can then be visualized in ordinations of ecologically meaningful dissimilarity spaces. Multinomial mixtures of data drawn from copula models also yield smooth power curves in dissimilarity‐based settings. Our proposed analysis pathway provides new opportunities to combine model‐based approaches with dissimilarity‐based methods to enhance understanding of ecological systems. We demonstrate implementation of the pathway through an ecological example, where associations among fish species were found to increase after the establishment of a marine reserve.     

SMAD3 Is Associated with the Total Burden of Radiographic Osteoarthritis: The Chingford Study

Background

A newly-described syndrome called Aneurysm-Osteoarthritis Syndrome (AOS) was recently reported. AOS presents with early onset osteoarthritis (OA) in multiple joints, together with aneurysms in major arteries, and is caused by rare mutations in SMAD3. Because of the similarity of AOS to idiopathic generalized OA (GOA), we hypothesized that SMAD3 is also associated with GOA and tested the hypothesis in a population-based cohort.

Methods

Study participants were derived from the Chingford study. Kellgren-Lawrence (KL) grades and the individual features of osteophytes and joint space narrowing (JSN) were scored from radiographs of hands, knees, hips, and lumbar spines. The total KL score, osteophyte score, and JSN score were calculated and used as indicators of the total burden of radiographic OA. Forty-one common SNPs within SMAD3 were genotyped using the Illumina HumanHap610Q array. Linear regression modelling was used to test the association between the total KL score, osteophyte score, and JSN score and each of the 41 SNPs, with adjustment for patient age and BMI. Permutation testing was used to control the false positive rate.

Results

A total of 609 individuals were included in the analysis. All were Caucasian females with a mean age of 60.9±5.8. We found that rs3825977, with a minor allele (T) frequency of 20%, in the last intron of SMAD3, was significantly associated with total KL score (β = 0.14, P_permutation = 0.002). This association was stronger for the total JSN score (β = 0.19, P_permutation = 0.002) than for total osteophyte score (β = 0.11, P_permutation = 0.02). The T allele is associated with a 1.47-fold increased odds for people with 5 or more joints to be affected by radiographic OA (P_permutation = 0.046).

Conclusion

We found that SMAD3 is significantly associated with the total burden of radiographic OA. Further studies are required to reveal the mechanism of the association.     

The post-translational processing and intracellular sorting of PC2 in the islets of Langerhans.

Proinsulin conversion in the insulin secretory granule is mediated by two sequence-specific endoproteases related to the Kex2 homologues, PC2 and PC3 (Bennett, D. L., Bailyes, E. M., Nielsen, E., Guest, P. C., Rutherford, N. G., Arden, S. D., and Hutton, J. C. (1992) J. Biol. Chem. 267, 15229-15236; Bailyes, E. M., Bennett, D. L., and Hutton, J. C. (1992) Enzyme, in press). Radiolabeling studies using isolated rat islets showed that PC2 was synthesized initially as a 76-kDa glycoprotein which was converted by limited proteolysis to the mature 64-66-kDa form. Conversion was initiated approximately 1 h after synthesis and proceeded via intermediates of 71, 68, and 66 kDa with a t1/2 of 140 min. Release of only the 66- and 64-66-kDa radiolabeled forms of PC2 was induced by glucose and then only at times more than 2 h following synthesis. Proinsulin conversion, by contrast, was more rapid (delay = 30 min, t1/2 = 60 min), and release commenced as soon as 1 h after synthesis with the secreted material being comprised of the precursor, intermediate, and mature forms of insulin. Ultrastructural analysis of islet beta cells showed that PC2 was concentrated in secretory granules. Subcellular fractionation combined with immunoblot analysis showed that insulinoma secretory granules contained only the mature 64-66-kDa form of PC2, whereas fractions enriched in Golgi and endoplasmic reticulum contained a mixture of the 76- and 66-kDa forms of the enzyme. These results indicate that post-translational proteolysis of PC2 is initiated before sorting into the regulated pathway of secretion and that the relative proportions of proinsulin and PC2 packaged into secretory granules will change with physiological conditions.     

Growth and survival of the superorganism: Ant colony macronutrient intake and investment

In this study, we used two common ant species (Lasius niger and Lasius neoniger) to assay how they translate variation in the diet (both in composition and frequency) into growth. We measured colony development for over 8 months and measured several phenotypic traits of the worker caste, and examined whether forager preference corresponded with diet quality. Optimal colony growth was a balance between survival and growth, and each of these was maximized with different nutrient regimes. Interestingly, forager preference was not totally aligned with the diet that maximized colony growth. Our results highlight that: (a) organism and superorganism size are controlled by the same nutrients, and this may reflect a common molecular basis for size across life's organizational levels, (b) there are nutrient trade‐offs that are associated with life‐history trade‐offs, likely leading to selection for a balanced diet, and (c) the connection between the preference of foragers for different nutrients and how nutrient combinations affect colony success and demographics are complex and only beginning to be understood.     

Umbilical Cord Blood Mononuclear Cell HIV-1 LTR Binding Activities

Vertically transmitted HIV disease constitutes a significant problem in pediatrics. In order to characterize some of the possible host factors involved in HIV replication in fetuses and newborns, we surveyed the HIV-1 LTR binding factors present in nuclear extracts from cord blood mononuclear cells. A series of electrophoretic mobility shift assays (EMSAs) showed that protein extracts from cord blood interacted with several regions of the HIV LTR. The most prominent binding activities involved the NF-kB sites, but other regions of the LTR also showed factor binding with the cord blood extracts. Some of these cord blood extract binding activities displayed qualitative differences when compared to adult peripheral blood mononuclear cell extracts in EMSA and UV cross-linking studies. Transient transfection experiments indicated that the NF-kB and Sp1 sequences were important for wild type levels of expression in cord blood cells, but that additional sequences 5 to the NF-kB sites also contributed activity. Thus, factors that interact with many of the well-known HIV LTR regulatory sites are present in cord blood cells. However, certain qualitative differences distinguished cord blood and adult peripheral blood binding activities and these may contribute to pathogenesis of HIV infection in neonates.     

Influence of the endocrine system on tryptic activity in female Aedes aegypti

In MNC-ablated or ovariectomized mosquitoes, blood-fed by enema, the tryptic activity of midgut homogenates was reduced by half. By sealing the anus after the blood meal, we showed that the reduction in enzyme activity was not due to premature or increased excretion of active enzyme in operated females. The enzyme activity was restored to the level of unoperated controls by either reimplantation of an ovary or injection of 20-hydroxy-ecdysone in a large, single dose shortly before the blood meal.The reduction in tryptic activity in MNC-ablated or ovariectomized females did not alter the rate of protein digestion as measured by the decrease of protein in midgut homogenates. We conclude that the neurosecretory system and the ovaries are required for maximal tryptic activity in normal females, and that the enzyme apparently is secreted in excess of that required for complete digestion of the blood meal.