Scaling of long bone fracture strength with animal mass

Most long bone fractures are the result of bending and/or torsional loading. To allometrically relate bone torsional and bending strength to animal mass (M), we define the bone strength index SB = J/dl where J = midshaft cross section polar moment of inertia, d = diameter, and l = length. In geometrically similar scaling, one would expect SB alpha M2/3. In this study, long bone geometric parameters were measured for 12 species of Artiodactyls. The relationships determined for length and diameter are similar to those reported by previous investigators (l alpha d3/4, l alpha M1/4). For the Artiodactyls studied, we found that SB alpha M0.82. Data previously collected by Biewener on a wide range of mammals (non-Artiodactyls) showed different scaling characteristics (l alpha d0.89, l alpha M0.31). However, our analysis of his data suggests roughly similar scaling of the torsional and bending strength index, SB alpha M0.77. It therefore appears that, in spite of differences in scaling of length and external diameter, the bending and torsional strengths scale similarly across a broad range of animals.     

Conservative Tests under Satisficing Models of Publication Bias

Publication bias leads consumers of research to observe a selected sample of statistical estimates calculated by producers of research. We calculate critical values for statistical significance that could help to adjust after the fact for the distortions created by this selection effect, assuming that the only source of publication bias is file drawer bias. These adjusted critical values are easy to calculate and differ from unadjusted critical values by approximately 50%—rather than rejecting a null hypothesis when the t-ratio exceeds 2, the analysis suggests rejecting a null hypothesis when the t-ratio exceeds 3. Samples of published social science research indicate that on average, across research fields, approximately 30% of published t-statistics fall between the standard and adjusted cutoffs.     

Global phylogeny determined by the combination of protein domains in proteomes

The majority of proteins consist of multiple domains that are either repeated or combined in defined order. In this study, we survey the combination of protein domains defined at fold and fold superfamily levels in 185 genomes belonging to organisms that have been fully sequenced and introduce a method that reconstructs rooted phylogenomic trees from the content and arrangement of domains in proteins at a genomic level. We find that the majority of domain combinations were unique to Archaea, Bacteria, or Eukarya, suggesting most combinations originated after life had diversified. Domain repeat and domain repeat within multidomain proteins increased notably in eukaryotes, mainly at the expense of single-domain and domain-pair proteins. This increase was mostly confined to Metazoa. We also find an unbalanced sharing of domain combinations which suggests that Eukarya is more closely related to Bacteria than to Archaea, an observation that challenges the widely assumed eukaryote-archaebacterial sisterhood relationship. The occurrence and abundance of the molecular repertoire (interactome) of domain combinations was used to generate phylogenomic trees. These global interactome-based phylogenies described organismal histories satisfactorily, revealing the tripartite nature of life, and supporting controversial evolutionary patterns, such as the Coelomata hypothesis, the grouping of plants and animals, and the Gram-positive origin of bacteria. Results suggest strongly that the process of domain combination is not random but curved by evolution, rejecting the null hypothesis of domain modules combining in the absence of natural selection or an optimality criterion.     

Akt1/PKBalpha is required for normal growth but dispensable for maintenance of glucose homeostasis in mice

The serine-threonine kinase Akt, also known as protein kinase B (PKB), is an important effector for phosphatidylinositol 3-kinase signaling initiated by numerous growth factors and hormones. Akt2/PKBbeta, one of three known mammalian isoforms of Akt/PKB, has been demonstrated recently to be required for at least some of the metabolic actions of insulin (Cho, H., Mu, J., Kim, J. K., Thorvaldsen, J. L., Chu, Q., Crenshaw, E. B., Kaestner, K. H., Bartolomei, M. S., Shulman, G. I., and Birnbaum, M. J. (2001) Science 292, 1728-1731). Here we show that mice deficient in another closely related isoform of the kinase, Akt1/PKBalpha, display a conspicuous impairment in organismal growth. Akt1(-/-) mice demonstrated defects in both fetal and postnatal growth, and these persisted into adulthood. However, in striking contrast to Akt2/PKBbeta null mice, Akt1/PKBalpha-deficient mice are normal with regard to glucose tolerance and insulin-stimulated disposal of blood glucose. Thus, the characterization of the Akt1 knockout mice and its comparison to the previously reported Akt2 deficiency phenotype reveals the non-redundant functions of Akt1 and Akt2 genes with respect to organismal growth and insulin-regulated glucose metabolism.     

On the power of some binomial modifications of the Bonferroni multiple test

Widely used in testing statistical hypotheses, the Bonferroni multiple test has a rather low power that entails a high risk to accept falsely the overall null hypothesis and therefore to not detect really existing effects. We suggest that when the partial test statistics are statistically independent, it is possible to reduce this risk by using binomial modifications of the Bonferroni test. Instead of rejecting the null hypothesis when at least one of n partial null hypotheses is rejected at a very high level of significance (say, 0.005 in the case of n = 10), as it is prescribed by the Bonferroni test, the binomial tests recommend to reject the null hypothesis when at least k partial null hypotheses (say, k = [n/2]) are rejected at much lower level (up to 30-50%). We show that the power of such binomial tests is essentially higher as compared with the power of the original Bonferroni and some modified Bonferroni tests. In addition, such an approach allows us to combine tests for which the results are known only for a fixed significance level. The paper contains tables and a computer program which allow to determine (retrieve from a table or to compute) the necessary binomial test parameters, i.e. either the partial significance level (when k is fixed) or the value of k (when the partial significance level is fixed).     

Reversible binding of platelet-derived growth factor-AA, -AB, and -BB isoforms to a similar site on the "slow" and "fast" conformations of alpha 2-macroglobulin.

The mechanism by which the platelet-derived growth factor (PDGF)-binding protein, alpha 2-macroglobulin (alpha 2M), modulates PDGF bioactivity is unknown, but could involve reversible PDGF-alpha 2M binding. Herein we report that greater than 70% of 125I-PDGF-BB or -AB complexed to alpha 2M was dissociated by SDS-denaturation followed by SDS-polyacrylamide gel electrophoresis, i.e. most of the binding was noncovalent. Reduction of the PDGF.alpha 2M complex following denaturation dissociated the cytokine from alpha 2M by greater than 90%, suggesting covalent disulfide bond formation. Approximately 50% of the growth factor was dissociated by lowering the pH from 7.5 to 4.0. 125I-PDGF-BB bound alpha 2M in a time-dependent manner (t1/2 = approximately 1 h), reaching equilibrium after 4 h. The 125I-PDGF.BB/alpha 2M complex dissociated more slowly (t1/2 = approximately 2.5 h). "Slow" and "fast" alpha 2M bound nearly equal amounts of PDGF-AB or -BB. Trypsin treatment converted PDGF-BB/alpha 2M complex to the fast conformation but did not release bound 125I-PDGF-BB. All PDGF-isoforms (AA, -AB, and -BB) competed for binding with 125I-PDGF-BB binding to slow alpha 2M and fast alpha 2M-methylamine by 65-80%. Other cytokines that bind alpha 2M (transforming growth factor-beta 1 and -beta 2, tumor necrosis factor-alpha, basic fibroblast growth factor, interleukin -1 beta, and -6) did not compete for 125I-PDGF-BB binding slow alpha 2M, but transforming growth factor-beta 1 and basic fibroblast growth factor inhibited 125I-PDGF-BB binding alpha 2M-methylamine by 30-50%. The reversible nature of the PDGF.alpha 2M complex could allow for targeted PDGF release near mesenchymal cells which possess PDGF receptors.     

RGS2 binds directly and selectively to the M1 muscarinic acetylcholine receptor third intracellular loop to modulate Gq/11alpha signaling

RGS proteins serve as GTPase-activating proteins and/or effector antagonists to modulate Galpha signaling events. In live cells, members of the B/R4 subfamily of RGS proteins selectively modulate G protein signaling depending on the associated receptor (GPCR). Here we examine whether GPCRs selectively recruit RGS proteins to modulate linked G protein signaling. We report the novel finding that RGS2 binds directly to the third intracellular (i3) loop of the G(q/11)-coupled M1 muscarinic cholinergic receptor (M1 mAChR; M1i3). This interaction is selective because closely related RGS16 does not bind M1i3, and neither RGS2 nor RGS16 binds to the G(i/o)-coupled M2i3 loop. When expressed in cells, RGS2 and M1 mAChR co-localize to the plasma membrane whereas RGS16 does not. The N-terminal region of RGS2 is both necessary and sufficient for binding to M1i3, and RGS2 forms a stable heterotrimeric complex with both activated G(q)alpha and M1i3. RGS2 potently inhibits M1 mAChR-mediated phosphoinositide hydrolysis in cell membranes by acting as an effector antagonist. Deletion of the N terminus abolishes this effector antagonist activity of RGS2 but not its GTPase-activating protein activity toward G(11)alpha in membranes. These findings predict a model where the i3 loops of GPCRs selectively recruit specific RGS protein(s) via their N termini to regulate the linked G protein. Consistent with this model, we find that the i3 loops of the mAChR subtypes (M1-M5) exhibit differential profiles for binding distinct B/R4 RGS family members, indicating that this novel mechanism for GPCR modulation of RGS signaling may generally extend to other receptors and RGS proteins.     

Brassinolide activities of 2alpha,3alpha-diols versus 3alpha,4alpha-diols in the bean second internode bioassay: explanation by molecular modeling methods

In general, the structural requirements postulated for a high brassinolide activity are: 2alpha,3alpha-diol, 6-ketone or better 7-oxalactone in B-ring, A/B trans fused ring junction, a cis C-22,C-23-diol preferentially with RR configurations, and a C-24 methyl or ethyl substituent [Takatsuto S, Yazawa N, Ikekawa N, Takematsu T, Takeuchi Y, Koguchi M. Structure-activity relationship of brassinosteroids. Phytochemistry 1983;22:2437-41; Thompson MJ, Meudt WJ, Mandava NB, Dutky SR, Lusby WR, Spaulding DW. Synthesis of brassinosteroids and relationship of structure to plant growth-promoting effects. Steroids 1982;39:89-105]. We found that the 3alpha,4alpha-diols 4, 6 and 8 are more active than the 2alpha,3alpha-diols 3, 5 and 7 [Sísa M, Budesínsky M, Kohout L. Synthesis of 7a-homo and 7a,7b-dihomo-5alpha-cholestane analogues of brassinolide. Collect Czech Chem Commun 2003;68:2171-89]. This fact is in strong contrast with the structure requirements mentioned above. Our hypothesis suggests that the lower activity of 2alpha,3alpha-diols and/or the higher activity of 3alpha,4alpha-diols could be explained by twisting and distortion of the molecule due to the seven- or eight-membered B-ring and also by the position of a carbonyl group relative to the A-ring diol. 3D-SAR computer methodologies as alignments and overlaps of GRID maps and 3D-QSAR analysis GRID-GOLPE (CoMFA-like) were used as an effort to explain the higher bioactivity of 3alpha,4alpha-diols 4, 6 and 8 in comparison with the 2alpha,3alpha-diols 3, 5 and 7 of B-ring enlarged brassinosteroids.     

The mid-domain effect cannot explain the diversity gradient of Nearctic birds

A recent explanation for diversity gradients proposes a ‘null model’ based on how species ranges are constrained by the geometry of bounded domains. We conduct a test of this hypothesis by comparing patterns predicted by two two‐dimensional geometric models against observed diversity patterns for terrestrially feeding Nearctic birds. Consistent with previous tests in two‐dimensional space, we find empirical support for the hypothesis to be very weak. We also point out a fundamental conceptual flaw in the hypothesis with respect to the key assumption that ranges can exist independently of the environment in which they are embedded that undermines its theoretical basis as well. We conclude that the mid‐domain effect has little empirical support and no theoretical support for its existence, and recommend that it be eliminated as a potential explanation for diversity gradients.     

Changes in the binding of "fast"-form alpha 2-macroglobulin to 3T3-L1 cells after differentiation to adipocytes

Human alpha 2-macroglobulin (alpha 2M)-CH3NH2 specifically binds to 3T3-L1 fibroblasts and adipocytes with an apparent Kd of 0.3 nM at 4 degrees C. Binding to fibroblasts follows first-order kinetics only for the first 20-30 min of reaction, k1 = 160 microM-1 h-1, and then proceeds in a non-first-order reaction that takes 28 h to reach steady state. Receptor activity is 120 fmol of alpha 2M-CH3NH2/mg of cell protein or 60 000 molecules/cell. Binding is nondissociable. In contrast, binding to adipocytes follows first-order kinetics, k1 = 720 microM-1 h-1, and reaches steady state in 6-8 h. Receptor activity is 35 fmol of alpha 2M-CH3NH2/mg of cell protein or 60 000 molecules/cell. Binding is reversible with a k2 of 0.4 h-1. Control studies with 3T3-C2 cells, which do not differentiate after hormone treatment, indicate that these differences are not due to hormone treatment alone. Binding to both fibroblasts and adipocytes is specific for "fast"-form alpha 2M but not for native alpha 2M. Inhibition studies with neoglycoproteins demonstrate that binding does not occur via any of the known carbohydrate receptors. Some cross-reactivity with antithrombin III-trypsin complexes is demonstrated. Both fibroblasts and adipocytes take up and degrade alpha 2M-CH3NH2 at 37 degrees C. For both cell types, the concentration of alpha 2M-CH3NH2 needed for half-maximal uptake is 65 nM.(ABSTRACT TRUNCATED AT 250 WORDS)     

The M3/M4 cytoplasmic loop of the alpha1 subunit restricts GABAARs lateral mobility: a study using fluorescence recovery after photobleaching

A crucial problem in neurobiology is how neurons are able to maintain neurotransmitter receptors at specific membrane domains. The large structural heterogeneity of gamma aminobutyric acid receptors (GABAARs) led to the hypothesis that there could be a link between GABAAR gene diversity and the targeting properties of the receptor complex. Previous studies using Fluorescence Recovery After Photobleaching (FRAP) have shown a restricted mobility in GABAARs containing the alpha1 subunit. The M3/M4 cytoplasmic loop is the region of the alpha1 subunit with the lowest sequence homology to other subunits. Therefore, we asked whether the M3/M4 loop is involved in cytoskeletal anchoring and GABAAR clustering. A series of alpha1 chimeric subunits was constructed: alpha1CH (control subunit), alpha1CD (Cytoplasmic loop deleted), alpha1CD2, and alpha1CD3 (alpha1 with the M3/M4 loop from the alpha2 and alpha3 subunits, respectively). Our results using FRAP indicate an involvement of the M3/M4 cytoplasmic loop of the alpha1 subunit in controlling receptor lateral mobility. On the other hand, inmunocytochemical approaches showed that this domain is not involved in subunit targeting to the cell surface, subunit-subunit assembly, or receptor aggregation.     

Fractal scale-invariant and nonlinear properties of cardiac dynamics remain stable with advanced age: a new mechanistic picture of cardiac control in healthy elderly

Heart beat fluctuations exhibit temporal structure with robust long-range correlations, fractal and nonlinear features, which have been found to break down with pathologic conditions, reflecting changes in the mechanism of neuroautonomic control. It has been hypothesized that these features change and even break down also with advanced age, suggesting fundamental alterations in cardiac control with aging. Here we test this hypothesis. We analyze heart beat interval recordings from the following two independent databases: 1) 19 healthy young (average age 25.7 yr) and 16 healthy elderly subjects (average age 73.8 yr) during 2 h under resting conditions from the Fantasia database; and 2) 29 healthy elderly subjects (average age 75.9 yr) during approximately 8 h of sleep from the sleep heart health study (SHHS) database, and the same subjects recorded 5 yr later. We quantify: 1) the average heart rate (); 2) the SD sigma(R-R) and sigma(DeltaR-R) of the heart beat intervals R-R and their increments DeltaR-R; 3) the long-range correlations in R-R as measured by the scaling exponent alpha(R-R) using the Detrended Fluctuation Analysis; 4) fractal linear and nonlinear properties as represented by the scaling exponents alpha(sgn) and alpha(mag) for the time series of the sign and magnitude of DeltaR-R; and 5) the nonlinear fractal dimension D(k) of R-R using the fractal dimension analysis. We find: 1) No significant difference in (P > 0.05); 2) a significant difference in sigma(R-R) and sigma(DeltaR-R) for the Fantasia groups (P < 10(-4)) but no significant change with age between the elderly SHHS groups (P > 0.5); and 3) no significant change in the fractal measures alpha(R-R) (P > 0.15), alpha(sgn) (P > 0.2), alpha(mag) (P > 0.3), and D(k) with age. Our findings do not support the hypothesis that fractal linear and nonlinear characteristics of heart beat dynamics break down with advanced age in healthy subjects. Although our results indeed show a reduced SD of heart beat fluctuations with advanced age, the inherent temporal fractal and nonlinear organization of these fluctuations remains stable. This indicates that the coupled cascade of nonlinear feedback loops, which are believed to underlie cardiac neuroautonomic regulation, remains intact with advanced age.     

Opposite changes in imidazoline I2 receptors and alpha2-adrenoceptors density in rat frontal cortex after induced gliosis

Opposite age-dependent changes in alpha2-adrenoceptor and imidazoline I2 receptor (I2-IRs) density have been related to brain gliosis development with aging. To check this hypothesis we applied in rats a model of reactive gliosis induced by heat. The specific binding of [3H]idazoxan (0.5-20 nM) in the presence of (-)adrenaline (5 x 10(-6) M) to membranes from rat brain cortex showed that the density of I(2)-IRs was significantly higher in membranes of injured cortex (Bmax=60+/-6 fmol/mg protein; n=9) than in control (Bmax=38+/-3 fmol/mg protein; n=9; p=0.0053). Conversely, the density of alpha2-adrenoceptors, measured by [3H]clonidine (0.25-16 nM), in the injured cortex (Bmax=75+/-4 fmol/mg protein; n=9) was significantly lower than in sham membranes (Bmax=103+/-7 fmol/mg protein; n=9; p=0.0035). No significant differences in receptor's affinity were observed between both groups. These results support the hypothesis that gliosis induces opposite changes in alpha2-adrenoceptor and I2-IR density.     

A phenological mid-domain effect in flowering diversity

In this paper, we test the mid-domain hypothesis as an explanation for observed patterns of flowering diversity in two sub-alpine communities of insect-pollinated plants. Observed species richness patterns showed an early-season increase in richness, a mid-season peak, and a late-season decrease. We show that a mid-domain null model can qualitatively match this pattern of flowering species richness, with R² values typically greater than 60%. We find significant or marginally significant departures from expected patterns of diversity for only 3 out of 12 year-site combinations. On the other hand, we do find a consistent pattern of departure when comparing observed versus null-model predicted flowering diversity averaged across years. Our results therefore support the hypothesis that ecological factors shape patterns of flowering phenology, but that the strength or nature of these environmental forcings may differ between years or the two habitats we studied, or may depend on species-specific characteristics of these plant communities. We conclude that mid-domain null models provide an important baseline from which to test departure of expected patterns of flowering diversity across temporal domains. Geometric constraints should be included first in the list of factors that drive seasonal patterns of flowering diversity.     

Cell surface sialylation and tumor metastasis. Metastatic potential of B16 melanoma variants correlates with their relative numbers of specific penultimate oligosaccharide structures

Numerous investigations suggest that cell surface glycoconjugates, and in particular sialic acids, are directly involved in determining the metastatic phenotype. To further evaluate this hypothesis, we have used a variety of techniques to probe the cell surfaces of several metastatic variants of the murine B16 melanoma that were selected for experimental lung-colonizing ability (Fidler, I. (1973) Nature 242, 148-149) or for their ability to spontaneously metastasize from the site of a subcutaneous injection (Stackpole, C. W., Alterman, A. L., and Fornabaio, D. M. (1985) Invasion & Metastasis 5, 125-142). Using a highly sensitive high performance liquid chromatography sialic acid assay in conjunction with Vibrio cholerae sialidase, we find that none of these metastatic variants differ significantly in their overall levels of cell surface sialic acid. Using highly purified, linkage-specific sialyltransferases, in conjunction with specific glycosidases, to probe the cell surface saccharide topography of specific penultimate oligosaccharides, we also find no significant differences between the efficient lung-colonizing variant, B16-F10 and the poorly-colonizing B16-F1 or B16-Flr variants. In contrast, the spontaneously metastatic variants examined contain substantially different levels of specific penultimate sialylation sites. The tumorigenic but nonmetastatic B16-LM3/G3.26 variant contains 4-fold more penultimate Gal beta 1-3GalNAc sialylation sites than the tumorigenic and highly metastatic B16-LM3/G3.12 variant when CMP[3H]NeuAc and the alpha 2-3Gal beta 1-3GalNAc sialyltransferase are used to probe the melanoma cell surfaces. Several prominent glycoconjugates of apparent Mr 43,000, 40,000, and 30,000 are especially evident upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the nonmetastatic cells. The nonmetastatic variant also contains 2-fold more Gal beta 1-4GlcNAc sialylation sites than the metastatic variant when the alpha 2-6Gal beta 1-4GlcNAc sialyltransferase is used as a cell surface probe. In this case, glycoconjugates of apparent Mr 74,000, 45,000, and 43,000 are more prominently observed on the cell surfaces of the nonmetastatic variant. These data indicate that the differences in lung-colonizing abilities of B16 melanoma metastatic variants do not correlate with the numbers or sialylation states of specific penultimate oligosaccharide structures on their surfaces. However, the relative levels of specific penultimate saccharide structures do correlate with the ability of the cells to undergo spontaneous metastasis from a subcutaneous tumor.     

Genetic factors influence cataract formation in alpha 3 connexin knockout mice

Connexin alpha 3 (Cx46 or Gja3) gene targeted null mice developed lens nuclear cataracts shortly after birth. A large variance in the cataracts was observed in alpha 3 null sibs on a mixed 129SvJae X C57BL/6J F3 background. This suggested that the genetic background might influence the cataract phenotype. Therefore, we placed the alpha 3 null mutation into a 129SvJae background, and also backcrossed the mutation for six generations into 129SvJ and C57BL/6J backgrounds. While alpha 3 nulls on the two 129 backgrounds contained severe cataracts associated with gamma crystallin cleavage, alpha 3 nulls on the C57B16 background had far milder cataracts with no detectable gamma crystallin cleavage. These findings suggest that a genetic modifier exists that influences gamma crystallin stability, and that gamma crystallin breakdown is associated with severe nuclear cataracts.     

Long-term cardiac allograft survival across an MHC mismatch after "pruning" of alloreactive CD4 T cells

Specific tolerance to allografts has been achieved by a variety of means. We have previously shown that ex vivo removal of dividing CD4(+) T cells from an MLR or "pruning" delays skin allograft rejection. We tested pruning of alloreactive T cells as a strategy for retaining a broad T cell repertoire while removing alloreactive T cells in a model of cardiac allograft transplant. Using CFSE staining of responder BALB/c cells with stimulator C57BL/6 cells in an MLR, SCID mice were reconstituted with either dividing (D) or nondividing (ND) CD4(+) T cells derived from an MLR and then challenged with heterotopic cardiac allografts. Mice reconstituted with D CD4(+) T cells rejected cardiac allografts from the stimulator strain with a median survival time (MST) of 29 days, while mice reconstituted with ND CD4(+) T cells maintained allografts from the stimulator strain (MST of >100 days) while rejecting third-party allografts (B10.BR) (MST = 11 days). ELISPOT assays demonstrate donor-specific hyporesponsiveness of the ND CD4(+) T cells. TCR beta-chain V region (TRBV) repertoire analysis demonstrates clonal expansion within both rejecting D cardiac allografts and ND cardiac allografts surviving for the long-term. Histology showed greater allograft infiltration by the D CD4(+) T cells. The surviving ND cardiac allografts demonstrated reduced cellular infiltration and reduced incidence of allograft vasculopathy, but with the development of chronic fibrosis. Thus, pruning of alloreactive T cells allows long-term-specific cardiac allograft survival while retaining the ability to reject third-party allografts.