Morphological study of the anthropoid thoracic cage: scaling of thoracic width and an analysis of rib curvature

While a relatively broad thorax and strongly curved ribs are widely regarded as common features of living hominoids, few studies have quantitatively examined these traits by methods other than calculating the chest index. The present study aims to quantify variations in thoracic cage morphology for living anthropoids. The odd-numbered ribs (first to eleventh) were articulated with the corresponding vertebrae and the cranial and lateral views subsequently photographed. Rib profiles were digitized in both views and line-fitted by a Bézier curve to create a three-dimensional morphological data set. When thoracic cage width was scaled against body mass, Hylobates (and possibly Pongo) plotted above non-hominoid anthropoids at almost all rib levels, while Pan did not differ from non-hominoid anthropoids. The overall pattern of the normalized thoracic width differed between Hylobates and other hominoids. In Hylobates, an upward convex curve was seen between the first and seventh ribs while a more linear pattern was observed in Pan and Pongo. This result quantitatively confirmed that the barrel-shaped thoracic cage in Hylobates can be distinguished from the funnel-shaped form in other hominoids. Conversely, all hominoids shared two distinct features in the upper half-thorax: (1) a pronounced dorsal protrusion of the proximal part of the rib in accordance with ventral displacement of the thoracic spine and (2) a relatively medially projecting sternal end. Although these features are likely to provide some mechanical advantage in orthograde and/or suspensory positional behaviors, they were barely present in the suspensory Ateles. An erratum to this article can be found at     

Textural characteristics of the iliac-femoral trabecular pattern in a bipedally trained Japanese macaque

Previous research has revealed that Japanese macaques (Macaca fuscata) trained in bipedal performance (Saru-mawashi) display a number of functionally related external skeletal changes, as well as some site-specific endostructural cortical and cancellous adaptations. Through radiography assisted by digital image processing, we investigated the trabecular pattern of the ilium and femoral neck of Sansuke, a macaque habitually bipedally trained for 8 years. A set of eight regions of interest on Sansuke were recorded for subtle structural characterization of the cancellous network and compared to a sample of 5 ilia and 23 femurs from 26 adult wild Japanese macaques. The measured variables include trabecular thickness, trabecular bone volume, and degree of anisotropy. As a whole, the site-specific textural characteristics of the cancellous network detected on the ilium and proximal femur of the bipedally trained macaque can be interpreted as functional adaptive responses to more compressive loads dissipated along the axis from the sacro-iliac to the coxo-femoral joint, and back.     

Variation in limb proportions between Jomon foragers and Yayoi agriculturalists from prehistoric Japan

Variation in limb proportions between prehistoric Jomon and Yayoi people of Japan are explored by this study. Jomon people were the descendents of Pleistocene nomads who migrated to the Japanese Islands around 30,000 yBP. Phenotypic and genotypic evidence indicates that Yayoi people were recent migrants to Japan from continental Northeast Asia who likely interbred with Jomon foragers. Limb proportions of Jomon and Yayoi people were compared using RMA regression and "Quick-Test" calculations to investigate relative variability between these two groups. Cluster and principal components analyses were performed on size-standardized limb lengths and used to compare Jomon and Yayoi people with other groups from various climatic zones. Elongated distal relative to proximal limb lengths were observed among Jomon compared to Yayoi people. Jomon limb proportions were similar to human groups from temperate/tropical climates at lower latitudes, while Yayoi limb proportions more closely resemble groups from colder climates at higher latitudes. Limb proportional similarities with groups from warmer environments among Jomon foragers likely reflect morphological changes following Pleistocene colonization of the Japanese Islands. Cold-derived limb proportions among the Yayoi people likely indicate retention of these traits following comparatively recent migrations to the Japanese Islands. Changes in limb proportions experienced by Jomon foragers and retention of cold-derived limb proportions among Yayoi people conform to previous findings that report changes in these proportions following long-standing evolution in a specific environment.     

Abnormal phosphorylation of Ser409/410 of TDP-43 in FTLD-U and ALS

A monoclonal antibody specific for phosphoserines 409 and 410 of TDP-43 (mAb pS409/410) has been produced. It strongly stained TDP-43-positive inclusions in brain of patients with frontotemporal lobar degeneration and amyotrophic lateral sclerosis, but did not stain nuclei, in which normal TDP-43 is localized. It did not recognize TDP-43 rapidly extracted from brains of rats at various developmental stages, strongly suggesting that phosphorylation of Ser409/410 is an abnormal event. Analysis of postmortem changes of TDP-43 revealed that the amounts of Sarkosyl-insoluble, urea-soluble full-length TDP-43 and a 35 kDa N-terminal fragment increased time-dependently.     

Structural insight into the specific interaction between murine SHPS-1/SIRP alpha and its ligand CD47

SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1 (SHPS-1 or SIRPα/BIT) is an immunoglobulin (Ig) superfamily transmembrane receptor and a member of the signal regulatory protein (SIRP) family involved in cell-cell interaction. SHPS-1 binds to its ligand CD47 to relay an inhibitory signal for cellular responses, whereas SIRPβ, an activating member of the same family, does not bind to CD47 despite sharing a highly homologous ligand-binding domain with SHPS-1. To address the molecular basis for specific CD47 recognition by SHPS-1, we present the crystal structure of the ligand-binding domain of murine SHPS-1 (mSHPS-1). Folding topology revealed that mSHPS-1 adopts an I2-set Ig fold, but its overall structure resembles IgV domains of antigen receptors, although it has an extended loop structure (C′E loop), which forms a dimer interface in the crystal. Site-directed mutagenesis studies of mSHPS-1 identified critical residues for CD47 binding including sites in the C′E loop and regions corresponding to complementarity-determining regions of antigen receptors. The structural and functional features of mSHPS-1 are consistent with the human SHPS-1 structure except that human SHPS-1 has an additional β-strand D. These results suggest that the variable complementarity-determining region-like loop structures in the binding surface of SHPS-1 are generally required for ligand recognition in a manner similar to that of antigen receptors, which may explain the diverse ligand-binding specificities of SIRP family receptors.     

Plk3 phosphorylates topoisomerase IIalpha at Thr(1342), a site that is not recognized by Plk1

The Plk (polo-like kinase) family is involved in cell-cycle machinery. Despite the possible overlapping involvement of Plk1 and Plk3 in cell-cycle distribution, the precise role of each Plk might be different. To investigate mechanisms that may differentiate their physiological roles, we compared the substrate specificities of Plk1 and Plk3 using synthetic peptides. Among these substrate peptides, topoisomerase IIalpha EKT(1342)DDE-containing synthetic peptide was strongly phosphorylated by Plk3 but not by Plk1. By modulating the topoisomerase IIalpha peptide, we identified residues at positions +1, +2 and +4 as determinants of differential substrate recognition between Plk1 and Plk3. Acidic residues at positions +2 and +4 appear to be a positive determinant for Plk3 but not Plk1. Variation at position +1 appears to be tolerated by Plk3, while a hydrophobic residue at +1 is critical for Plk1 activity. The direct phosphorylation of Thr(1342) of topoisomerase IIalpha by Plk3 was demonstrated with an in vitro kinase assay, and overexpression of Plk3 induced the phosphorylation of Thr(1342) in cellular topoisomerase IIalpha. Furthermore, the physical interaction between Plk3 and topoisomerase IIalpha was also demonstrated in cells in addition to phosphorylation. These data suggest that topoisomerase IIalpha is a novel physiological substrate for Plk3 and that Plk1 and Plk3 play different roles in cell-cycle regulation.     

Activation of c-Src and Fyn kinases by protein-tyrosine phosphatase RPTPalpha is substrate-specific and compatible with lipid raft localization

Src family tyrosine kinases (SFKs) function in multiple signaling pathways, raising the question of how appropriate regulation and substrate choice are achieved. SFK activity is modulated by several protein-tyrosine phosphatases, among which RPTPalpha and SHP2 are the best established. We studied how RPTPalpha affects substrate specificity and regulation of c-Src and Fyn in response to epidermal growth factor and platelet-derived growth factor. We find that RPTPalpha, in a growth factor-specific manner, directs the specificity of these kinases toward a specific subset of SFK substrates, particularly the focal adhesion protein Paxillin and the lipid raft scaffolding protein Cbp/PAG. A significant fraction of RPTPalpha is present in lipid rafts, where its targets Fyn and Cbp/PAG reside, and growth factor-mediated SFK activation within this compartment is strictly dependent on RPTPalpha. Forced concentration of RPTPalpha into lipid rafts is compatible with activation of Fyn. Finally, RPTPalpha-induced phosphorylation of Paxillin and Cbp/PAG induces recruitment of the SFK inhibitory kinase Csk, indicative of negative feedback loops limiting SFK activation by RPTPalpha. Our findings indicate that individual SFK-controlling PTPs play important and specific roles in dictating SFK substrate specificity and regulatory mechanism.     

Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems

The wobble uridine in yeast cytosolic tRNA(Lys2)(UUU) and tRNA(Glu3)(UUC) undergoes a thio-modification at the second position (s(2) modification) and a methoxycarbonylmethyl modification at the fifth position (mcm(5) modification). We previously demonstrated that the cytosolic and mitochondrial iron-sulfur (Fe/S) cluster assembly machineries termed CIA and ISC, including a cysteine desulfurase called Nfs1, were essential for the s(2) modification. However, the cytosolic component that directly participates in this process remains unclear. We found that ubiquitin-like protein Urm1 and ubiquitin-activating enzyme-like protein Uba4, as well as Tuc1 and Tuc2, were strictly required for the s(2) modification. The carboxyl-terminal glycine residue of Urm1 was critical for the s(2) modification, indicating direct involvement of the unique ubiquitin-related system in this process. We also demonstrated that the s(2) and mcm(5) modifications in cytosolic tRNAs influence each other's efficiency. Taken together, our data indicate that the s(2) modification of cytosolic tRNAs is a more complex process that requires additional unidentified components.     

Hepatitis C virus NS3 helicase forms oligomeric structures that exhibit optimal DNA unwinding activity in vitro

HCV NS3 helicase exhibits activity toward DNA and RNA substrates. The DNA helicase activity of NS3 has been proposed to be optimal when multiple NS3 molecules are bound to the same substrate molecule. NS3 catalyzes little or no measurable DNA unwinding under single cycle conditions in which the concentration of substrate exceeds the concentration of enzyme by 5-fold. However, when NS3 (100 nm) is equimolar with the substrate, a small burst amplitude of approximately 8 nm is observed. The burst amplitude increases as the enzyme concentration increases, consistent with the idea that multiple molecules are needed for optimal unwinding. Protein-protein interactions may facilitate optimal activity, so the oligomeric properties of the enzyme were investigated. Chemical cross-linking indicates that full-length NS3 forms higher order oligomers much more readily than the NS3 helicase domain. Dynamic light scattering indicates that full-length NS3 exists as an oligomer, whereas NS3 helicase domain exists in a monomeric form in solution. Size exclusion chromatography also indicates that full-length NS3 behaves as an oligomer in solution, whereas the NS3 helicase domain behaves as a monomer. When NS3 was passed through a small pore filter capable of removing protein aggregates, greater than 95% of the protein and the DNA unwinding activity was removed from solution. In contrast, only approximately 10% of NS3 helicase domain and approximately 20% of the associated DNA unwinding activity was removed from solution after passage through the small pore filter. The results indicate that the optimally active form of full-length NS3 is part of an oligomeric species in vitro.