Three-dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by cross-linking and molecular modelling

SMC proteins are essential components of three protein complexes that are important for chromosome structure and function. The cohesin complex holds replicated sister chromatids together, whereas the condensin complex has an essential role in mitotic chromosome architecture. Both are involved in interphase genome organization. SMC-containing complexes are large (more than 650 kDa for condensin) and contain long anti-parallel coiled-coils. They are thus difficult subjects for conventional crystallographic and electron cryomicroscopic studies. Here, we have used amino acid-selective cross-linking and mass spectrometry combined with structure prediction to develop a full-length molecular draft three-dimensional structure of the SMC2/SMC4 dimeric backbone of chicken condensin. We assembled homology-based molecular models of the globular heads and hinges with the lengthy coiled-coils modelled in fragments, using numerous high-confidence cross-links and accounting for potential irregularities. Our experiments reveal that isolated condensin complexes can exist with their coiled-coil segments closely apposed to one another along their lengths and define the relative spatial alignment of the two anti-parallel coils. The centres of the coiled-coils can also approach one another closely in situ in mitotic chromosomes. In addition to revealing structural information, our cross-linking data suggest that both H2A and H4 may have roles in condensin interactions with chromatin.     

Body mass in large extant and extinct carnivores

Body mass in six species of Plio-Pleistocene carnivores was estimated based on the relationship between mass and cross-sectional geometric properties, distal articular surface area, lengths and circumferences of proximal limb bones (femur and humerus) in 28 species of extant carnivores. All measures, except lengths, were found to give congruent body mass estimates. Two of the extinct carnivores ( Smilodon fatalis and Panthera atrox ) are estimated to be as much as one and a half times heavier than previously thought. Based on these results inferences are made concerning possible prey species.     

Covalent cross-linking of proteins without chemical reagents

A facile method for the formation of zero-length covalent cross-links between protein molecules in the lyophilized state without the use of chemical reagents has been developed. The cross-linking process is performed by simply sealing lyophilized protein under vacuum in a glass vessel and heating at 85 degrees C for 24 h. Under these conditions, approximately one-third of the total protein present becomes cross-linked, and dimer is the major product. Chemical and mass spectroscopic evidence obtained shows that zero-length cross-links are formed as a result of the condensation of interacting ammonium and carboxylate groups to form amide bonds between adjacent molecules. For the protein examined in the most detail, RNase A, the cross-linked dimer has only one amide cross-link and retains the enzymatic activity of the monomer. The in vacuo cross-linking procedure appears to be general in its applicability because five different proteins tested gave substantial cross-linking, and co-lyophilization of lysozyme and RNase A also gave a heterogeneous covalently cross-linked dimer.     

Transmissible and nontransmissible components of anthropometric variation in the Alexanderwohl Mennonites: I. Description and familial correlations

Data on 34 anthropometric measures from the Alexanderwohl Mennonite congregations of Kansas and Nebraska are presented. A factor analysis of these traits shows that body length and body width measures are distinct from each other as well as from measures of the head and face. Moreover, familial correlations estimated by maximum likelihood for all 34 traits tend to separate from each other along factor lines with correlations for body lengths being the highest and those for skinfolds and circumferences being the lowest. These results suggest the presence of various body "fields" which are under differing degrees of genetic and environmental control. We offer the term "functional multifactorial complex" as a means of referring to the joint genetic and environmental influences on these fields.     

Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry

Recent work using chemical cross-linking to define interresidue distance constraints in proteins has shown that these constraints are useful for testing tertiary structural models. We applied this approach to the G-protein-coupled receptor bovine rhodopsin in its native membrane using lysine- and cysteine-targeted bifunctional cross-linking reagents. Cross-linked proteolytic peptides of rhodopsin were identified by combined liquid chromatography and FT-ICR mass spectrometry with automated data-reduction and assignment software. Tandem mass spectrometry was used to verify cross-link assignments and locate the exact sites of cross-link attachment. Cross-links were observed to form between 10 pairs of residues in dark-state rhodopsin. For each pair, cross-linkers with a range of linker lengths were tested to determine an experimental distance-of-closest-approach (DCA) between reactive side-chain atoms. In all, 28 cross-links were identified using seven different cross-linking reagents. Molecular mechanics procedures were applied to published crystal structure data to calculate energetically achievable theoretical DCAs between reactive atoms without altering the position of the protein backbone. Experimentally measured DCAs are generally in good agreement with the theoretical DCAs. However, a cross-link between C316 and K325 in the C-terminal region cannot be rationalized by DCA simulations and suggests that backbone reorientation relative to the crystal coordinates occurs on the timescale of cross-linking reactions. Biochemical and spectroscopic data from other studies have found that the C-terminal region is highly mobile in solution and not fully represented by X-ray crystallography data. Our results show that chemical cross-linking can provide reliable three-dimensional structural information and insight into local conformational dynamics in a membrane protein.     

Telomere length and age in pinnipeds: The endangered Australian sea lion as a case study

Telomeres are the protective caps at the ends of all eukaryotic chromosomes. Because DNA replication of chromosome ends is incomplete, telomeres undergo sequence loss with each cell division resulting in the progressive shortening of their lengths. Telomere shortening with age is known from terrestrial mammals. We test whether this pattern is shared by marine mammals, by comparing telomere lengths between age classes in a pinniped species, the Australian sea lion (Neophoca cinerea). Telomere lengths were measured using a real‐time quantitative polymerase chain reaction (PCR) method in specimens from three age classes: pup (<1.5 yr), juvenile (1.5–5 yr), and adult (>5 yr). Mean telomere lengths of the adults were significantly shorter than the juvenile and pup classes. However, we were unable to differentiate between pups and juveniles. These findings confirm that the Australian sea lion shares the general pattern of shortening telomere lengths with age as documented in terrestrial mammals. The application of telomere lengths as an age determinant requires considerable development to refine the scale of the age estimates derived, which will require the use of known‐aged individuals. Nonetheless, measures of telomere lengths have the potential to become valuable tools in molecular ecology and forensics for assessing compliance in harvesting situations.     

X-Ray Crystal Structure of a Highly Functionalized Thiophene as a New Backbone Amide Linker for Solid-phase Peptide Synthesis. Relationship between Crystal Structure and Reactivity

The development of new linkers (handles) for solid-phase synthesis provides new chemical opportunities for peptide synthesis. To understand the chemical properties of a recently developed backbone amide linker from a structural perspective, the crystal structure of S-((5-formyl-3,4-ethylenedioxy)thiophene-2-yl)-3-thiopropionic acid (T-BAL2) was studied. Specifically, we wished to address whether this highly substituted thiophene retained planarity in the aromatic ring as well as between the aromatic ring and the aldehyde carbonyl. Furthermore, we sought an explanation for the relatively low reactivity in reductive aminations of the thienylaldehyde with amines in solution and on solid phase. Based on the crystal structure of T-BAL2, the thienyl-C (aldehyde) and C–O (aldehyde) bond lengths were applied as measures for the electron-deficiency (electrophilicity) of the aldehyde and compared to similar bond lengths found in previously reported formylated homo- and hetero-aromatic systems, which show significantly higher reactivity towards imine formation. The bond lengths found in the present structure are in accordance with normal C–C single bond and C–O double bond lengths. The high similarity in aldehyde bond lengths in the present system and in the reported systems indicates similar electron distribution in these systems. The lower reactivity of the present system may therefore not be attributed to electronic factors.     

Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site

The relative efficiencies of the maximum-likelihood (ML), neighbor- joining (NJ), and maximum-parsimony (MP) methods in obtaining the correct topology and in estimating the branch lengths for the case of four DNA sequences were studied by computer simulation, under the assumption either that there is variation in substitution rate among different nucleotide sites or that there is no variation. For the NJ method, several different distance measures (Jukes-Cantor, Kimura two- parameter, and gamma distances) were used, whereas for the ML method three different transition/transversion ratios (R) were used. For the MP method, both the standard unweighted parsimony and the dynamically weighted parsimony methods were used. The results obtained are as follows: (1) When the R value is high, dynamically weighted parsimony is more efficient than unweighted parsimony in obtaining the correct topology. (2) However, both weighted and unweighted parsimony methods are generally less efficient than the NJ and ML methods even in the case where the MP method gives a consistent tree. (3) When all the assumptions of the ML method are satisfied, this method is slightly more efficient than the NJ method. However, when the assumptions are not satisfied, the NJ method with gamma distances is slightly better in obtaining the correct topology than is the ML method. In general, the two methods show more or less the same performance. The NJ method may give a correct topology even when the distance measures used are not unbiased estimators of nucleotide substitutions. (4) Branch length estimates of a tree with the correct topology are affected more easily than topology by violation of the assumptions of the mathematical model used, for both the ML and the NJ methods. Under certain conditions, branch lengths are seriously overestimated or underestimated. The MP method often gives serious underestimates for certain branches. (5) Distance measures that generate the correct topology, with high probability, do not necessarily give good estimates of branch lengths. (6) The likelihood-ratio test and the confidence-limit test, in Felsenstein's DNAML, for examining the statistical of branch length estimates are quite sensitive to violation of the assumptions and are generally too liberal to be used for actual data. Rzhetsky and Nei's branch length test is less sensitive to violation of the assumptions than is Felsenstein's test. (7) When the extent of sequence divergence is < or = 5% and when > or = 1,000 nucleotides are used, all three methods show essentially the same efficiency in obtaining the correct topology and in estimating branch lengths.(ABSTRACT TRUNCATED AT 400 WORDS)      

Extension of neurites on axons is impaired by antibodies against specific neural cell surface glycoproteins

We have developed an in vitro assay which measures the ability of growth cones to extend on an axonal substrate. Neurite lengths were compared in the presence or absence of monovalent antibodies against specific neural cell surface glycoproteins. Fab fragments of antibodies against the neural cell adhesion molecule, NCAM, have an insignificant effect on the lengths of neurites elongating on either an axonal substrate or a laminin substrate. Fab fragments of polyclonal antibodies against two new neural cell surface antigens, defined by mAb G4 and mAb F11, decrease the lengths of neurites elongating on an axonal substrate, but have no effect on the lengths of neurites elongating on a laminin substrate. G4 antigen is related to mouse L1, while F11 antigen appears to be distinct from all known neural cell surface glycoproteins. Our results suggest that the G4 and F11 antigens help to promote the extension of growth cones on axons.     

Sex dimorphism in digital formulae of children

This paper presents results of a study designed to: 1) test for a sex difference in the relative lengths of the finger bones, including the second-to-fourth digit ratio (2D:4D), using left-hand radiographs taken in young children, 2) test whether sex differences can be explained by sex differences in fetal growth, and 3) test the serial stability of sex differences in relative digit lengths, including 2D:4D. Results are presented from 1,060 subjects of the California Child Health and Development Studies. One serial replication at about 9 years old is available from 271 subjects. Results indicate that relative digit lengths are sex-dimorphic in children (Manning et al. [1998] Hum. Reprod. 13:3000-3004, [2004] Early Hum. Dev. 80:161-168). Sex differences in digit length ratios are more pronounced within sibships, where shared family factors are controlled, and are not strongly associated with gross measures of fetal growth, like birth length or weight. Thus, sex differences in the fetal growth of the body are not implicated in sex differences in digital formulae, leaving open the possibility of more direct hormonal and/or genetic causation. However, 2D:4D declined between ages 6-8 in a longitudinal sample, and was a less consistent sex-dimorphic marker than 3D:4D across ethnic groups, suggesting that 3D:4D may be a better marker of perinatal sex differentiation. Prior conflicting findings about 2D:4D may be partly explained by variations in age and ethnicity of populations studied.     

Tree shape‐based approaches for the comparative study of cophylogeny

Cophylogeny is the congruence of phylogenetic relationships between two different groups of organisms due to their long‐term interaction. We investigated the use of tree shape distance measures to quantify the degree of cophylogeny. We implemented a reverse‐time simulation model of pathogen phylogenies within a fixed host tree, given cospeciation probability, host switching, and pathogen speciation rates. We used this model to evaluate 18 distance measures between host and pathogen trees including two kernel distances that we developed for labeled and unlabeled trees, which use branch lengths and accommodate different size trees. Finally, we used these measures to revisit published cophylogenetic studies, where authors described the observed associations as representing a high or low degree of cophylogeny. Our simulations demonstrated that some measures are more informative than others with respect to specific coevolution parameters especially when these did not assume extreme values. For real datasets, trees’ associations projection revealed clustering of high concordance studies suggesting that investigators are describing it in a consistent way. Our results support the hypothesis that measures can be useful for quantifying cophylogeny. This motivates their usage in the field of coevolution and supports the development of simulation‐based methods, i.e., approximate Bayesian computation, to estimate the underlying coevolutionary parameters.     

Variation in CAG repeat length of the androgen receptor gene predicts variables associated with intrasexual competitiveness in human males

An expanding body of research suggests that circulating androgens regulate the allocation of energy between mating and survival effort in human males, with higher androgen levels promoting greater investment in mating effort. Because variations in the number of CAG codon repeats in the human androgen receptor (AR) gene appear to modulate the phenotypic effects of androgens - with shorter repeat lengths associated with greater androgenic effects per unit androgen - polymorphisms in this gene may predict trait-like individual differences in the degree to which men are calibrated toward greater mating effort. Consistent with this, men in the present study with shorter CAG repeat lengths exhibited greater upper body strength and scored higher on self-report measures of dominance and prestige, all of which are argued to be indices of mating effort. Repeat length failed to predict sociosexual orientation (i.e. pursuit of short-term mating relationships), however, suggesting that the traits correlated with this polymorphism may be primarily associated with intrasexual competitiveness in the service of long-term mating effort. None of these measures of mating effort was related to baseline testosterone concentrations (either as main effects or as interactions with CAG repeat length), implying that long-term androgen exposure associated with AR gene polymorphisms may account for more variance in some androgen-dependent traits than does current testosterone concentration. These findings provide further evidence for the importance of the CAG repeat polymorphism in the AR gene in explaining a broad range of individual differences in human males.     

Branch-length prior influences Bayesian posterior probability of phylogeny

The Bayesian method for estimating species phylogenies from molecular sequence data provides an attractive alternative to maximum likelihood with nonparametric bootstrap due to the easy interpretation of posterior probabilities for trees and to availability of efficient computational algorithms. However, for many data sets it produces extremely high posterior probabilities, sometimes for apparently incorrect clades. Here we use both computer simulation and empirical data analysis to examine the effect of the prior model for internal branch lengths. We found that posterior probabilities for trees and clades are sensitive to the prior for internal branch lengths, and priors assuming long internal branches cause high posterior probabilities for trees. In particular, uniform priors with high upper bounds bias Bayesian clade probabilities in favor of extreme values. We discuss possible remedies to the problem, including empirical and full Bayesian methods and subjective procedures suggested in Bayesian hypothesis testing. Our results also suggest that the bootstrap proportion and Bayesian posterior probability are different measures of accuracy, and that the bootstrap proportion, if interpreted as the probability that the clade is true, can be either too liberal or too conservative.     

Recombinant human erythropoietin (rHuEPO): cross-linking with disuccinimidyl esters and identification of the interfacing domains in EPO.

Several amino groups of recombinant human erythropoietin are selectively cross-linked by specific cross-linkers including disuccinimidyl suberate or dithiobis(succinimidyl propionate). Intramolecular cross-linkings are obtained without significant change of the protein conformation using appropriate concentrations (0.2 mM) of the cross-linkers, which possess an 11-12-A length of a spacer between two reacting groups. Intramolecularly cross-linked peptides obtained suggest that several amino groups in erythropoietin (EPO) are positioned at a distance of near 12 A in the solution state. These interfacing amino groups include Lys 20-Lys 154, Lys 45-Lys 140, Lys 52-Lys 154, Lys 52-Lys 140, and Ala 1-Lys 116. A comparison of the cross-linking results between nonglycosylated EPO and glycosylated EPO suggests that both proteins retain high similarity regarding protein conformation. These results fit a structural model similar to that of human growth hormone, in which four alpha-helical bundles and a long stretch of beta-sheet structure are involved in the active protein.     

Distance measures in terms of substitution processes.

Phylogenetic reconstruction from DNA or amino acid sequences relies heavily on suitable distance measures. A number of new distance measures (asynchronous, LogDet, and paralinear distances) which possess the desired property of tree additivity under fairly general models of sequence evolution have been proposed recently, but they are not well understood from a mechanistic point of view. We review them here in a unifying framework, which is the substitution process in continuous time. The emerging interpretation will also clarify the relationship among these distance measures. We also tackle situations with site-to-site variation of substitution rates which is well known to cause non-additive distances and inconsistent branch lengths. For homogeneous, stationary, time-reversible models, this may be repaired provided that the distribution of rates is known. In contrast, we will show that, for non-stationary models, different tree topologies may produce identical joint distributions of letters in pairs of sequences, given the same distribution of rates. This precludes the existence of any tree-additive pairwise distance measure.     

Poor growth prior to early childhood: decreased health and life-span in the adult

Previous studies in animal populations have shown that stunted neural and thymolymphatic growth early in development may result in permanently impaired neural and immune function, decreased body growth, vertebral wedging, and decreased life-span. In the human adult, small vertebral neural canal (VNC) diameters may reflect early stunted neural and immune development and impaired function that leads to decreased health (inferred by greater vertebral wedging) and life-span in the adult. VNC, which complete their growth by early childhood (age 4), are markers of early development in adults. On the other hand, features following general body growth, such as height, weight (represented here by vertebral body height) continues to grow until young adulthood. They are less reliable, because they readily experience catch-up growth (even in chronically stressed populations) and, unlike VNC, may mask poor early growth. To test associations between early growth and adult health and life-span in humans, we measured 2,060 VNC, vertebral heights, vertebral wedging, nerve-root tunnel lengths, severity of vertebral osteophytosis, and ages at death in 90 adult (aged 15-55 years) prehistoric skeletons (950-1300 A.D.). Tibial lengths were also measured in a subsample (n = 30). Multivariate, bivariate, and nonparametric analyses showed that small VNC are significantly associated with greater vertebral wedging and decreased life-span (P less than 0.05-0.00001). VNC are independent of vertebral body heights and tibial lengths (general body growth). VNC, but not statural components, are useful in predicting adult health, presumably because they reflect neural and immune development and do not readily experience catch-up growth. Thus, longitudinal retrospective measures of early growth and adult health were systematically linked within individuals regardless of confounding factors operating over the 350-year time period. Since this research was completed, this model has repeatedly been independently confirmed in four living urban industrial populations. Longitudinal retrospective analysis was employed together with direct measures of VNC, neural and immune function. Together these results suggested that it may be essential to improve growth prior to early childhood in order to maximize adult health and life-span.     

Nodal distances for rooted phylogenetic trees

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M_n(\mathbb R){\mathcal{M}_n(\mathbb {R})} of real-valued n × n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L ^p metrics on M_n(\mathbb R){\mathcal{M}_n(\mathbb {R})}, with ${p \in \mathbb {R}_{ >0 }}${p \in \mathbb {R}_{ >0 }}.     

Unearthing the molecular phylodiversity of desert soil green algae (Chlorophyta)

Deserts are not usually considered biodiversity hotspots, but desert microbiotic crust communities exhibit a rich diversity of both eukaryotic and prokaryotic life forms. Like many communities dominated by microscopic organisms, they defy characterization by traditional species-counting approaches to assessing biodiversity. Here we use exclusive molecular phylodiversity (E) to quantify the amount of evolutionary divergence unique to desert-dwelling green algae (Chlorophyta) in microbiotic crust communities. Given a phylogenetic tree with branch lengths expressed in units of expected substitutions per site, E is the total length of all tree segments representing exclusively desert lineages. Using MCMC to integrate over tree topologies and branch lengths provides 95% Bayesian credible intervals for phylodiversity measures. We found substantial exclusive molecular phylodiversity based on 18S rDNA data, showing that desert lineages are distantly related to their nearest aquatic relatives. Our results challenge conventional wisdom, which holds that there was a single origin of terrestrial green plants and that green algae are merely incidental visitors rather than indigenous components of desert communities. We identify examples of lineage diversification within deserts and at least 12 separate transitions from aquatic to terrestrial life apart from the most celebrated transition leading to the embryophyte land plants. [Bayesian phylogenetics; biodiversity; exclusive molecular phylodiversity; microbiotic crusts.].     

Do migrant birds have more pointed wings?: A comparative study

Summary Do birds that migrate over longer distances have more pointed wings than more sedentary birds? Within several bird genera, species differ considerably in their migration distances. This makes it possible to study the extent to which different taxa show similar morphological solutions to common selection pressures. I selected 14 species, two from each of seven passerine genera, to maximize within-genus differences in migration distance. Wing lengths and the lengths of eight primary feathers around the wing tip were measured to assess wing length and shape. Primary lengths were transformed to take into account the allometric relationship between the length of each feather and wing length and then collapsed into summary measures of shape by principal component analysis. I used the method of independent contrasts to address the effects of phylogeny. Wing length showed no relationship with migration distance. There was a correlation between migration distance and wing shape. It is concluded that long-distance migration has resulted in convergent morphological evolution of long distal and short proximal primaries, resulting in wing tips close to the leading edge of the wing.     

不同沙地生境下黄柳(Salix gordejevii)种群若干数量特征的比较研究

对分布于３种不同沙地生境（半固定沙丘、固定沙丘、丘间低地）黄柳灌丛的个体形态、生长和群体数量特征进行了比较研究,同时测定了灌丛下草本层植物种类组成及频率。结果显示：分布于丘间低地的黄柳灌丛当年枝平均长度增加缓慢,短枝条的比例较高,枝长频度分布（当年枝）峰值偏左,分枝也较多,叶片短而狭,长宽比大;与之相比,分布于半固定沙丘上的灌丛当年枝平均长度增加较快,长枝条比例较高,枝长频度分布趋于正态分布,分枝