REMARKABLE CONSERVATION OF INTERNALLY TRANSCRIBED SPACER SEQUENCES OF ARTHROSPIRA (“SPIRULINA” ) (CYANOPHYCEAE,CYANOBACTERIA) STRAINS FROM FOUR CONTINENTS AND OF RECENT AND 30‐YEAR‐OLD DRIED SAMPLES FROM AFRICA1

The internally transcribed spacer (ITS) sequences of 21 Arthrospira clonal strains from four continents and assigned to four different species (A. platensis, A. maxima, A. fusiformis, A. indica) in the culture collections were determined. Two main clusters, I and II, were differentiated by 49 positions out of 475 nt or 477 nt, respectively. Each cluster was further subdivided into two subclusters. Subclusters I.A and I.B were separated by two substitutions, whereas subclusters II.A and II.B were distinguished by four substitutions. After direct sequencing of the PCR products, three dried samples from Chad aged between 3 months and 35 years yielded a sequence belonging to subcluster I.A, as did a recent commercial product. The strains grown in production plants belonged to the same (sub)clusters as strains from culture collections, mainly I.A and II. PCR primers specific for each cluster and subcluster were designed and tested with crude cell lysates of Arthrospira strains. One dried sample (“dihé” 1) and a herbarium sample from Lake Sonachi (Kenya) only contained I.A sequences, whereas the commercial product was a mixture of the four genotypes and the other two dried samples contained minor polymorphisms characteristic of different clusters. Five clonal Arthrospira strains, thought to be duplicates, showed the simultaneous presence of the two forms of the four diagnostic positions that distinguish subclusters genotype II.A and genotype II.B. This is likely to be caused by multiple copies of the rDNA operon, in a intermediate stage of homogenization between subcluster II.A and subcluster II.B. The high conservation of ITS sequences is in contrast with the assignment to four different species, the great morphological variability of the strains, and their wide geographic distribution.     

植物分枝模型

从生物体总是最有效地利用物质的思想出发,对植物分枝形状建立了一个数学模型。该模型认为,当主干与侧枝的截面积之间存在类似平行四边形法则的关系时,分枝的体积取极小值。该模型揭示植物分枝形态不仅符合力学平衡的原则,在进化上也有显著生物学意义。根据实测数据提出了偏移度的概念,认为分枝形态建成与个体内部枝条相互作用有关,植物分枝取向受空间效应影响时仍满足体积最小的原则。由于此模型具有随机性,遵循此模型的分枝可呈现千变万化的形式。模型将分枝角度与分枝截面积有机结合起来,可作为计算机模拟植物的方法。     

Sample size considerations for stepped wedge designs with subclusters

The stepped wedge cluster randomized trial (SW-CRT) is an increasingly popular design for evaluating health service delivery or policy interventions. An essential consideration of this design is the need to account for both within-period and between-period correlations in sample size calculations. Especially when embedded in health care delivery systems, many SW-CRTs may have subclusters nested in clusters, within which outcomes are collected longitudinally. However, existing sample size methods that account for between-period correlations have not allowed for multiple levels of clustering. We present computationally efficient sample size procedures that properly differentiate within-period and between-period intracluster correlation coefficients in SW-CRTs in the presence of subclusters. We introduce an extended block exchangeable correlation matrix to characterize the complex dependencies of outcomes within clusters. For Gaussian outcomes, we derive a closed-form sample size expression that depends on the correlation structure only through two eigenvalues of the extended block exchangeable correlation structure. For non-Gaussian outcomes, we present a generic sample size algorithm based on linearization and elucidate simplifications under canonical link functions. For example, we show that the approximate sample size formula under a logistic linear mixed model depends on three eigenvalues of the extended block exchangeable correlation matrix. We provide an extension to accommodate unequal cluster sizes and validate the proposed methods via simulations. Finally, we illustrate our methods in two real SW-CRTs with subclusters.     

Germ cell cluster formation in insect ovaries

Three different ovariole types exist in insects: panoistic, polytrophic- and telotrophic-meroistic. Their ontogenetic development is comparable to all insect orders. Each ovariole is composed of somatic tissues and germ cells.Panoistic ovarioles can be developed: (1) by totally blocking germ cell cluster division (e.g. in “primitive” insect orders; and (2) after germ cell cluster formation by final cleavage of cystocytes, which develop as oocytes (e.g. in stoneflies or thrips).Polytrophic-meroistic ovaries, showing a set of identical characters, are found among hemirnetabolous and holometabolous insects, indicating a “basic type” of common origin. One characteristic feature is the differentiation of only one oocyte, which is derived from one central cell of the cluster, whereas all other siblings are transformed into nurse cells.Telotrophic ovaries differ from polytrophic ovaries by retention of all nurse cells in the anterior trophic chamber. In addition, oocyte-nurse cell determination can be shifted towards more oocytes in a cluster, and clusters or subclusters can fuse by cell membrane reduction among nurse cells. This type of ovary developed independently 3 times from polytrophic ancestors and once in mayflies directly from panoistic ancestors.     

Development of a general method for designing microvascular networks using distribution of wall shear stress

In the present study, theoretical formulations for calculation of optimal bifurcation angle and relationship between the diameters of mother and daughter vessels using the power law model for non-Newtonian fluids are developed. The method is based on the distribution of wall shear stress in the mother and daughter vessels. Also, the effect of distribution of wall shear stress on the minimization of energy loss and flow resistance is considered. It is shown that constant wall shear stress in the mother and daughter vessels provides the minimum flow resistance and energy loss of biological flows. Moreover, the effects of different wall shear stresses in the mother and daughter branches, different lengths of daughter branches in the asymmetric bifurcations and non-Newtonian effect of biological fluid flows on the bifurcation angle and the relationship between the diameters of mother and daughter branches are considered. Using numerical simulations for non-Newtonian models such as power law and Carreau models, the effects of optimal bifurcation angle on the pressure drop and flow resistance of blood flow in the symmetric bifurcation are investigated. Numerical simulations show that optimal bifurcation angle decreases the pressure drop and flow resistance especially for bifurcations at large Reynolds number.     

Amorphic kinds: Cluster’s last stand?

I raise a puzzle case for “cluster” accounts of natural kinds—the homeostatic property cluster and stable property cluster accounts, especially—on the basis of their expected treatment of the metaphysics of certain disease kinds. Some kinds, I argue, fail to exhibit the co-instantiated property clusters these cluster views take to be (partly) constitutive of natural kinds. Some genetic diseases, for example, have archetypical instances with few or none of the pathological processes or symptoms associated with the kind: their instances are typified by a single dispositional property. I dub such kinds ‘amorphic’, owing to their limited morphology, and try out a number of ways in which these kinds might be treated in terms of property clusters, adapting responses cluster theorists have offered to the problem of polymorphic species. Finding these responses wanting, I conclude that cluster accounts are unlikely to be the best account of the metaphysics of amorphic kinds.     

Hox cluster organization in the jawless vertebrate Petromyzon marinus

Large-scale gene amplifications may have facilitated the evolution of morphological innovations that accompanied the origin of vertebrates. This hypothesis predicts that the genomes of extant jawless fish, scions of deeply branching vertebrate lineages, should bear a record of these events. Previous work suggests that nonvertebrate chordates have a single Hox cluster, but that gnathostome vertebrates have four or more Hox clusters. Did the duplication events that produced multiple vertebrate Hox clusters occur before or after the divergence of agnathan and gnathostome lineages? Can investigation of lamprey Hox clusters illuminate the origins of the four gnathostome Hox clusters? To approach these questions, we cloned and sequenced 13 Hox cluster genes from cDNA and genomic libraries in the lamprey, Petromyzon marinus. The results suggest that the lamprey has at least four Hox clusters and support the model that gnathostome Hox clusters arose by a two-round-no-cluster-loss mechanism, with tree topology [(AB)(CD)]. A three-round model, however, is not rigorously excluded by the data and, for this model, the tree topologies [(D(C(AB))] and [(C(D(AB))] are most parsimonious. Gene phylogenies suggest that at least one Hox cluster duplication occurred in the lamprey lineage after it diverged from the gnathostome lineage. The results argue against two or more rounds of duplication before the divergence of agnathan and gnathostome vertebrates. If Hox clusters were duplicated in whole-genome duplication events, then these data suggest that, at most, one whole genome duplication occurred before the evolution of vertebrate developmental innovations.     

Sample Size Considerations for GEE Analyses of Three‐Level Cluster Randomized Trials

Summary Cluster randomized trials in health care may involve three instead of two levels, for instance, in trials where different interventions to improve quality of care are compared. In such trials, the intervention is implemented in health care units (“clusters”) and aims at changing the behavior of health care professionals working in this unit (“subjects”), while the effects are measured at the patient level (“evaluations”). Within the generalized estimating equations approach, we derive a sample size formula that accounts for two levels of clustering: that of subjects within clusters and that of evaluations within subjects. The formula reveals that sample size is inflated, relative to a design with completely independent evaluations, by a multiplicative term that can be expressed as a product of two variance inflation factors, one that quantifies the impact of within‐subject correlation of evaluations on the variance of subject‐level means and the other that quantifies the impact of the correlation between subject‐level means on the variance of the cluster means. Power levels as predicted by the sample size formula agreed well with the simulated power for more than 10 clusters in total, when data were analyzed using bias‐corrected estimating equations for the correlation parameters in combination with the model‐based covariance estimator or the sandwich estimator with a finite sample correction.     

No more than 14: the end of the amphioxus Hox cluster

The Hox gene cluster has been a key paradigm for a generation of developmental and evolutionary biologists. Since its discovery in the mid-1980's, the identification, genomic organization, expression, colinearity, and regulation of Hox genes have been immediate targets for study in any new model organism, and metazoan genome projects always refer to the structure of the particular Hox cluster(s). Since the early 1990's, it has been dogma that vertebrate Hox clusters are composed of thirteen paralogous groups. Nonetheless, we showed that in the otherwise prototypical cephalochordate amphioxus (Branchiostoma floridae), the Hox cluster contains a fourteenth Hox gene, and very recently, a 14(th) Hox paralogous group has been found in the coelacanth and the horn shark, suggesting that the amphioxus cluster was anticipating the finding of Hox 14 in some vertebrate lineages. In view of the pivotal place that amphioxus occupies in vertebrate evolution, we thought it of considerable interest to establish the limits of its Hox gene cluster, namely resolution of whether more Hox genes are present in the amphioxus cluster (e.g., Hox 15). Using two strategies, here we report the completion and characterization of the Hox gene content of the single amphioxus Hox cluster, which encompasses 650 kb from Hox1 to Evx. Our data have important implications for the primordial Hox gene cluster of chordates: the prototypical nature of the single amphioxus Hox cluster makes it unlikely that additional paralogous groups will be found in any chordate lineage. We suggest that 14 is the end.     

Diameter asymmetry of porcine coronary arterial trees: structural and functional implications

The coronary vasculature is characterized by highly asymmetric diameters at bifurcations, which may be an important determinant of flow distribution. To facilitate accurate reconstruction of the coronary network for hemodynamic analysis, we introduce a statistical data set of the diameter asymmetry at bifurcations based on morphometric data of the porcine coronary arterial and venous trees. The bifurcation asymmetry data were represented by the diameter ratio of the daughters relative to mother vessel and by an area expansion ratio (AER) at each bifurcation. A novel asymmetry ratio matrix was introduced to describe the diameter asymmetry of daughters to mother vessels. The relations between AER and flow velocity, and asymmetry ratio matrix and flow distribution, were considered. The results indicate that the ratio of large daughter to mother vessel has a minimum value at order 5 (mean diameter of approximately 70 microm), whereas the ratio of small daughter to mother vessel decreases monotonically with increase in order number. The AER was found to be fairly uniform for larger vessels and to increase from order 5 toward the capillaries. At order 5, we observe a transition in asymmetric bifurcation pattern that may mark a hemodynamic transition from transmural to perfusion subnetworks. The functional implications of these structural transitions are considered.     

A striking example of developmental bias in an evolutionary process: The “domestication syndrome”

The question of whether “developmental bias” can influence evolution is still controversial, despite much circumstantial evidence and a good theoretical argument. Here, I will argue that the domestication of mammalian species, which took place independently more than two dozen times, provides a particularly convincing example of developmental bias in evolution. The singular finding that underlies this claim is the repeated occurrence in domesticated mammals of a set of distinctive traits, none of which were deliberately selected. This phenomenon has been termed “the domestication syndrome”. In this article, I will: (a) describe the properties of the domestication syndrome; (b) show how it can be explained in terms of the operation of a specific genetic regulatory network, that which governs neural crest cell development; and (c) discuss Dmitry Belyaev's idea of “destabilizing selection,” which holds that selecting for a new behavior often entails neuroendocrine alterations that alter many aspects of development. Finally, I will argue for the potential general significance of such destabilizing selection, in combination with developmental bias, in animal evolution.     

Identification and Comparative Analysis of the Protocadherin Cluster in a Reptile,the Green Anole Lizard

Background

The vertebrate protocadherins are a subfamily of cell adhesion molecules that are predominantly expressed in the nervous system and are believed to play an important role in establishing the complex neural network during animal development. Genes encoding these molecules are organized into a cluster in the genome. Comparative analysis of the protocadherin subcluster organization and gene arrangements in different vertebrates has provided interesting insights into the history of vertebrate genome evolution. Among tetrapods, protocadherin clusters have been fully characterized only in mammals. In this study, we report the identification and comparative analysis of the protocadherin cluster in a reptile, the green anole lizard (Anolis carolinensis).

Methodology/Principal Findings

We show that the anole protocadherin cluster spans over a megabase and encodes a total of 71 genes. The number of genes in the anole protocadherin cluster is significantly higher than that in the coelacanth (49 genes) and mammalian (54–59 genes) clusters. The anole protocadherin genes are organized into four subclusters: the δ, α, β and γ. This subcluster organization is identical to that of the coelacanth protocadherin cluster, but differs from the mammalian clusters which lack the δ subcluster. The gene number expansion in the anole protocadherin cluster is largely due to the extensive gene duplication in the γb subgroup. Similar to coelacanth and elephant shark protocadherin genes, the anole protocadherin genes have experienced a low frequency of gene conversion.

Conclusions/Significance

Our results suggest that similar to the protocadherin clusters in other vertebrates, the evolution of anole protocadherin cluster is driven mainly by lineage-specific gene duplications and degeneration. Our analysis also shows that loss of the protocadherin δ subcluster in the mammalian lineage occurred after the divergence of mammals and reptiles. We present a model for the evolutionary history of the protocadherin cluster in tetrapods.     

Hox, ParaHox, ProtoHox: facts and guesses

The Hox gene cluster has captivated the imagination of evolutionary and developmental biologists worldwide. In this review, the origin of the Hox and ParaHox gene clusters by duplication of a ProtoHox gene cluster, and the changes in their gene numbers in major Metazoan Transitions are reviewed critically. Re-evaluation of existing data and recent findings in Cnidarians, Acoels, and critical stages of vertebrate evolution suggest alternative scenarios for the origin, structure, and changes in Hox gene numbers in relevant events of Metazoan evolution. I discuss opposing views and propose that (i) the ProtoHox cluster had only two genes, and not four as commonly believed: a corollary is that the origin of Bilaterians was coincident with the invention of new Hox and ParaHox gene classes, which may have facilitated such a transition; (ii) the ProtoHox cluster duplication was a cis duplication event, rather than a trans duplication event, as previously suggested, and (iii) the ancestral vertebrate cluster possessed 14 Hox genes, and not the 13 generally assumed. These hypotheses could be verified or refuted in the near future, but they may help critical discussion of the evolution of the Hox/ParaHox family in the metazoan kingdom.     

Differentiation of species in the Bacillus brevis group and the Bacillus aneurinolyticus group based on the electrophoretic whole-cell protein pattern

Ninety strains of eleven Bacillus species in the Bacillus brevis group and the Bacillus aneurinolyticus group were compared with the electrophoretic whole-cell protein pattern. The strains were separated into two clusters at the similarity of 55%. One cluster (cluster 1) was consisted of strains from the B. brevis group, and another cluster (cluster 2) was composed of strains from the B. aneurinolyticus group. The cluster 1 was separated into eight subclusters. Out of eight subclusters, seven subclusters contain strains from B. brevis, B. laterosporus, B. agri, B. reuszeri, B. choshinensis, B. formosus, and B. borstelensis. Another subcluster was further separated into two related clusters, which corresponded to B. centrosporus and B. parabrevis, and they were fused at the similarity of 76%. Cluster 2 was separated into two subclusters, which corresponded to B. aneurinolyticus and B. migulanus. The above eleven species showed characteristic patterns distinct from one another, and this correlated well with the published DNA relatedness data. The comparison of the electrophoretic whole-cell protein pattern proved to be useful for evaluation of taxonomic relationships among these taxa.     

Local and global bifurcations at infinity in models of glycolytic oscillations

 We investigate two models of glycolytic oscillations. Each model consists of two coupled nonlinear ordinary differential equations. Both models are found to have a saddle point at infinity and to exhibit a saddle-node bifurcation at infinity, giving rise to a second saddle and a stable node at infinity. Depending on model parameters, a stable limit cycle may blow up to infinite period and amplitude and disappear in the bifurcation, and after the bifurcation, the stable node at infinity then attracts all trajectories. Alternatively, the stable node at infinity may coexist with either a stable sink (not at infinity) or a stable limit cycle. This limit cycle may then disappear in a heteroclinic bifurcation at infinity in which the unstable manifold from one saddle at infinity joins the stable manifold of the other saddle at infinity. These results explain prior reports for one of the models concerning parameter values for which the system does not admit any physical (bounded) behavior. Analytic results on the scaling of amplitude and period close to the bifurcations are obtained and confirmed by numerical computations. Finally, we consider more realistic modified models where all solutions are bounded and show that some of the features stemming from the bifurcations at infinity are still present. Received 4 September 1995; received in revised form 18 September 1996     

Which diameter and angle rule provides optimal flow patterns in a coronary bifurcation?

The branching angle and diameter ratio in epicardial coronary artery bifurcations are two important determinants of atherogenesis. Murray's cubed diameter law and bifurcation angle have been assumed to yield optimal flows through a bifurcation. In contrast, we have recently shown a 7/3 diameter law (HK diameter model), based on minimum energy hypothesis in an entire tree structure. Here, we derive a bifurcation angle rule corresponding to the HK diameter model and critically evaluate the streamline flow through HK and Murray-type bifurcations. The bifurcations from coronary casts were found to obey the HK diameter model and angle rule much more than Murray's model. A finite element model was used to investigate flow patterns for coronary artery bifurcations of various types. The inlet velocity and pressure boundary conditions were measured by ComboWire. Y-bifurcation of Murray type decreased wall shear stress-WSS (10%-40%) and created an increased oscillatory shear index-OSI in atherosclerosis-prone regions as compared with HK-type bifurcations. The HK-type bifurcations were found to have more optimal flow patterns (i.e., higher WSS and lower OSI) than Murray-type bifurcations which have been traditionally believed to be optimized. This study has implications for changes in bifurcation angles and diameters in percutaneous coronary intervention.     

Were there any “misassignments” among iron–sulfur clusters N4, N5 and N6b in NADH-quinone oxidoreductase (complex I)?

NADH-quinone oxidoreductase (complex I) in bovine heart mitochondria has a molecular weight of approximately 1 million Da composed of 45 distinct subunits. It is the largest energy transducing complex so far known. Bacterial complex I is simpler and smaller, but the essential redox components and the basic mechanisms of electron and proton translocation are the same. Over the past three decades, Ohnishi et al. have pursued extensive EPR studies near liquid helium temperatures and characterized most of the iron–sulfur clusters in complex I. Recently, Yakovlev et al. [G. Yakovlev, T. Reda, J. Hirst, Reevaluating the relationship between EPR spectra and enzyme structure for the iron-sulfur clusters in NADH:quinone oxidoreductase, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 12720–12725] challenged Ohnishi's group by claiming that there were EPR “misassignments” among clusters N4, N5 and N6b (in order to prevent confusion, we used current consensus nomenclature, as the nickname). They claimed that we misassigned EPR signals arising from cluster N5 to cluster N4, and signals from cluster N6b to cluster N4. They also proposed that cluster N5 has (4Cys)-ligands. Based on the accumulated historical data and recent results of our site-specific mutagenesis experiments, we confirmed that cluster N5 has (1His + 3Cys)-ligands as we had predicted. We revealed that E. coli cluster N5 signals could be clearly detected at the sample temperature around 3 K with microwave power higher than 5 mW. Thus Hirst's group could not detect N5 signals under any of their EPR conditions, reported in their PNAS paper. It seems that they misassigned the signals from cluster N4 to N5. As to the claim of “misassignment” between clusters N4 and N6b, that was not a possibility because our mutagenesis systems did not contain cluster N6b. Therefore, we believe that we have not made any “misassignment” in our work.     

EVOLUTION AND MORPHOGENETIC RULES: THE SHAPE OF THE VERTEBRATE LIMB IN ONTOGENY AND PHYLOGENY

The notion of a “developmental constraint” has become a catchphrase for a collection of poorly defined notions about how ontogeny affects phylogeny. In this paper, we shall attempt to define this idea more precisely by examining the vertebrate limb from three viewpoints. First, theoretical models of morphogenesis suggest several generalizations about how limb geometry is laid down during development. Comparative studies and experimental manipulations of developing limbs independently confirm these generalizations, which amount to a set of “construction rules” for determining how the major features of limb architecture are established in ontogeny. Armed with these rules, we can inquire how limb morphology can be varied during evolution and suggest a more precise operational definition of “developmental constraints” on morphological evolution.     

Bifurcation control of the Morris–Lecar neuron model via a dynamic state-feedback control

In this paper, we address the control problem of bifurcations in the Morris–Lecar (ML) neuron model. With the use of a dynamic state-feedback control, two Hopf bifurcation points in the ML neuron model with Type II excitability can be relocated to new desired locations simultaneously. Also, with the proposed control law, the neuronal excitability characteristics can be transformed from Type I excitability to Type II excitability by changing the type of bifurcation, in which the neuron goes from quiescence to periodic spiking from a saddle node on an invariant circle bifurcation to a Hopf bifurcation. Simulation results are provided.