Simple diagnostic statistical tests of models for DNA substitution

The accuracy of models for DNA substitution used in phylogenetic analyses is becoming more important with the increasing availability and analysis of molecular sequence data. It is natural to look for ways of improving these models, and to do this in a planned manner it is useful to be able to identify features of sequences that may not be described adequately. In this paper, I describe three statistics which may give useful diagnostic information on departures from models' predictions. The statistical distributions of these statistics are discussed and simple significance tests are derived. These tests are based on the (estimated) phylogeny of the sequences and so have the advantage of using the information contained in this tree. Examples are given of the application of the new tests to Markov chain models describing the evolution of primate pseudogene sequences and small-subunit RNA sequences.Abbreviations b(N,p) binomial distribution of N trials, each with probability p of success - m(N,p ₁,p ₂, ..., p _r ) multinomial distribution of N trials, with r possible outcomes having probabilities p ₁, p ₂, ..., p_r, respectively - N(, ²) Normal distribution with mean and variance ² - p() Poisson distribution with mean - bp base pairs - cdf cumulative distribution function - i.i.d. independent, identical distribution     

WT1 peptide vaccination combined with BCG-CWS is more efficient for tumor eradication than WT1 peptide vaccination alone

A Wilms tumor gene WT1 is expressed at high levels not only in most types of leukemia but also in various types of solid tumors, including lung and breast cancer. WT1 protein has been reported to serve as a target antigen for tumor-specific immunotherapy both in vitro in human systems and in vivo in murine models. We have shown that mice immunized with WT1 peptide or WT1 cDNA could reject a challenge from WT1-expressing tumor cells (a prophylactic model). However, it was not examined whether WT1 peptide vaccination had the potency to reject tumor cells in a therapeutic setting. In the present study, we demonstrated for the first time that WT1 peptide vaccination combined with Mycobacterium bovis bacillus Calmette-Guérin cell wall skeleton (BCG-CWS) was more effective for eradication of WT1-expressing tumor cells that had been implanted into mice before vaccination (a therapeutic model) compared with WT1 peptide vaccination alone. An intradermal injection of BCG-CWS into mice, followed by that of WT1 peptide at the same site on the next day, generated WT1-specific cytotoxic T lymphocytes (CTLs) and led to rejection of WT1-expressing leukemia or lung cancer cells. These results showed that BCG-CWS, which was well known to enhance innate immunity, could enhance WT1-specific immune responses (acquired immunity) in combination with WT1 peptide vaccination. Therefore, WT1 peptide vaccination combined with BCG-CWS may be applied to cancer immunotherapy in clinical settings.H. Nakajima and K. Kawasaki contributed equally to this study.     

Evolutionary origin of the class A and class C β-lactamases

Summary The protein sequences of 18 class A -lactamases and 2 class C -lactamases were analyzed to produce a rooted phylogenetic tree using the DD peptidase of Streptomyces R61 as an outgroup. This tree supports the penicillin-binding proteins as the most likely candidate for the ancestoral origin of the class A and class C -lactamases, these proteins diverging from a common evolutionary origin close to the DD peptidase. The actinomycetes are clearly shown as the origin of the class A -lactamases found in other non-actinomycete species. The tree also divides the -lactamases from the Streptomyces into two subgroups. One subgroup is closer to the DD peptidase root. The other Streptomyces subgroup shares a common branch point with the rest of the class A -lactamases, showing this subgroup as the origin of the non-actinomycete class A -lactamases. The non-actinomycete class A -lactamase phylogenetic tree suggests a spread of these -lactamases by horizontal transfer from the Streptomyces into the non-actinomycete gram-positive bacteria and thence into the gram-negative bacteria. The phylogenetic tree of the Streptomyces class A -lactamases supports the possibility that horizontal transfer of class A -lactamases occurred within the Streptomyces.     

Light adaptation in cone photoreceptors: The occurrence and significance of unitary adaptive strength

The behavior of peak response-log intensity functions generated by the dark glasses model is examined and is shown to describe previously observed light adapted behavior in cone photoreceptors. The models of Boynton and Whitten (1970) and Norman and Werblin (1974) are closely related to the dark glasses model — the Boynton-Whitten model being more specific and the Normann-Werblin model more general. For the models, a certain parameter relationship will produce systems which have optimal intensity discriminative capacities. When the data are fitted, this parameter relationship — unitary adaptive strengh — seems to emerge. Possible evolutionary and psychophysical implications are discussed.     

Testing population genetic structure using parametric bootstrapping and M<Emphasis Type="SmallCaps">IGRATE-N</Emphasis>

We present a method for investigating genetic population structure using sequence data. Our hypothesis states that the parameters most responsible for the formation of genetic structure among different populations are the relative rates of mutation () and migration (M). The evolution of genetic structure among different populations requires rates of M because this allows population-specific mutation to accumulate. Rates of M will result in populations that are effectively panmictic because genetic differentiation will not develop among demes. Our test is implemented by using a parametric bootstrap to create the null distribution of the likelihood of the data having been produced under an appropriate model of sequence evolution and a migration rate sufficient to approximate panmixia. We describe this test, then apply it to mtDNA data from 243 plethodontid salamanders. We are able to reject the null hypothesis of no population structure on all but smallest geographic scales, a result consistent with the apparent lack of migration in Plethodon idahoensis. This approach represents a new method of investigating population structure with haploid DNA, and as such may be particularly useful for preliminary investigation of non-model organisms in which multi-locus nuclear data are not available.     

Asymmetries in population growth regulated by intraspecific competition: Empirical studies and model tests

Summary The linearity assumption in the logistic model of population growth is violated for nearly all organisms. Two simple models, the -logistic and the -Ricker, are shown to account for asymmetric patterns of population growth for 27 species of Drosophila and for a variety of other organisms, where the data were derived from the literature. These models are developed so as to aid laboratory and field ecologists to anticipate the dynamics of various experimental organisms. Potential problems of data gathering and model applications for experimental ecologists and wild life management biologists are identified. Intraspecific asymmetries offer alternative explanations to the habitat selection model, and the higher order interactions or coalitions model, for interspecific competition.     

Large scale preparation of PA-oligosaccharides from glycoproteins using an improved extraction method

We have developed a new method for the large scale preparation of pyridylaminated (PA-) oligosaccharides from glycoproteins. Phenol/chloroform extration was adapted for the removal of protein and excess 2-aminopyridine, improving the efficiency of preparation. From a 2.5 g sample of human apo-transferrin, 25–30 mol of agalacto biantennary PA-oligosaccharide could be obtained. By increasing the concentration of PA-oligosaccharide substrate, we were able to detect a very low level ofN-acetylglucosaminlytransferase IV activity in CHO cell extracts.Abbreviations PA 2-aminopyridine - SDS sodium dodecyl sulfate - GlcNAc N-acetylglucosamine - GnT N-acetylglucosaminyltransferase - Gn,Gn-bi-PA GlcNAc1-2Man1-3(GlcNAc1-2Man1-6)Man1-4GlcNAc1-4GlcNAc-2-aminopyridine - Gn,Gn,Gn-tri-PA GlcNAc1-2(GlcNAc1-4)Man1-3(GlcNAc1-2Man1-6)Man1-4GlcNAc1-4GlcNAc-2-aminopyridine - Gn,Gn,Gn-trí-PA GlcNAc1-2Man1-3({GlcNAc1-2(GlcNAc1-6)Man1-6})Man1-4GlcNac1-4GlcNAc-2-aminopyridine - Gn,(Gn),Gn-bi-PA GlcNAc1-2Man1-3(GlcNAc1-4)(GlcNAc1-2Man1-6)Man1-4GlcNAc1-4GlcNAc-2-aminopyridine     

Notes on the Mechanism of ATP Synthesis

The most commonly quoted mechanism of the coupling between the electrochemical proton gradient and the formation of ATP from ADP and P_i assumes that all states of the F₁ portion of the ATP synthase have subunits in tight, loose, and open conformations. Models based on this assumption are inconsistent with some of the available experimental evidence. A mechanism that includes an additional subunit conformation, closed, observed in the rat liver structure overcomes these difficulties.     

Disease and illness Distinctions between professional and popular ideas of sickness

The dysfunctional consequences of the Cartesian dichotomy have been enhanced by the power of biomedical technology. Technical virtuosity reifies the mechanical model and widens the gap between what patients seek and doctors provide.Patients suffer illnesses; doctors diagnose and treat diseases. Illnesses are experiences of discontinuities in states of being and perceived role performances. Diseases, in the scientific paradigm of modern medicine, are abnormalities in the function and/or structure of body organs and systems. Traditional healers also redefine illness as disease: because they share symbols and metaphors consonant with lay beliefs, their healing rituals are more responsive to the psychosocial context of illness.Psychiatric disorders offer an illuminating perspective on the basic medical dilemma. The paradigms for psychiatric practice include multiple and ostensibly contradictory models: organic, psychodynamic, behavioural and social. This melange of concepts stems from the fact that the fundamental manifestations of psychosis are disordered behaviours. The psychotic patient remains a person; his self-concept and relationships with others are central to the therapeutic encounter, whatever pharmacological adjuncts are employed.The same truths hold for all patients. The social matrix determines when and how the patient seeks what kind of help, his compliance with the recommended regimen and, to a significant extent, the functional outcome. When physicians dismiss illness because ascertainable disease is absent, they fail to meet their socially assigned responsibility. It is essential to reintegrate scientific and social concepts of disease and illness as a basis for a functional system of medical research and care.Harvard Medical School     

The relationships between the structure of paddy levees and the plant species diversity in cultural landscapes on the west side of Lake Biwa,Shiga, Japan

Paddy levees form networks of narrow linear habitats and play various roles in cultural landscapes. Traditional landscapes on the west side of Lake Biwa consist of paddy field terraces and both stone and soil levees that have been maintained by paddy field management using local resources. Paddy levees in this study site are principally classified into five different types. Our study points out how differences in paddy levee structure as well as in management practices influence the plant species. Seventeen paddy levee transects were split into four habitat types based on their species components by TWINSPAN. Spatial characteristics and physical structures of paddy levees depended on natural conditions and human activities. The species–area curves of each levee type showed a clear distinction: the soil, stone and abandoned curves were steep, while the concrete and consolidated ones were gentle. The vegetation on consolidated levees was utterly different from the vegetation on traditional levee types from the aspect of species richness and species components. Soil type levees contained various woody plant species and included more diverse and indigenous plant species than abandoned type levees.     

Hepatic α1 and β adrenergic receptors in various animal species

Summary Plasma membranes were isolated from the livers of various animal species representing the four vertebrate classes: Amphibia, Reptilia, Aves and Mammalia. These liver plasma membranes displayed comparable levels of purity as judged by marker enzyme analysis. The activities of the two marker enzymes, 5-nucleotidase and -glutamyltranspeptidase displayed striking, and quite different, species-dependent differences, with no apparent relationship to phylogeny. ₁ and -adrenergic receptors were characterized in isolated liver plasma membranes by radioligand binding techniques. The hepatic -adrenergic receptor was found to be expressed in all animals studied; the hepatic ₁-adrenergic receptor was absent in Amphibia and Reptilia, co-expressed with the receptor in Aves, and dominant over the receptor in Mammalia. These results suggest that, in liver, the -adrenergic receptor is more primitive while the ₁-adrenergic receptor is of a more recent phylogenetic origin. It is proposed that the latter may have evolved in conjunction with hepatic sympathetic innervation.     

Computational constraints that may have favoured the lamination of sensory cortex

At the transition from early reptilian ancestors to primordial mammals, the areas of sensory cortex that process topographic modalities acquire the laminar structure of isocortex. A prominent step in lamination is granulation, whereby the formerly unique principal layer of pyramidal cells is split by the insertion of a new layer of excitatory, but intrinsic, granule cells, layer IV. I consider the hypothesis that granulation, and the differentiation between supra- and infra-granular pyramidal layers, may be advantageous to support fine topography in their sensory maps. Fine topography implies a generic distinction between where information, explicitly mapped on the cortical sheet, and what information, represented in a distributed fashion as a distinct firing pattern across neurons. These patterns can be stored on recurrent collaterals in the cortex, and such memory can help substantially in the analysis of current sensory input. The simulation of a simplified network model demonstrates that a non-laminated patch of cortex must compromise between transmitting where information or retrieving what information. The simulation of a modified model including differentiation of a granular layer shows a modest but significant quantitative advantage, expressed as a less severe trade-off between what and where. The further connectivity differentiation between infra-granular and supra-granular pyramidal layers is shown to match the mix of what and where information optimal for their respective target structures.     

A model of visual development

There is now abundant evidence that the structure of the mammalian visual cortex is not innately determined but can be altered by visual experiences during a certain period at an early age. A model based on the evidence is proposed that will explain some aspects of the developmental process in the visual cortex. The model self-organizingly forms a simple cell which responds to bars and edges of a certains orientation and retinal position. The total system of the model corresponds to a hyper column which contains a complete cycle of orientational selectiviy. The model has the following three original points. i) A hyper column is finally formed in the model. ii) Most of the cells do not have orientation selectivity in the initial state. iii) It is hypothesized that the orientation continuity of the hyper column is caused by similar orientations of successive input stimuli. The results of computer simulation show that the model has the expected performance.     

Assortative mating and the genetic correlation

Summary The effect of assortative mating on the genetic correlation between traits X and Y is considered. Assortation on trait X changes the magnitude of the genetic correlation but not its sign. There are two situations depending on the signs of the correlation between mates () and of the random mating genetic correlation (): 1) if sign () = sign (), then >, where is the genetic correlation at equilibrium after continued assortation, and 2) if sign () = sign (), then < . However, negative assortative mating is virtually powerless to alter the magnitude of the genetic correlation. The consequences of a mixed assortation model, e.g., high milk production females mated to fast growing males and lesser productive females mated to slower growing sires, were also studied. Mixed positive assortation always increases the genetic correlation, but negative assortation decreases it. The implications of assortative mating on correlated responses to selection and on the equilibrium covariances between relatives for pairs of traits are discussed.     

Regime Shifts in the Sahara and Sahel: Interactions between Ecological and Climatic Systems in Northern Africa

The Sahara and Sahel regions of northern Africa have complex environmental histories punctuated by sudden and dramatic regime shifts in climate and ecological conditions. Here we review the current understanding of the causes and consequences of two environmental regime shifts in the Sahara and Sahel. The first regime shift is the sudden transition from vegetated to desert conditions in the Sahara about 5500 years ago. Geologic data show that wet environmental conditions in this region—giving rise to extensive vegetation, lakes, and wetlands—came to an abrupt end about 5500 years ago. Explanations for climatic changes in northern Africa during the Holocene have suggested that millennial-scale changes in the Earths orbit could have caused the wet conditions that prevailed in the early Holocene and the dry conditions prevalent today. However, the orbital hypothesis, by itself, does not explain the sudden regime shift 5500 years ago. Several modeling studies have proposed that strong, nonlinear feedbacks between vegetation and the atmosphere could amplify the effects of orbital variations and create two alternative stable states (or regimes) in the climate and ecosystems of the Sahara: a green Sahara and a desert Sahara. A recent coupled atmosphere-ocean-land model confirmed that there was a sudden shift from the green Sahara to the desert Sahara regime approximately 5500 years ago. The second regime shift is the onset of a major 30-year drought over the Sahel around 1969. Several lines of evidence have suggested that the interactions between atmosphere and vegetation act to reinforce either a wet Sahel or a dry Sahel climatic regime, which may persist for decades at a time. Recent modeling studies have indicated that the shift from a wet Sahel to a dry Sahel regime was caused by strong feedbacks between the climate and vegetation cover and may have been triggered by slow changes in either land degradation or sea-surface temperatures. Taken together, we conclude that the existence of alternative stable states (or regimes) in the climate and ecosystems of the Sahara and Sahel may be the result of strong, nonlinear interactions between vegetation and the atmosphere. Although the shifts between these regimes occur rapidly, they are made possible by slow, subtle changes in underlying environmental conditions, including slow changes in incoming solar radiation, sea-surface temperatures, or the degree of land degradation.     

Architecture of the Alzheimer’s AβP Ion Channel Pore

We have proposed that the cytotoxic action of Alzheimers amyloid beta protein might be initiated by the interaction with the neuronal cell membrane, and subsequent formation of toxic ion channels. Consequently, AP toxicity can be explained on the basis of harmful ion fluxes across AP channels. The conformation of AP in membranes is not known. However, several models suggests that a transmembrane annular polymeric structure is responsible for the ion channel properties of the membrane-bound AP. To identify that portion of the AP molecule making up the conducting pore we have hypothesized that the region of the AP sequence in the vicinity of the hypothetical pore might interact with complementary regions in the adjacent AP subunits. We have further hypothesized that an interaction by a peptide segment would block AP conductance. To test this hypothesis we synthesized peptides that encompass the histidine dyad (H-H) previously hypothesized to line the pore. We report here that peptides designed to most closely match the proposed pore are, in fact, the most effective at blocking ion currents through the membrane-incorporated AP channel. As previously shown for Zn²⁺ blockade, peptide blockade is also asymmetric. The results also provide additional evidence for the asymmetric insertion of the AP molecules into lipid membranes, and give support to the concept that rings of histidines line the entry to one side of the AP pore.     

Electrophoretic variation between class II molecules expressed on HLA-DRw8 homozygous typing cells reveals multiple distinct haplotypes

Two-dimensional (2D) gel electrophoresis of immunoprecipitated HLA-DR antigens from eight homozygous typing cells (HTC) expressing the HLA-DRw8 specificity revealed a clustering of polymorphic chain patterns into distinct electrophoretic variants. The variant patterns correlate with three discrete HLA-D clusters that are defined in the mixed leukocyte culture reaction (MLR) using DRw8-positive HTC. These HLA-D clusters have been provisionally designated Dw8.1, detected primarily in Caucasoids, Dw8.2, detected primarily in American Indians, and Dw8.3, detected predominantly in Orientals. All three HLA-Dw8.1 cell lines express a single DR-locus product as defined by immunoprecipitation with a DR-specific monoclonal antibody, P4.1. This DR chain is identical among the Dw8.1 cell lines and different from the DR chains of the Dw8.2 and Dw8.3 cell lines. Two separate Dw8.2 HTC express a shared DR chain that is slightly more basic than the 8.1 DR molecule; interestingly, one of these lines also expresses an additional DR-like chain not found in the other cells. Thus, the two lines defining the Dw8.2 cluster share one distinct class 11 molecule, but differ in another and therefore are not biochemically HLA-identical. Cells from the Dw8.3 cluster are likewise distinct from all other Dw8 clusters. One additional DRw8-positive HTC has been analyzed and found to be distinct from the Dw8.1, 8.2 and 8.3 clusters by both MLR and 2D gels. lmmunoprecipitates using monoclonal antibody 1B5 [anti-DR and anti-DQ(DS)] identify additional polymorphic class II variants among the cell lines tested. These data indicate that HLA-DRw8 is a public serologic specificity present on class II molecules expressed on multiple distinct haplotypes. These haplotypes differ from each other in expression of polymorphic class II molecules encoded by at least two HLA loci. They also differ in HLA-D, even though they all type as HLA-DRw8 homozygous. In Dw8.2, variation in expressed chains is not reflected in variation in HLA-D, indicating that MLR, as well as serologic typing, does not detect the full degree of allelic polymorphism within HLA.     

Production of a novel syrup containing neofructo-oligosaccharides by the cells of Penicillium citrinum

A novel syrup containing neofructo-oligosaccharides was produced from sucrose (Brix 70) by whole cells of Penicillium citrinum. The efficiency of fructo-oligosaccharides production was more than 55% and those of the main carbohydrate components, 1-kestose (Fruf 21Fruf 21 Glc), nystose (Fruf 21Fruf 21 Fruf 21 Glc) and neokestose (Fruf 26 Glc12 Fruf), were 22, 14 and 11%, respectively.     

Adoptions expérimentales de larves entre des fourmis de genres différents:Leptothorax nylanderi Förster etSolenopsis fugax Latreille

Résumé En l'absence de son propre couvain,Solenopsis fugax a élevé des larves deLeptothorax nylanderi, à la température de 22°C. Les ouvrières deSolenopsis détruisirent une partie de ces larves mais nourrirent celles qu'elles épargnèrent; ces dernières grossirent lentement pendant cinq à six mois, sans atteindre le stade prénymphe. Lorsque les ouvrières deS. fugax et les larves deL. nylanderi furent soumises ensemble à un hivernage préalable, elles donnèrent les mêmes résultats que sans hivernage. La présence d'une jeune reine deSolenopsis fut défavorable aux larves deLeptothorax.Inversement,L. nylanderi fut capable d'élever, à la température de 22°C, des larves deS. fugax et de les amener jusqu'au stade adulte. En présence de leurs propres larves, les ouvrières deL. nylanderi détruisirent tapidement toutes les larves deS. fugax introduites dans leur nid. D'autre part, un jeune couvain deLeptothorax remplaçait plus ou moins rapidement les larves deLeptothorax enlevées au préalable; sa présence était alors défavorable au développement des larves deSolenopsis. Un hivernage en début d'expérience fut plutôt favorable auxS. fugax, de même que la présence d'une reine féconde deLeptothorax. LesSolenopsis ainsi obtenus n'ont pas vécu plus de sept semaines. Ils étaient tous de caste ouvrière et de taille très petite.

---

Summary When its own eggs and larvae missed,Solenopsis fugax bred larvae ofLeptothorax nylanderi, at a temperature of 22°C. TheSolenopsis workers killed some of this larvae and fed the others; these slowly grew bigger during five or six months but never reached the pre-pupa stage. The result was the same if the workers ofS. fugax and the larvae ofL. nylanderi overwintered together or not at all. A youngSolenopsis queen being there was noxious to the larvae ofLeptothorax.On the contrary,L. nylanderi has been able to breed larvae ofS. fugax up to the imago stage, at a temperature of 22°C. When its own larvae were in the nest, together with larvae ofS. fugax, the workers ofL. nylanderi killed the larvae ofS. fugax. On the other hand, new eggs and young larvae ofLeptothorax had to replace, more or less quickly, the larvae which had been taken away, and that was noxious to the growth ofSolenopsis larvae. An overwintering at the beginning of the experiment was rather favourable toS. fugax as was the presence of a fecundLeptothorax queen. TheSolenopsis thus obtained lived no longer than seven weeks. They all were workers and very small.

---

S. Fugax L. Nylanderi 22° . Leptothorax , , , , . . S. Fugax Leptothorax.,L. Nylanderi 22° S. Fugax . L. Nylanderi ( )Leptothorax ; S. Fugax Solenopsis, Leptothorax. S. Fugax . .

     

Cation permeation at the amphibian motor end-plate

Summary Measurements of acetylcholine-induced single-channel conductance and null potentials at the amphibian motor end-plate in solutions containing Na, K, Li and Cs ions (Gage & Van Helden, 1979;J. Physiol. (London) (in press) were analyzed in terms of three models. Two of these models, the neutral site channel model and the charged site channel model were developed to cater for three cations. Both were shown to be able to explain the dependence of single-channel conductance on membrane potential and gave the following sequences of equilibrium constants and mobilities.K _Li/K _Na/K _K/K _Cs=71.710.9 andu _Cs/u _K/u _Na/u _Li=1.410.580.13 at 8 °C. Similar sequences were obtained at 20 °C. Although the neutral model fitted the data for relative conductances in Li-, Cs-and Na-solutions slightly better than the charged model, experiments done in normal [NaCl] and [NaCl]/2 solutions could only be fitted by the neutral model. In contrast, the third model, the Constant Field Equation, was unable to fit the conductance data in any of the above situations. The data available suggests that permeation is through long neutral channels, lined with high field-strength negative polar groups and including one or possibly more high resistance barriers for anions.