Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications

Tobamoviruses, mostly isolated from solanaceous plants, may represent ancient virus lineages that have codiverged with their hosts. Recently completed nucleotide sequences of six nonsolanaceous tobamoviruses allowed assessment of the codivergence hypothesis and support a third subgroup within tobamoviruses. The genomic sequences of 12 tobamoviruses and the partial sequences of 11 others have been analyzed. Comparisons of the predicted protein sequences revealed three clusters of tobamoviruses, corresponding to those infecting solanaceous species (subgroup 1), those infecting cucurbits and legumes (subgroup 2), and those infecting crucifers. The orchid-infecting odontoglossum ringspot tobamovirus was associated with subgroup 1 genomes by its coat and movement protein sequences, but with the crucifer-pathogenic tobamoviruses by the remainder of its genome, suggesting that it is the progeny of a recombinant. For four of five genomic regions, subgroup 1 and 3 genomes were equidistant from a subgroup 2 genome chosen for comparison, suggesting uniform rates of evolution. A phylogenetic tree of plant families based on the tobamoviruses they harbor was congruent with that based on rubisco sequences but had a different root, suggesting that codivergence was tempered by rare events of viruses of one family colonizing another family. The proposed subgroup 3 viruses probably have an origin of virion assembly in the movement protein gene, a large (25-codon) overlap of movement and coat protein open reading frames, and a comparably shorter genome. Codon-position-dependent base compositions and codon prevalences suggested that the coat protein frame of the overlap region was ancestral. Bootstrapped parsimony analysis of the nucleotides in the overlap region and of the sequences translated from the -1 frame (the subgroup 3 movement protein frame) of this region produced trees inconsistent with those deduced from other regions. The results are consistent with a model in which a no or short overlap organization was ancestral. Despite encoding of subgroup 2 and 3 movement protein C-termini by nonhomologous nucleotides, weak similarities between their amino acid sequences suggested convergent sequence evolution.     

Translocations of acrocentric chromosomes and their implications in the evolution of sheep (Ovis)

Cytogenetic evidence suggests that the caprids (sheep and goats) evolved from a common ancestor with a 2n=60 karyotype. Although goats (Capra) retained the primitive 2n=60 karyotype, sheep (Ovis) underwent a sequential reduction in the number of chromosomes by means of acrocentric translocation. The formation of the first metacentric autosome (M1) occurred in the aoudad (Ammotragus) and urial (O. vignei), resulting in a 2n=58 karyotype. The G-bands are homologous, which implies both genotypes arose from a common ancestor, possibly a rupicaprid. Based on G-bands, acrocentric chromosomes 1 and 7 of the 2n=60 karyotype formed the M1. The X chromosome, which is the second longest acrocentric in the 2n=60 karyotype, became the longest acrocentric in Ammotragus and Ovis (2n=58). The second pair of metacentrics to evolve, which is ranked in the M3 position of the 2n=54 karotype, resulted from the translocations of acrocentric chromosomes 4 and 14 or 15 in the 2n=60 karyotype. The M2 was the third pair of metacentrics to be formed and resulted from the translocations of acrocentric chromosomes 3 and 12 or 13 in the 2n=60 karyotype. The G-bands of all 2n=54 karyotypes are homologous, which indicates origin from a common ancestor. Evidence is presented that suggests a prezygotic selection is bringing about a reduction in diploid chromosome numbers. The possible roles of fission and fusion in the karyotypic evolution of Ovis are discussed.     

An upper dentition of Aframonius dieides (Primates) from the Fayum, Egyptian Eocene

The first known upper dentitions--an adult and subadult--of the cercamoniine adapiform Aframonius dieides are described. Comparisons show that A. dieides has an upper molar morphology resembling that of other cercamoniine adapids but the species lacks some of their typical specializations. The new dental material confirms that Aframonius stands closer to Mahgarita from west Texas and Cercamonius from Europe than it does to Schizarodon and Omanodon from Oman-all of which have been ranked as cercamoniines. Affinities of the latter two genera probably lie with the Anchomomys group. The presence of a cercamoniine adapid in the Eocene of Egypt supports the view that early African anthropoideans evolved not in isolation, but concomitantly with a contemporary Eocene prosimian radiation.     

Tripartite model of anxiety and depression: Psychometric evidence and taxonomic implications.

Reviews psychometric and other evidence relevant to mixed anxiety-depression. Properties of anxiety and depression measures, including the convergent and discriminant validity of self- and clinical ratings, and interrater reliability, are examined in patient and normal samples. Results suggest that anxiety and depression can be reliably and validly assessed; moreover, although these disorders share a substantial component of general affective distress, they can be differentiated on the basis of factors specific to each syndrome. L. A. Clark and D. Watson also review evidence for these specific factors, examining the influence of context and scale content on ratings, factor analytic studies, and the role of low positive affect in depression. With these data, Clark and Watson argue for a tripartite structure consisting of general distress, physiological hyperarousal (specific anxiety), and anhedonia (specific depression), and they propose a diagnosis of mixed anxiety-depression. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

T lymphocytes and their cytokines in human immunodeficiency virus (HIV) infection: implications for associated neoplasias

Infection with the human immunodeficiency virus (HIV) results in gradual immunosuppression due to the loss of CD4+ T cells. In the wake of immune system breakdown, infected individuals may acquire multiple opportunistic infections and develop certain malignancies which ultimately account for the vast majority of deaths in these persons. A limited number of malignancies are directly associated with HIV infection and suggest a common tie between these tumors. Inappropriate immune surveillance resulting in insufficient inhibition of virus replication and inadequate control of the growth of transformed cells may contribute to the development of malignancies in HIV-infected individuals. Alternatively, malignancies in HIV infection may be the consequence of immune dysregulation. Cellular immune responses mediated by antigen-specific cytotoxic T lymphocytes (CTL) are of particular importance for immunologic control of viral infections and substantial information has been gathered about theses cells in HIV infection. The goal of this review is therefore to summarize recent findings regarding the cellular immune response to HIV with a particular focus on cytokines released by HIV-specific CTL.     

Daily smoking patterns, their determinants, and implications for quitting.

In this article, the authors examine daily temporal patterns of smoking in relation to environmental restrictions on smoking and cessation outcomes. Time-series methods were used for analyzing cycles in 351 smokers who monitored their smoking in real time for 2 weeks. The waking day was divided into 8 "bins" of approximately 2 hr, cigarette counts were tallied for each bin, and temporal patterns of smoking and restriction were analyzed. Cluster analyses of smoking patterns by time of day resulted in 4 clusters: daily decline (n = 30; 9%), morning high (n = 43; 12%), flatline (n = 247; 70%), and daily dip-evening incline (n = 31; 9%). Clusters differed in baseline demographic, smoking, and psychosocial variables. Results suggest that smoking behavior can be characterized by regular patterns of smoking frequency during the waking day: Smoking in the flatline cluster was within ±0.5 standard deviation at all times. For the other clusters, smoking was high in the morning (daily dip-evening incline: +1.7 standard deviations; morning high: +2.8 standard deviations; daily decline: +1.7 standard deviations); moderate (morning high: -0.8 standard deviations; daily decline: +0.3 standard deviations) or low (daily dip-evening incline: -1.0 standard deviations) midday; and high (daily dip-evening incline: +2.0 standard deviations), moderate (morning high: +0.5 standard deviations), or low (daily decline: -1.5 standard deviations) in the evening. Daily smoking patterns were related to environmental smoking restrictions, but the strength of this relationship differed among clusters and by time of day. Clusters differed in lapse risk. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Restoration of the type and palate of Ankarapithecus meteai: taxonomic and phylogenetic implications

A small number of large hominoid specimens are known from the late Miocene of Turkey. (This paper focuses on the two specimens known until 1996. New fossils described by Alpagut et al. ([1996] Nature 382:349-351) are briefly discussed in this paper as well.) Among these, a fragmentary mandible is the type specimen of Ankarapithecus meteai. Another specimen, a partial face, is from the same taxon. Based on the morphology of this face, Ankarapithecus meteai was synonymized with Sivapithecus (Andrews and Tekkaya [1980], Paleontology 23:85-95). The facial specimen was recently restored by the authors, exposing much anatomy that had previously been obscured. The new anatomical details reveal many important differences from Sivapithecus and justify a revision of the nomen Ankarapithecus. Ankarapithecus was a large hominid (great apes and humans) in the clade that also includes Sivapithecus and Pongo. Sivapithecus and Pongo share derived characters not found in Ankarapithecus, which is thus the sister clade to the Sivapithecus-Pongo clade. While the results of this analysis support the sister relationship of Sivapithecus and Pongo, there is some uncertainty regarding paleobiogeographic and taxonomic relationships to the large hominids from the Siwaliks. An Ankarapithecus-like taxon may have been ancestral to Sivapithecus, or an early Siwalik (Chinji formation) taxon, which predates both Sivapithecus sensu stricto and Ankarapithecus, may be ancestral to both.     

Nuclear gene trees and the phylogenetic relationships of the mangabeys (Primates: Papionini)

Phylogenetic relationships of mangabeys within the Old World monkey tribe Papionini are inferred from analyses of nuclear DNA sequences from five unlinked loci. The following conclusions are strongly supported, based on congruence among trees derived for the five separate gene regions: (1) mangabeys are polyphyletic within the Papionini; (2) Cercocebus is the sister taxon to the genus Mandrillus; and (3) Lophocebus belongs to a clade with Papio and Theropithecus, with Papio as its most likely sister taxon. Morphologically based phylogenies positing mangabey monophyly were evaluated by mapping the sequences for each locus on these trees. The data seem to fit these trees poorly in both maximum-parsimony and likelihood analyses. Incongruence among nuclear gene trees occurred in the interrelationships among Lophocebus, Papio, and Theropithecus. Several factors that may account for this incongruence are discussed, including sampling error, random lineage sorting, and introgression.     

Molecular phylogeny of the New World monkeys (Platyrrhini, primates) based on two unlinked nuclear genes: IRBP intron 1 and epsilon-globin sequences

Nuclear sequences of the 1.8 kilobase (kb) long intron 1 of the interstitial retinol-binding protein gene (IRBP), previously determined for 11 of the 16 extant genera of New World monkeys (superfamily Ceboidea, infraorder Platyrrhini), have now been determined for the remaining 5 genera. The maximum parsimony trees found, first with IRBP sequences alone and then with tandemly combined IRBP and epsilon-globin gene sequences from the same species, supported a provisional cladistic classification with the following clusters. Subtribes Callitrichina (Callithrix, Cebuella), Callimiconina (Callimico), Leontopithecina (Leontopithecus) and Saguina (Saguinus) constitute subfamily Callitrichinae, and subfamilies Callitrichinae, Aotinae (Aotus), and Cebinae (Cebus, Saimiri) constitute family Cebidae. Subtribes Chiropotina (Chiropotes, Cacajao) and Pitheciina (Pithecia) constitute tribe Pitheciini; and tribes Pitheciini and Callicebini (Callicebus) constitute subfamily Pitheciinae. Subtribes Brachytelina (Brachyteles, Lagothrix) and Atelina (Ateles) constitute tribe Atelini, and tribes Atelini and Alouattini (Alouatta) constitute subfamily Atelinae. The parsimony results were equivocal as to whether Pitheciinae should be grouped with Atelinae in family Atelidae or have its own family Pitheciidae. The cladistic groupings of extant ceboids were also examined by different stochastic evolutionary models that employed the same stochastic process of nucleotide substitutions but alternative putative phylogenetic trees on which the nucleotide substitutions occurred. Each model, i.e., each different tree, predicted a different multinomial distribution of nucleotide character patterns for the contemporary sequences. The predicted distributions that were closest to the actual observed distributions identified the best fitting trees. The cladistic relationships depicted in these best fitting trees agreed in almost all cases with those depicted in the maximum parsimony trees.     

Biochemical polymorphisms in wild rats (Rattus norvegicus) captured in Oita city, Japan

The investigation of biochemical markers in wild rats (Rattus norvegicus) is thought to be useful in the efficient establishment of inbred strains with a wide range of genetic variability of wild rats. In this study, 21 marker proteins were analyzed by electrophoresis in nine wild rats captured in Oita city. It was found that eleven marker samples in six animals were heterogeneous. We further found that the investigated wild rat population possessed the interesting polymorphisms of esterase-4 (ES-4) with high frequency, which are very rare in laboratory rats.     

Social class, political power, and the state: their implications in medicine--part III

This is the third part of an article on the distribution of power and the nature of the state in Western industrialized societies and their implications in medicine. Parts I and II were published in the preceding issue of this Journal. Part I presented a critique of contemporary theories of the Western system of power; discussed the countervailing pluralist and power of elite theories, as well as those of bureaucratic and professional control; and concluded with an examination of the Marxist theories of economic determinism, structural determinism, and corporate statism. Part II presented a Marxist theory of the role, nature, and characteristics of state intervention. Part III focuses on the mode of that intervention and the reasons for its growth, with an added analysis of the attributes of state intervention in the health sector, and of the dialectical relationship between its growth and the current fiscal crisis of the state. In all three parts, the focus is on Western European countries and on North America, with many examples and categories from the area of medicine.     

Mortality invariants and their genetic implications

Old noninbred fly mortality decreases according to the inverse linear law and reduces to a single suborder-specific age. Relative child mortality (the mortality at a given age related to the mortality at 10 years) from 1 mo to 11 years is the same with 8% mean accuracy for all humans, independent of race, country, sex, and birth year (from 1780 to 1995), in contrast to birth mortality, which in developed countries changed fiftyfold during the last century. The concept of invariants, which is very powerful in physics, is applied to mortality of species as remote as humans and flies. It provides quantitative estimates for the selection of hereditary Methuselahs, who live, e.g., over six-mean lifespans and who may be relatively young biologically. It also demonstrates that old fly and relative child mortality are determined genetically and that the former is related to genetic heterogeneity.     

Manganese superoxide dismutase (MnSOD) genetic polymorphisms, dietary antioxidants, and risk of breast cancer

Oxidative stress, resulting from the imbalance between prooxidant and antioxidant states, damages DNA, proteins, cell membranes, and mitochondria and seems to play a role in human breast carcinogenesis. Dietary sources of antioxidants (chemical) and endogenous antioxidants (enzymatic), including the polymorphic manganese superoxide dismutase (MnSOD), can act to reduce the load of oxidative stress. We hypothesized that the valine-to-alanine substitution that seems to alter transport of the enzyme into the mitochondrion, changing its efficacy in fighting oxidative stress, was associated with breast cancer risk and that a diet rich in sources of antioxidants could ameliorate the effects on risk. Data were collected in a case-control study of diet and breast cancer in western New York from 1986 to 1991. Caucasian women with incident, primary, histologically confirmed breast cancer were frequency-matched on age and county of residence to community controls. Blood specimens were collected and processed from a subset of participants in the study (266 cases and 295 controls). Using a RFLP that distinguishes a valine (V) to alanine (A) change in the -9 position in the signal sequence of the protein for MnSOD, we characterized MnSOD genotypes in relation to breast cancer risk. We also evaluated the effect of the polymorphism on risk among low and high consumers of fruits and vegetables. Premenopausal women who were homozygous for the A allele had a 4-fold increase in breast cancer risk in comparison to those with 1 or 2 V alleles (odds ratio, 4.3; 95% confidence interval, 1.7-10.8). Risk was most pronounced among women below the median consumption of fruits and vegetables and of dietary ascorbic acid and alpha-tocopherol, with little increased risk for those with diets rich in these foods. Relationships were weaker among postmenopausal women, although the MnSOD AA genotype was associated with an almost 2-fold increase in risk (odds ratio, 1.8; confidence interval, 0.9-3.6). No appreciable modification of risk by diet was detected for these older women. These data support the hypothesis that MnSOD and oxidative stress play a significant role in breast cancer risk, particularly in premenopausal women. The finding that risk was greatest among women who consumed lower amounts of dietary antioxidants and was minimal among high consumers indicates that a diet rich in sources of antioxidants may minimize the deleterious effects of the MnSOD polymorphism, thereby supporting public health recommendations for the consumption of diets rich in fruits and vegetables as a preventive measure against cancer.     

西藏甲玛过铝质花岗岩的地球化学特征及成因意义

探讨了西藏甲玛中新世花岗斑岩的地球化学特征及意义.通过对岩体(脉)进行的野外地质调查、岩相学研究、全岩地球化学分析及同位素分析,结果表明甲玛花岗斑岩表现过铝质花岗岩的特征,整体表现为:Na2O/K2O<1,A/CNK>1.1,刚玉标准分子(w(C-norm))>1%;轻稀土元素富集,重稀土元素亏损,负Eu、Ce异常不明显,高Sr,低Y、Yb,但Sr/Y值相对较低,不具有埃达克岩的地球化学特征;此外,富集大离子亲石元素,尤其是Rb、Cs、Th、U、K等元素,而高场强元素,尤其是Sc、Ti则强烈亏损;Pb-Sr-Nd同位素均显示其下地壳的物质来源,并受到地幔物质(EMⅡ)的混染.甲玛过铝质花岗斑岩形成于亚洲-印度大陆"后碰撞"造山运动早期阶段的构造活动.