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Physiological variation in insects: large-scale patterns and their implications.

In this paper we demonstrate how broad scale comparative physiology has an important role to play in informing a variety of assumptions made in macroecology. We do so by examining large-scale geographic variation in insect development, thermal tolerance and metabolic rate. From these studies, and those from the literature on insect water loss and thermoregulation, we show that there is often a bias to the geographic extent of available empirical data. Studies of cold hardiness are most usually undertaken at high latitudes, while investigations of upper thermal tolerances and water loss are most common in warm arid regions. Likewise, we demonstrate that much variation in insect physiological tolerances is partitioned at higher taxonomic levels, which has important implications for comparative physiology. Intriguingly, data on the full range of variables we review are available for only three species. We also show that, despite its importance, body size is regularly reported in only some kinds of investigations (metabolic rate, water loss rate), whereas in others (upper lethal temperature, cold hardiness, development) this variable is often ignored. In short, although large-scale comparative physiology can contribute considerable understanding to both physiology and ecology, there is much that remains to be done.

Animals↗

Phylogenetic taxonomy of Leishmania (Viannia) braziliensis based on isoenzymatic study of 137 isolates.

Biochemical characterization of 137 Leishmania braziliensis isolates from South and Central America, and from selected endemic foci in Bolivia, Brazil and Colombia, performed by isoenzymatic electrophoresis using 10 enzymatic systems, showed a high enzymatic polymorphism (44 zymodemes obtained) based on the variation of a small number of enzymes. Cladistic analysis showed close links between the zymodemes within the L. braziliensis s.s. cluster. The position of 2 Colombian zymodemes obtained (MON*204 and MON*205) justify the inclusion of L. peruviana within the L. braziliensis cluster.

Americas↗

[Genetic diagnosis of acute leukemias--a practical guide].

Acute leukemias are the consequence of accumulation of immature precursor cells. Genetic alterations are cause of uncontrolled cell proliferation. They can be detected by conventional cytogenetics and molecular methods at diagnosis. Classification of acute leukemias according to the World Health Organization depend on the knowledge of the presence of these aberrations. Furthemore they are important prognostic parameters influencing therapy intensity. Genetic abnormalities can be targets of novel therapeutic strategies. Detection and monitoring of genetic abnormalities in acute leukemias are of major importance for correct management of patients.

Acute Disease↗

A new look at dietary carbohydrate: chemistry, physiology and health. Paris Carbohydrate Group.

The current view of dietary carbohydrates as simply providing us with energy is outdated. Because of their varied chemistry and physical form the rate and extent to which the different types are digested in and absorbed from the small intestine varies. This in turn leads to affects on satiety, blood glucose and insulin, protein glycosylation, lipids and bile acids. Some carbohydrates reach the colon where they are fermented and affect many aspects of large bowel function, colonocyte and hepatic metabolism. A new framework for classifying and measuring food carbohydrates is needed to allow a greater understanding of the role of individual species in health and to inform the public of their importance. A classification based primarily on molecular size (degree of polymerisation) into sugars, oligosaccharides and polysaccharides, is suggested, with sub-groups identified by the nature of the monosaccharides. Greater knowledge of the chemical and physical properties of carbohydrates allow a more precise relation with physiology and health to be drawn. The Carbohydrate Group met in Paris in December 1995 at the invitation of Gerard Pascal, Director of CNERNA. Financial support for the meeting was provided by CNERNA.

Carbohydrates↗

T-cell receptor gene rearrangements as markers of lineage and clonality in T-cell neoplasms.

Ig gene rearrangements represent markers of lineage, clonality, and differentiation of B cells, allowing a molecular diagnosis and immunogenotypic classification of B-cell neoplasms. We sought to apply a similar approach to the study of T-cell populations by analyzing rearrangements of the T-cell receptor beta-chain (T beta) gene. Our analysis, by Southern blotting hybridization using T beta-specific probes of DNAs from polyclonal T cells and from 12 T-cell tumors, indicates that T beta gene rearrangement patterns can be used as markers of (i) lineage, allowing the identification of polyclonal T-cell populations, and (ii) clonality, allowing the detection of monoclonal T-cell tumors. In addition, our data indicate that T beta gene rearrangements represent early and general markers of T-cell differentiation since they are detectable in histologically different tumors at all stages of T-cell development. The ability to determine lineage, clonality, and stage of differentiation has significant implications for future experimental and clinical studies on normal and neoplastic T cells.

Cell Differentiation↗

Classification of environmental pollutants for global mobility potential.

The environmental behaviour of global organic contaminants is known to be controlled by the physico-chemical properties of the compounds themselves. The principal component analysis of some physico-chemical properties, particularly relevant in determining mobility potential (vapour pressure, Henry's law constant, water solubility, K(OW), K(OA) and melting point) allows a multivariate approach to a ranking of organic pollutants according to their intrinsic tendency towards mobility, and the definition of four a priori mobility classes for screening purposes. Quantitative structure-property relationships (QSPRs) were used to predict missing values for octanol/air partition coefficients. Finally, a classification method employing theoretical molecular descriptors was used to assign studied chemicals to four mobility classes. The proposed approach assesses, directly and simply, a pollutant's inherent tendency towards mobility using only knowledge of the pollutant's molecular structure; the approach is particularly useful for a preliminary screening and the prioritisation of organic pollutants of emerging environmental concern.

Air Movements↗

Bayesian estimation of ancestral character states on phylogenies.

Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors.

Animals↗

Biogeographic interpretation of splits graphs: least squares optimization of branch lengths.

Although most often used to represent phylogenetic uncertainty, network methods are also potentially useful for describing the phylogenetic complexity expected to characterize recent species radiations. One network method with particular advantages in this context is split decomposition. However, in its standard implementation this approach is limited by a conservative criterion for branch length estimation. Here we extend the utility of split decomposition by introducing a least squares optimization technique for correcting branch lengths that may be underestimated by the standard implementation. This optimization of branch lengths is generally expected to improve divergence time estimates calculated from splits graphs. We illustrate the effect of least squares optimization on such estimates using the Australasian Myosotis and the Hawaiian silversword alliance as examples. We also discuss the biogeographic interpretation and limitations of splits graphs.

Boraginaceae↗

Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods.

Many phylogenetic methods produce large collections of trees as opposed to a single tree, which allows the exploration of support for various evolutionary hypotheses. However, to be useful, the information contained in large collections of trees should be summarized; frequently this is achieved by constructing a consensus tree. Consensus trees display only those signals that are present in a large proportion of the trees. However, by their very nature consensus trees require that any conflicts between the trees are necessarily disregarded. We present a method that extends the notion of consensus trees to allow the visualization of conflicting hypotheses in a consensus network. We demonstrate the utility of this method in highlighting differences amongst maximum likelihood bootstrap values and Bayesian posterior probabilities in the placental mammal phylogeny, and also in comparing the phylogenetic signal contained in amino acid versus nucleotide characters for hexapod monophyly.

Algorithms↗

Phylogenetic relationships in Bupleurum (apiaceae) based on nuclear ribosomal DNA its sequence data.

BACKGROUND AND AIMS: The genus Bupleurum has long been recognized as a natural group, but its infrageneric classification is controversial and has not yet been studied in the light of sequence data. METHODS: Phylogenetic relationships among 32 species (35 taxa) of the genus Bupleurum were investigated by comparative sequencing of the ITS region of the 18-26S nuclear ribosomal DNA repeat. Exemplar taxa from all currently accepted sections and subsections of the genus were included, along with outgroups from four other early branching Apioideae genera (Anginon, Heteromorpha, Physospermum and Pleurospermum). RESULTS: Phylogenies generated by maximum parsimony, maximum likelihood, and neighbour-joining methods show similar topologies, demonstrating monophyly of Bupleurum and the division of the genus into two major clades. This division is also supported by analysis of the 5.8S coding sequence alone. The first branching clade is formed by all the species of the genus with pinnate-reticulate veined leaves and B. rigidum with a unique type of leaf venation. The other major clade includes the remaining species studied, all of which have more or less parallel-veined leaves. CONCLUSIONS: These phylogenetic results do not agree with any previous classifications of the genus. Molecular data also suggest that the endemic Macaronesian species B. salicifolium is a neoendemic, as the sequence divergence between the populations in Madeira and Canary Islands, and closer mainland relatives in north-west Africa is small. All endemic north-west African taxa are included in a single unresolved but well-supported clade, and the low nucleotide variation of ITS suggests a recent radiation within this group. The only southern hemisphere species, B. mundii (southern Africa), is shown to be a neoendemic, apparently closely related to B. falcatum, a Eurasian species.

Bupleurum↗

IGCN: integrative graph convolution networks for patient level insights and biomarker discovery in multi-omics integration.

MOTIVATION: Developing computational tools for integrative analysis across multiple types of omics data has been of immense importance in cancer molecular biology and precision medicine research. While recent advancements have yielded integrative prediction solutions for multi-omics data, these methods lack a comprehensive and cohesive understanding of the rationale behind their specific predictions. To shed light on personalized medicine and unravel previously unknown characteristics within integrative analysis of multi-omics data, we introduce a novel integrative neural network approach for cancer molecular subtype and biomedical classification applications, named Integrative Graph Convolutional Networks (IGCN). RESULTS: To demonstrate the superiority of IGCN, we compare its performance with other state-of-the-art approaches across different cancer subtype and biomedical classification tasks. Our experimental results show that our proposed model outperforms the state-of-the-art and baseline methods. IGCN identifies which types of omics data receive more emphasis for each patient when predicting a specific class. Additionally, IGCN has the capability to pinpoint significant biomarkers from a range of omics data types. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/bozdaglab/IGCN.

Humans↗

Cigarette smoking and risk of acute leukemia: associations with morphology and cytogenetic abnormalities in bone marrow.

BACKGROUND: Cigarette smoking may be a risk factor for leukemia. No detailed biological mechanism has been proposed, but a causal link is made plausible by evidence of systemic effects of cigarette smoke and the presence in cigarette smoke of chemicals that have been associated with leukemia risk. PURPOSE: Our purpose was to investigate the leukemia risk associated with cigarette smoking in a multicenter case-control study of acute leukemias in adults. METHODS: Adults aged 18-79 with newly diagnosed leukemia were contacted to participate in this epidemiologic study when they entered a clinical trial to be treated under protocols sponsored by Cancer and Leukemia Group B. Smoking histories for 610 patients with acute leukemia and 618 population control subjects were obtained by telephone interviews. We examined bone marrow samples and classified patients by morphology of leukocyte precursor cells according to the French-American-British (FAB) classification system and, for 378 patients, by the presence or absence of specific clonal chromosome abnormalities. We calculated odds ratios (ORs) for risk of leukemia associated with smoking cigarettes. ORs were adjusted for age, race, and sex. RESULTS: Smoking was associated with only a modest increase in risk for leukemia overall (adjusted OR = 1.13; 95% confidence interval [CI] = 0.89-1.44). However, among participants aged 60 and older, smoking was associated with a twofold increase in risk for acute myeloid leukemia (AML) (OR = 1.96; 95% CI = 1.17-3.28) and a threefold increase in risk for acute lymphocytic leukemia (ALL) (OR = 3.40; 95% CI = 0.97-11.9). Among older persons, risks increased with amount and duration of smoking. Smoking was associated with increased risk for AML classified as FAB type M2 at all ages, with ORs of 1.70 (95% CI = 1.00-2.90) for those younger than 60 and 3.50 (95% CI = 1.53-8.03) for those aged 60 and older. Smoking was also associated with ALL type L2 at all ages, with ORs of 1.72 (95% CI = 0.90-3.27) for those younger than 60 and 5.34 (95% CI = 1.03-27.6) for those who were older. Smoking was more common among patients with specific chromosome abnormalities in AML [-7 or 7q-, -Y, +13] and in ALL [t(9;22)(q34;q11)]. CONCLUSIONS: Cigarette smoking is associated with increased risk for leukemia and may lead to leukemias of specific morphologic and chromosomal types. The association varies with age. IMPLICATION: Examining discrete subtypes of disease may permit more accurate assessment of risk. As standardized morphologic classification and cytogenetic and molecular evaluation of leukemia patients becomes more common, epidemiologic studies that take advantage of these advances will begin to contribute to the identification of additional risk factors and mechanisms in acute leukemia.

Acute Disease↗

Loss of imprinting of insulin-like growth factor-II (IGF2) gene in distinguishing specific biologic subtypes of Wilms tumor.

BACKGROUND: Loss of imprinting (LOI) of the insulin-like growth factor-II (IGF2) gene, an epigenetic alteration associated with expression of the normally silent maternal allele, was observed first in Wilms tumor. Although LOI has subsequently been detected in most adult tumors, the biologic role of LOI in cancer remains obscure. We analyzed the imprinting status of Wilms tumors with respect to pathologic subtype, stage, and patient's age at diagnosis and examined the expression of genes potentially affected by LOI. METHODS: Of 60 Wilms tumors examined, 25 were informative for an ApaI polymorphism in the IGF2 gene, allowing analysis of allele-specific gene expression, and could be classified by pathologic subtype. Gene expression was measured quantitatively by real-time polymerase chain reaction, and pathologic analysis was blinded for genetic status. All statistical tests were two-sided. RESULTS: We observed LOI of IGF2 in nine (90%) of 10 Wilms tumors classified as having a pathologic subtype associated with a later stage of renal development and in only one (6.7%) of 15 Wilms tumors with a pathologic subtype associated with an earlier stage of renal development (P< .001). LOI was associated with a 2.2-fold increase (95% confidence interval [CI] = 1.6-fold to 3.1-fold) in IGF2 expression (P< .001). Children whose Wilms tumors displayed LOI of IGF2 were statistically significantly older at diagnosis (median = 65 months; interquartile range [IQR] = 47-83 months) than children whose tumors displayed normal imprinting (median = 24 months; IQR = 13-35 months; P< .001). CONCLUSIONS: These data demonstrate a clear relationship between LOI and altered expression of IGF2 in Wilms tumors and provide a molecular basis for understanding the divergent pathogenesis of this cancer. Analysis of LOI could provide a valuable molecular tool for the classification of Wilms tumor.

Age of Onset↗

Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?

A recent phylogenomic study reported that the animal phylogeny was unresolved despite the use of 50 genes. This lack of resolution was interpreted as "a positive signature of closely spaced cladogenetic events." Here, we propose that this lack of resolution is rather due to the mutual cancellation of the phylogenetic signal (historical) and the nonphylogenetic signal (due to systematic errors) that results from inadequate taxon sampling and/or model of sequence evolution. Starting with a data set of comparable size, we use 3 different strategies to reduce the nonphylogenetic signal: 1) increasing the number of species; 2) replacing a fast-evolving species by a slowly evolving one; and 3) using a better model of sequence evolution. In all cases, the phylogenetic resolution is markedly improved, in agreement with our hypothesis that the originally reported lack of resolution was artifactual.

Algorithms↗