Determinants of expression variability

The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.     

Morphogenia: a new genus of the Neotropical tribe Jubini (Coleoptera,Staphylinidae, Pselaphinae) from the Brazilian Amazon

A new genus and species of the large Neotropical pselaphine tribe Jubini is described from Manaus, Brazil, based on material preserved in the Natural History Museum, London. Morphogenia struhli gen. et sp. n. represents the possible sister taxon of the abundant and speciose genus Barrojuba Park, sharing with it the putatively derived condition of anterolaterally shifted vertexal foveae, producing a smoothly convex vertex devoid of fovea or sulci. However, unlike Barrojuba, Morphogenia retains a plesiomorphic antebasal sulcus on the pronotum in both sexes, and additionally lacks elaborate abdominal fovea-like pockets and teeth on the lateral margins of the pronotum that are typical of Barrojuba. The genus is also unusual among jubine genera in lacking the characteristic V- or Y-shaped gular carina. In contrast to the commonly-collected Barrojuba, specimens of Morphogenia are absent in extensive jubine collections housed in museums in the United States, indicating that the new taxon may be relatively scarce or localised.     

Subunit composition of a high molecular weight oligomer: Limulus polyphemus hemocyanin

The hemocyanin of Limulus polyphemus is a 48-subunit aggregate. This 3.3 × 10⁶-dalton oligomer is composed of structurally and functionally heterogeneous subunits. Using polyacrylamide electrophoresis J. Markl, A. Markl, W. Schartau, and B. Linzen (J. Comp. Physiol. Ser. B130,283–292, 1979) observed 12 bands; while using immunoelectrophoresis, M. Hoylaerts, G. Preaux, R. Witters, and R. Lontie (Arch. Int. Physiol. Biochem.87, 417–418, 1979) and J. Lamy, J. Lamy, J. Weill, J. Bonaventura, C. Bonaventura, and M. Brenowitz. (Arch. Biochem. Biophys.196, 324–339, 1979) observed 8 subunits. To proceed with an analysis of subunit roles in assembly it is first necessary to determine the number of distinct subunits. Refinement of the chromatographic separation procedures has led to the isolation of 8 immunologically distinct subunits as well as additional charge isomers which cannot be distinguished immunologically. Alkaline electrophoresis revealed 15 bands and isoelectric focusing up to 17. On the basis of extensive control experiments, including composit acrylamide-agarose immunoelectrophoresis and checks for conformational isomers, aggregation, proteolysis, and other types of degradation, we conclude that the electrophoretic heterogeneity of immunologically identical subunits is not artifactual. We have extended the nomenclature used by Lamy et al. (1979) to include the electrophoretic heterogeneity by using primes (′) to denote electrophoretically distinguishable subunits which are immunologically identical. A number of patterns have become apparent by correlating the results obtained by the different techniques. For example, immunologically pure subunit II, which shows 3 bands on alkaline electrophoresis, is in fact a mixture of electrophoretically distinct subunits II, II′, II″. Except for subunits II, II′, and II″ immunoelectrophoretically identical subunits are typically homogeneous on sodium dodecyl sulfate-gels. However, slight differences in the apparent molecular weight are observed on high-resolution gels between immunologically unrelated subunits. The immunological identity and electrophoretic differences suggest that the charge isomers which are immunologically identical have similar antigenic surfaces. If a charge substitution is not in a critical location, we would expect the electrophoretically distinct but immunologically identical subunits to have identical assembly roles. Comparison of the results for Limulus hemocyanin with the hemocyanin of related species Eurypelma californicum and Androctanus australis, which have 7 and 8 immunologically distinct subunits, respectively, suggests that the calcium-mediated aggregation from 24 to 48 subunits of Limulus does not require more extensive subunit complexity.     

Noninvasive Assessment of Tumor VEGF Receptors in Response to Treatment with Pazopanib: A Molecular Imaging Study

Vascular endothelial growth factor (VEGF) and its receptors (VEGFRs) drive angiogenesis, and several VEGFR inhibitors are already approved for use as single agents or in combination with chemotherapy. Although there is a clear benefit with these drugs in a variety of tumors, the clinical response varies markedly among individuals. Therefore, there is a need for an efficient method to identify patients who are likely to respond to antiangiogenic therapy and to monitor its effects over time. We have recently developed a molecular imaging tracer for imaging VEGFRs known as scVEGF/^99mTc; an engineered single-chain (sc) form of VEGF radiolabeled with technetium Tc 99m (^99mTc). After intravenous injection, scVEGF/^99mTc preferentially binds to and is internalized by VEGFRs expressed within tumor vasculature, providing information on prevalence of functionally active receptors. We now report that VEGFR imaging readily detects the effects of pazopanib, a small-molecule tyrosine kinase inhibitor under clinical development, which selectively targets VEGFR, PDGFR, and c-Kit in mice with HT29 tumor xenografts. Immunohistochemical analysis confirmed that the changes in VEGFR imaging reflect a dramatic pazopanib-induced decrease in the number of VEGFR-2⁺/CD31⁺ endothelial cells (ECs) within the tumor vasculature followed by a relative increase in the number of ECs at the tumor edges. We suggest that VEGFR imaging can be used for the identification of patients that are responding to VEGFR-targeted therapies and for guidance in rational design, dosing, and schedules for combination regimens of antiangiogenic treatment.     

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THE EFFECT OF TEMPERATURE UPON FACET NUMBER IN THE BAR-EYED MUTANT OF DROSOPHILA : PART III.

Three strains of the bar-eyed mutant of Drosophila melanogaster Meig have been reared at constant temperatures over a range of 15–31°C. The mean facet number in the bar-eyed mutant varies inversely with the temperature at which the larvæ develop. The temperature coefficient (Q₁₀) is of the same order as that for chemical reactions. The facet-temperature relations may be plotted as an exponential curve for temperatures from 15–31°. The rate of development of the immature stages gives a straight line temperature curve between 15 and 29°. Beyond 29° the rate decreases again with a further rise in temperature. The facet curve may be readily superimposed on the development curve between 15 and 27°. The straight line feature of the development curve is probably due to the flattening out of an exponential curve by secondary factors. Since both the straight line and the exponential curve appear simultaneously in the same living material, it is impractical to locate the secondary factors in enzyme destruction, differences in viscosity, or in the physical state of colloids. Differential temperature coefficients for the various separate processes involved in development furnish the best basis for an explanation of the straight line feature of the curve representing the effect of temperature on the rate of physiological processes. Facet number in the full-eyed wild stock is not affected by temperature to a marked degree. The mean facet number for fifteen full-eyed females raised at 27° is 859.06. The mean facet number for the Low Selected Bar females at 27° is 55.13; for the Ultra-bar females at 27° it is 21.27. A consistent sexual difference appears in all the bar stocks, the females having fewer facets. This relation may be expressed by the sex coefficient, the average value of which is 0.791. The average observed difference in mean facet number for a difference of 1°C. in the environment in which the flies developed is 3.09 for the Ultra-bar stock and 14.01 for the Low Selected stock. The average proportional differences in the mean for a difference of 1°C. are 9.22 per cent for Ultra-bar, and 14.51 for Low Selected. The differences in the number of facets per °C. are greatest at the low and least at the high temperatures. The difference in the number of facets per °C. varies with the mean. The proportional differences in the mean per °C. are greatest at the lower (15–17.5°) and higher (29–31°) temperatures and least at the intermediate temperatures. Temperature is a factor in determining facet number only during a relatively short period in larval development. This effective period, at 27°, comes between the end of the 3rd and the end of the 4th day. At 15°, this period is initiated at the end of 8 days following a 1st day at 27°. At 27° this period is approximately 18 hours long. At 15° it is approximately 72 hours long. The number of facets and the length of the immature stage (egg-larval-pupal) appear related when the whole of development is passed at one temperature. That the number of facets is not dependent upon the length of the immature stage is shown by experiments in which only a part of development was passed at one temperature and the remainder at another. Temperature affects the reaction determining the number of facets in approximately the same way that it affects the other developmental reactions, hence the apparent correlation between facet number and the length of the immature stage. Variability as expressed by the coefficient of variability has a tendency to increase with temperature. Standard deviation, on the other hand, appears to decrease with rise in temperature. Neither inheritance nor induction effects are exhibited by this material. This study shows that environment may markedly affect the somatic expression of one Mendelian factor (bar eye), while it has no visible influence on another (white eye).