The GP problem: quantifying gene-to-phenotype relationships

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.     

Characterization of a lysyl aminopeptidase activity associated with phosphoglucose isomerase of Vibrio vulnificus

Phosphoglucose isomerase (PGI) is a multifunctional enzyme involved in glycolysis and gluconeogenesis and, in mammalian cells, functions as neuroleukin, autocrine motility factor (AMF), and differentiation and maturation factor (MF). We isolated and characterized PGI with a novel lysyl aminopeptidase (LysAP) activity (PGI-LysAP) from Vibrio vulnificus. Mass spectrometry revealed that PGI-LysAP is a heterodimer consisting of 23.4- and 60.8-kDa subunits. Only the heterodimer displayed LysAP activity. PGI-LysAP has a pI around 6.0 and high specificity toward the synthetic, fluorogenic substrate l-lysyl-7-amino-4-methylcoumarin. LysAP activity is optimal at pH 8.0, is 64% higher at 37 degrees C than at 21 degrees C, does not directly correlate with virulence, and is strongly inhibited by serine protease and metalloprotease inhibitors. PGI-LysAP was also identified in Vibrio parahaemolyticus and V. cholerae, but was absent from non-Vibrio human pathogens. Sequencing of the pgi gene revealed 1653 bp coding for a 550-amino-acid protein. Cloned and expressed PGI formed a homodimer with isomerase activity, but not LysAP activity. The finding of LysAP activity associated with heterodimeric PGI should foster a broad search for putative substrates in an effort to elucidate the role of PGI-LysAP in bacteria and its roles in the pathophysiology of diseases.     

Regulated conformation of myosin V

We have found that myosin V, an important actin-based vesicle transporter, has a folded conformation that is coupled to inhibition of its enzymatic activity in the absence of cargo and Ca(2+). In the absence of Ca(2+) where the actin-activated MgATPase activity is low, purified brain myosin V sediments in the analytical ultracentrifuge at 14 S as opposed to 11 S in the presence of Ca(2+) where the activity is high. At high ionic strength it sediments at 10 S independent of Ca(2+), and its regulation is poor. These data are consistent with myosin V having a compact, inactive conformation in the absence of Ca(2+) and an extended conformation in the presence of Ca(2+) or high ionic strength. Electron microscopy reveals that in the absence of Ca(2+) the heads and tail are both folded to give a triangular shape, very different from the extended appearance of myosin V at high ionic strength. A recombinant myosin V heavy meromyosin fragment that is missing the distal portion of the tail domain is not regulated by calcium and has only a small change in sedimentation coefficient, which is in the opposite direction to that seen with intact myosin V. Electron microscopy shows that its heads are extended even in the absence of calcium. These data suggest that interaction between the motor and cargo binding domains may be a general mechanism for shutting down motor protein activity and thereby regulating the active movement of vesicles in cells.     

Uptake and transport of high-density lipoprotein (HDL) and HDL-associated alpha-tocopherol by an in vitro blood-brain barrier model

The present study aimed to investigate pathways that contribute to uptake and transcytosis of high-density lipoproteins (HDLs) and HDL-associated alpha-tocopherol (alpha TocH) across an in vitro model of the blood-brain barrier (BBB). In primary porcine brain capillary endothelial cells HDL-associated alpha TocH was taken up in 10-fold excess of HDL holoparticles, indicating efficient selective uptake, a pathway mediated by scavenger receptor class B, type I (SR-BI). SR-BI was present in caveolae of brain capillary endothelial cells and expressed almost exclusively at the apical membrane. Disruption of caveolae with methyl-beta-cyclodextrin (CDX) resulted in (mis)sorting of SR-BI to the basolateral membrane. Immunohistochemistry of porcine brain cryosections revealed SR-BI expression on brain capillary endothelial cells and presumably astrocytic endfeet. HDL-associated [(14)C]alpha TocH taken up by brain capillary endothelial cells was recovered in sucrose gradient fractions containing the majority of cellular caveolin-1, the major caveolae-associated protein. During mass transfer studies using alpha TocH-enriched HDL, approximately 50% of cellular alpha TocH was recovered with the bulk of cellular caveolin-1 and SR-BI. Efflux experiments revealed that a substantial amount of cell-associated [(14)C]alpha TocH could be mobilized into the culture medium. In addition, apical-to-basolateral transport of HDL holoparticles and HDL-associated alpha TocH was saturable. Results from the present study suggest that part of cerebral apolipoprotein A-I and alpha TocH originates from plasma HDL transcytosed across the BBB and that caveolae-located SR-BI facilitates selective uptake of HDL-associated alpha TocH at the BBB.     

Turnover of carbon isotopes in tail hair and breath CO<Subscript>2</Subscript> of horses fed an isotopically varied diet

Temporal stable isotope records derived from animal tissues are increasingly studied to determine dietary and climatic histories. Despite this, the turnover times governing rates of isotope equilibration in specific tissues following a dietary isotope change are poorly known. The dietary isotope changes recorded in the hair and blood bicarbonate of two adult horses in this study are found to be successfully described by a model having three exponential isotope pools. For horse tail hair, the carbon isotope response observed following a dietary change from a C₃ to a C₄ grass was consistent with a pool having a very fast turnover rate (t _1/2~0.5 days) that made up ~41% of the isotope signal, a pool with an intermediate turnover rate (t _1/2 ~4 days) that comprised ~15% of the isotope signal, and a pool with very slow turnover rate (t _1/2 ~140 days) that made up ~44% of the total isotope signal. The carbon isotope signature of horse blood bicarbonate, in contrast, had a different isotopic composition, with ~67% of the isotope signal coming from a fast turnover pool (t _1/2 0.2 days), ~17% from a pool with an intermediate turnover rate (t _1/2 ~3 days) and ~16% from a pool with a slow turnover rate (t _1/2 ~50 days). The constituent isotope pools probably correspond to one exogenous and two endogenous sources. The exogenous source equates to our fast turnover pool, and the pools with intermediate and slow turnover rates are thought to derive from the turnover of metabolically active tissues and relatively inactive tissues within the body, respectively. It seems that a greater proportion of the amino acids available for hair synthesis come from endogenous sources compared to the compounds undergoing cellular catabolism in the body. Consequently, the isotope composition of blood bicarbonate appears to be much more responsive to dietary isotope changes, whereas the amino acids in the blood exhibit considerable isotopic inertia.     

Oxidation and ring cleavage of dibenzofuran by the filamentous fungus <Emphasis Type="Italic">Paecilomyces lilacinus</Emphasis>

The ability of the imperfect soil fungus Paecilomyces lilacinus to transform the environmental pollutant dibenzofuran was investigated. Transformation of dibenzofuran and related derivatives lead to 14 products, which were identified by UV spectroscopy, mass spectrometry, and proton nuclear magnetic resonance spectroscopy. Biotransformation was initiated by two separate hydroxylation steps, leading to the accumulation of 4-monohydroxylated and 4-dihydroxylateddibenzofurans. Hydroxylation at both aromatic rings produced 2,7-dihydroxydibenzofuran, 3,7-dihydroxydibenzofuran, and 2,8-dihydroxydibenzofuran. Further oxidation yields ring cleavage of dibenzofuran, which has not been described before for filamentous fungi. The ring fission products were identified as benzo[b]furo[3,2-d]-2-pyrone-6-carboxylic acid and [2-(1-carboxy-methylidene)-benzofuran-3-ylidene]-hydroxy-acetic acid and its derivatives hydroxylated at carbon 7 and 8 at the non-cleaved ring. Other metabolites were riboside-conjugates of 2-hydroxydibenzofuran and 3-hydroxydibenzofuran. The results showed that P. lilacinus transforms the hydrophobic compound dibenzofuran by phase I/phase II reactions to produce hydroxylated products and excretable sugar conjugates.     

Genetic evidence for unequal effective population sizes of human females and males

The time to the most recent common ancestor (TMRCA) of the human mitochondria (mtDNA) is estimated to be older than that of the nonrecombining portion of the Y chromosome (NRY). Surveys of variation in globally distributed humans typically result in mtDNA TMRCA values just under 200 thousand years ago (kya), whereas those for the NRY range between 46 and 110 kya. A favored hypothesis for this finding is that natural selection has acted on the NRY, leading to a recent selective sweep. An alternate hypothesis is that sex-biased demographic processes are responsible. Here, we re-examine the disparity between NRY and mtDNA TMRCAs using data collected from individual human populations--a sampling strategy that minimizes the confounding influence of population subdivision in global data sets. We survey variation at 782 bp of the mitochondrial cytochrome c oxidase subunit 3 gene as well as at 26.5 kb of noncoding DNA from the NRY in a sample of 25 Khoisan, 24 Mongolians, and 24 Papua New Guineans. Data from both loci in all populations are best described by a model of constant population size, with the exception of Mongolian mtDNA, which appears to be experiencing rapid population growth. Taking these demographic models into account, we estimate the TMRCAs for each locus in each population. A pattern that is remarkably consistent across all three populations is an approximately twofold deeper coalescence for mtDNA than for the NRY. The oldest TMRCAs are observed for the Khoisan (73.6 kya for the NRY and 176.5 kya for mtDNA), whereas those in the non-African populations are consistently lower (averaging 47.7 kya for the NRY and 92.8 kya for mtDNA). Our data do not suggest that differential natural selection is the cause of this difference in TMRCAs. Rather, these results are most consistent with a higher female effective population size.