Cellular proteasome activity facilitates herpes simplex virus entry at a postpenetration step

Herpes simplex virus (HSV) entry into cells is a multistep process that engages the host cell machinery. The proteasome is a large, ATP-dependent, multisubunit protease that plays a critical role in the maintenance of cell homeostasis. A battery of assays were used to demonstrate that proteasome inhibitors blocked an early step in HSV entry that occurred after capsid penetration into the cytosol but prior to capsid arrival at the nuclear periphery. Proteasome-dependent viral entry was not reliant on host or viral protein synthesis. MG132, a peptide aldehyde that competitively inhibits the degradative activity of the proteasome, had a reversible inhibitory effect on HSV entry. HSV can use endocytic or nonendocytic pathways to enter cells. These distinct entry routes were both dependent on proteasome-mediated proteolysis. In addition, HSV successfully entered cells in the absence of a functional host ubiquitin-activating enzyme, suggesting that viral entry is ubiquitin independent. We propose that proteasomal degradation of virion and/or host proteins is required for efficient delivery of incoming HSV capsids to the nucleus.     

A data based parsimony method of cophylogenetic analysis

Phylogenies of closely interacting groups, such as hosts and parasites, are seldom completely congruent. Incongruence can arise from biologically meaningful differences in the histories of the two groups, or can be generated by artifactual differences that are merely the result of incorrect phylogenies with weakly supported nodes. We present a method that distinguishes between these sources of incongruence and identifies lineages that are responsible for significant differences between phylogenies. We use the logic of conditional combination in that we first test for statistically significant incongruence using the partition homogeneity test. Then we remove all possible combinations of taxa until a non-significant result of this test is achieved. Finally, we construct a 'combined evidence' phylogeny and then reposition the incongruent taxa. This method produces trees for final comparison using reconciliation methods, but it includes only as many incongruence events as can be statistically justified from the data sets. We apply this method to a host–parasite (gopher–louse) data set and identify many fewer incongruence events than do topology based analyses alone. Our method is broadly applicable to comparisons of phylogenies of interacting taxa, such as hosts and parasites, or mutualists. The method should also be useful for other problems involving comparisons of phylogenies, such as multiple gene trees or cladistic biogeography.     

RUNAWAY COEVOLUTION: ADAPTATION TO HERITABLE AND NONHERITABLE ENVIRONMENTS

Populations evolve in response to the external environment, whether abiotic (e.g., climate) or biotic (e.g., other conspecifics). We investigated how adaptation to biotic, heritable environments differs from adaptation to abiotic, nonheritable environments. We found that, for the same selection coefficients, the coadaptive process between genes and heritable environments is much faster than genetic adaptation to an abiotic nonheritable environment. The increased rate of adaptation results from the positive association generated by reciprocal selection between the heritable environment and the genes responding to it. These associations result in a runaway process of adaptive coevolution, even when the genes creating the heritable environment and genes responding to the heritable environment are unlinked. Although tightening the degree of linkage accelerates the coadaptive process, the acceleration caused by a comparable amount of inbreeding is greater, because inbreeding has a cumulative effect on reducing functional recombination over generations. Our results suggest that that adaptation to local abiotic environmental variation may result in the rapid diversification of populations and subsequent reproductive isolation not directly but rather via its effects on heritable environments and the genes responding to them.     

Energetics of swelling in isolated hepatocytes: A comprehensive study

Cell swelling is now admitted as being a new principle of metabolic control but little is known about the energetics of cell swelling. We have studied the influence of hypo- or hyperosmolarity on both isolated hepatocytes and isolated rat liver mitochondria. Cytosolic hypoosmolarity on isolated hepatocytes induces an increase in matricial volume and does not affect the myxothiazol sensitive respiratory rate while the absolute value of the overall thermodynamic driving force over the electron transport chain increases. This points to an increase in kinetic control upstream the respiratory chain when cytosolic osmolarity is decreased. On isolated rat liver mitochondria incubated in hypoosmotic potassium chloride media, energetic parameters vary as in cells and oxidative phosphorylation efficiency is not affected. Cytosolic hyperosmolarity induced by sodium co-transported amino acids, per se, does not affect either matrix volume or energetic parameters. This is not the case in isolated rat liver mitochondria incubated in sucrose hyperosmotic medium. Indeed, in this medium, adenine nucleotide carrier is inhibited as the external osmolarity increases, which lowers the state 3 respiration close to state 4 level and consequently leads to a decrease in oxidative phosphorylation efficiency. When isolated rat liver mitochondria are incubated in KCl hyperosmotic medium, state 3 respiratory rate, matrix volume and membrane electrical potential vary as a function of time. Indeed, matrix volume is recovered in hyperosmotic KCl medium and this recovery is dependent on Pi-Kentry. State 3 respiratory rate increases and membrane electrical potential difference decreases during the first minutes of mitochondrial incubation until the attainment of the same value as in isoosmotic medium. This shows that matrix volume, flux and force are regulated as a function of time in KCl hyperosmotic medium. Under steady state, neither matrix volume nor energetic parameters are affected. Moreover, NaCl hyperosmotic medium allows matrix volume recovery but induces a decrease in state 3 respiratory flux. This indicates that potassium is necessary for both matrix volume and flux recovery in isolated mitochondria. We conclude that hypoosmotic medium induces an increase in kinetic control both upstream and on the respiratory chain and changes the oxidative phosphorylation response to forces. At steady state, hyperosmolarity, per se, has no effect on oxidative phosphorylation in either isolated hepatocytes or isolated mitochondria incubated in KCl medium. Therefore, potassium plays a key role in matrix volume, flux and force regulation.     

On Extrapolating Past the Range of Observed Data When Making Statistical Predictions in Ecology

Ecologists are increasingly using statistical models to predict animal abundance and occurrence in unsampled locations. The reliability of such predictions depends on a number of factors, including sample size, how far prediction locations are from the observed data, and similarity of predictive covariates in locations where data are gathered to locations where predictions are desired. In this paper, we propose extending Cook’s notion of an independent variable hull (IVH), developed originally for application with linear regression models, to generalized regression models as a way to help assess the potential reliability of predictions in unsampled areas. Predictions occurring inside the generalized independent variable hull (gIVH) can be regarded as interpolations, while predictions occurring outside the gIVH can be regarded as extrapolations worthy of additional investigation or skepticism. We conduct a simulation study to demonstrate the usefulness of this metric for limiting the scope of spatial inference when conducting model-based abundance estimation from survey counts. In this case, limiting inference to the gIVH substantially reduces bias, especially when survey designs are spatially imbalanced. We also demonstrate the utility of the gIVH in diagnosing problematic extrapolations when estimating the relative abundance of ribbon seals in the Bering Sea as a function of predictive covariates. We suggest that ecologists routinely use diagnostics such as the gIVH to help gauge the reliability of predictions from statistical models (such as generalized linear, generalized additive, and spatio-temporal regression models).     

Genome Wide DNA Methylation Profiles Provide Clues to the Origin and Pathogenesis of Germ Cell Tumors

The cell of origin of the five subtypes (I-V) of germ cell tumors (GCTs) are assumed to be germ cells from different maturation stages. This is (potentially) reflected in their methylation status as fetal maturing primordial germ cells are globally demethylated during migration from the yolk sac to the gonad. Imprinted regions are erased in the gonad and later become uniparentally imprinted according to fetal sex. Here, 91 GCTs (type I-IV) and four cell lines were profiled (Illumina’s HumanMethylation450BeadChip). Data was pre-processed controlling for cross hybridization, SNPs, detection rate, probe-type bias and batch effects. The annotation was extended, covering snRNAs/microRNAs, repeat elements and imprinted regions. A Hidden Markov Model-based genome segmentation was devised to identify differentially methylated genomic regions. Methylation profiles allowed for separation of clusters of non-seminomas (type II), seminomas/dysgerminomas (type II), spermatocytic seminomas (type III) and teratomas/dermoid cysts (type I/IV). The seminomas, dysgerminomas and spermatocytic seminomas were globally hypomethylated, in line with previous reports and their demethylated precursor. Differential methylation and imprinting status between subtypes reflected their presumed cell of origin. Ovarian type I teratomas and dermoid cysts showed (partial) sex specific uniparental maternal imprinting. The spermatocytic seminomas showed uniparental paternal imprinting while testicular teratomas exhibited partial imprinting erasure. Somatic imprinting in type II GCTs might indicate a cell of origin after global demethylation but before imprinting erasure. This is earlier than previously described, but agrees with the totipotent/embryonic stem cell like potential of type II GCTs and their rare extra-gonadal localization. The results support the common origin of the type I teratomas and show strong similarity between ovarian type I teratomas and dermoid cysts. In conclusion, we identified specific and global methylation differences between GCT subtypes, providing insight into their developmental timing and underlying developmental biology. Data and extended annotation are deposited at GEO (GSE58538 and GPL18809).