Pharmacologic modulation of RNA splicing enhances anti-tumor immunity

1. Download : Download high-res image (217KB)
2. Download : Download full-size image

     

Assembly of Recombinant Israeli Acute Paralysis Virus Capsids

The dicistrovirus Israeli Acute Paralysis Virus (IAPV) has been implicated in the worldwide decline of honey bees. Studies of IAPV and many other bee viruses in pure culture are restricted by available isolates and permissive cell culture. Here we show that coupling the IAPV major structural precursor protein ORF2 to its cognate 3C-like processing enzyme results in processing of the precursor to the individual structural proteins in a number of insect cell lines following expression by a recombinant baculovirus. The efficiency of expression is influenced by the level of IAPV 3C protein and moderation of its activity is required for optimal expression. The mature IAPV structural proteins assembled into empty capsids that migrated as particles on sucrose velocity gradients and showed typical dicistrovirus like morphology when examined by electron microscopy. Monoclonal antibodies raised to recombinant capsids were configured into a diagnostic test specific for the presence of IAPV. Recombinant capsids for each of the many bee viruses within the picornavirus family may provide virus specific reagents for the on-going investigation of the causes of honeybee loss.     

Macrophage Gene Expression Associated with Remodeling of the Prepartum Rat Cervix: Microarray and Pathway Analyses

As the critical gatekeeper for birth, prepartum remodeling of the cervix is associated with increased resident macrophages (Mφ), proinflammatory processes, and extracellular matrix degradation. This study tested the hypothesis that expression of genes unique to Mφs characterizes the prepartum from unremodeled nonpregnant cervix. Perfused cervix from prepartum day 21 postbreeding (D21) or nonpregnant (NP) rats, with or without Mφs, had RNA extracted and whole genome microarray analysis performed. By subtractive analyses, expression of 194 and 120 genes related to Mφs in the cervix from D21 rats were increased and decreased, respectively. In both D21 and NP groups, 158 and 57 Mφ genes were also more or less up- or down-regulated, respectively. Mφ gene expression patterns were most strongly correlated within groups and in 5 major clustering patterns. In the cervix from D21 rats, functional categories and canonical pathways of increased expression by Mφ gene related to extracellular matrix, cell proliferation, differentiation, as well as cell signaling. Pathways were characteristic of inflammation and wound healing, e.g., CD163, CD206, and CCR2. Signatures of only inflammation pathways, e.g., CSF1R, EMR1, and MMP12 were common to both D21 and NP groups. Thus, a novel and complex balance of Mφ genes and clusters differentiated the degraded extracellular matrix and cellular genomic activities in the cervix before birth from the unremodeled state. Predicted Mφ activities, pathways, and networks raise the possibility that expression patterns of specific genes characterize and promote prepartum remodeling of the cervix for parturition at term and with preterm labor.     

Oh,SNAP! How enteroviruses redirect autophagic traffic away from degradation

Picornaviruses, one of the major causes of human diseases ranging from the common cold to acute flaccid paralysis, have a short cytosolic lifecycle that, in cultured cells, ends in cell lysis. For years, the prevailing model was that these viruses exit from cells exclusively through cell lysis. However, over the last several years it has become apparent that for some picornaviruses, a macroautophagy/autophagy-related pathway can result in release of virus particles wrapped in a membrane containing autophagic markers. It has been proposed that this enveloped release predominates within hosts, allowing cell-to-cell movement of virus while minimizing exposure to the immune system. One reason that picornaviruses induce the autophagy pathway is to provide membrane scaffolds for RNA replication complexes. Perhaps more importantly, acidified autophagosomes (known as amphisomes) provide havens for maturation of new viral particles into infectious viruses. In back-to-back papers recently published in Cell Reports, our labs investigated a basic question: if picornavirus particles are maturing inside amphisomes, then how are they avoiding the typical degradative fate of autophagic cargo and exiting the cell intact?     

Moralizing regulation: the implications of policing “good” versus “bad” immigrants

Recently, the US has dramatically expanded immigration enforcement. At the same time, some advocates have sought to support “good” immigrants. This paper considers how the resulting good/bad binaries affect undocumented immigrants. I examine a case study in Los Angeles, where policing intertwined with protection. Based on participant observation and interviews, I show that respondents believed state agents classified them either as “bad” criminals or “good”, immigrants. To the extent immigrants identified as “good”, they credited the US with offering them “freedom” and hoped for political inclusion. At the same time, in what I call moralizing regulation, they also performed “good” behaviour and distinguished themselves from those seen as “bad”. Some also tied “good” behaviour to femininity and “acting white”. At the extreme, they blamed other migrants for inviting state mistreatment. The effects were ambivalent: while immigrants appreciated US support, they also adopted and adapted to the state’s moral norms.     

The decapod researcher’s guide to the galaxy of sex determination

The objective of this study was to assess the frequency of use of marine resources in recruitment of Southern Hemisphere native riverine fish Galaxias maculatus from rivers across a latitudinal gradient. To do this, we analysed the concentrations of δ³⁴S in vertebral column tissues from fish collected in ten Chilean river systems across latitudes 36°–47°S. The analyses of δ³⁴S signatures in these rivers suggest that the use of marine resources by riverine populations of G. maculatus in large river systems in Chile is variable, with marine resources playing a limited role in more northern large rivers, characterised by warmer temperatures and predictable flow regimes and floodplain inundations. This is in contrast to life histories described for G. maculatus in rivers from New Zealand and Australia, where riverine populations are believed to be characterised by an obligatory recruitment phase in marine environments. Recruitment of G. maculatus in Chilean large rivers appears to depend on their freshwater productivity driven by climate as well as both longitudinal (headwaters lakes-estuary) and lateral (main channel-floodplains) hydrologic connectivities.     

Evaluation of genes involved in Norway lobster (<Emphasis Type="Italic">Nephrops norvegicus</Emphasis>) female sexual maturation using transcriptomic analysis

In marine ecosystems, the most significant migration observed in terms of biomass distribution is the one connected with the vertical movements in the water column. In the present study, the vertical profiles of the mesopelagic shrimps Gennadas elegans, Eusergestes arcticus, Sergia robusta, and the epipelagic Parasergestes vigilax in the Balearic Sea (western Mediterranean), during the stratified (summer) and non-stratified (autumn) hydrographic conditions, were investigated through their ontogeny, from the larval to adult stages. The mesopelagic adults were observed to move down to the deeper layers during the night more than during the daylight hours. Most larvae aggregated within the limits of the upper water column. The P. vigilax larvae were collected only during the stratified period. The first two larval stages vertical distribution indicates that the mesopelagic crustacean spawning could occur at greater depths. During the non-stratified period, the larvae of the mesopelagic species tended to remain at about 500 m depth at night, rising towards the upper layers at sunrise. Vertical patterns are discussed, as strategies associated with predator–prey trade-offs. To our knowledge, the present study is the first such attempt to jointly analyze the vertical migrations of the developmental stages of the pelagic shrimps in the Mediterranean Sea.     

A Bayesian multinomial logistic exposure model for estimating probabilities of competing sources of nest failure

Understanding causes of nest loss is critical for the management of endangered bird populations. Available methods for estimating nest loss probabilities to competing sources do not allow for random effects and covariation among sources, and there are few data simulation methods or goodness‐of‐fit (GOF) tests for such models. We developed a Bayesian multinomial extension of the widely used logistic exposure (LE) nest survival model which can incorporate multiple random effects and fixed‐effect covariates for each nest loss category. We investigated the performance of this model and the accompanying GOF test by analysing simulated nest fate datasets with and without age‐biased discovery probability, and by comparing the estimates with those of traditional fixed‐effects estimators. We then exemplify the use of the multinomial LE model and GOF test by analysing Piping Plover Charadrius melodus nest fate data (n = 443) to explore the effects of wire cages (exclosures) constructed around nests, which are used to protect nests from predation but can lead to increased nest abandonment rates. Mean parameter estimates of the random‐effects multinomial LE model were all within 1 sd of the true values used to simulate the datasets. Age‐biased discovery probability did not result in biased parameter estimates. Traditional fixed‐effects models provided estimates with a high bias of up to 43% with a mean of 71% smaller standard deviations. The GOF test identified models that were a poor fit to the simulated data. For the Piping Plover dataset, the fixed‐effects model was less well‐supported than the random‐effects model and underestimated the risk of exclosure use by 16%. The random‐effects model estimated a range of 1–6% probability of abandonment for nests not protected by exclosures across sites and 5–41% probability of abandonment for nests with exclosures, suggesting that the magnitude of exclosure‐related abandonment is site‐specific. Our results demonstrate that unmodelled heterogeneity can result in biased estimates potentially leading to incorrect management recommendations. The Bayesian multinomial LE model offers a flexible method of incorporating random effects into an analysis of nest failure and is robust to age‐biased nest discovery probability. This model can be generalized to other staggered‐entry, time‐to‐hazard situations.