Do human transposable element small RNAs serve primarily as genome defenders or genome regulators?

It is currently thought that small RNA (sRNA) based repression mechanisms are primarily employed to mitigate the mutagenic threat posed by the activity of transposable elements (TEs). This can be achieved by the sRNA guided processing of TE transcripts via Dicer-dependent (e.g., siRNA) or Dicer-independent (e.g., piRNA) mechanisms. For example, potentially active human L1 elements are silenced by mRNA cleavage induced by element encoded siRNAs, leading to a negative correlation between element mRNA and siRNA levels. On the other hand, there is emerging evidence that TE derived sRNAs can also be used to regulate the host genome. Here, we evaluated these two hypotheses for human TEs by comparing the levels of TE derived mRNA and TE sRNA across six tissues. The genome defense hypothesis predicts a negative correlation between TE mRNA and TE sRNA levels, whereas the genome regulatory hypothesis predicts a positive correlation. On average, TE mRNA and TE sRNA levels are positively correlated across human tissues. These correlations are higher than seen for human genes or for randomly permuted control data sets. Overall, Alu subfamilies show the highest positive correlations of element mRNA and sRNA levels across tissues, although a few of the youngest, and potentially most active, Alu subfamilies do show negative correlations. Thus, Alu derived sRNAs may be related to both genome regulation and genome defense. These results are inconsistent with a simple model whereby TE derived sRNAs reduce levels of standing TE mRNA via transcript cleavage, and suggest that human cells efficiently process TE transcripts into sRNA based on the available message levels. This may point to a widespread role for processed TE transcripts in genome regulation or to alternative roles of TE-to-sRNA processing including the mitigation of TE transcript cytotoxicity

A 150MG magnetic white dwarf in the cataclysmic variable RX J1554.2+2721

We report the detection of Zeeman-split Lalpha absorption pi and sigma+ lines in the far-ultraviolet Hubble Space Telescope/Space Telescope Imaging Spectrograph spectrum of the magnetic cataclysmic variable RX J1554.2+2721. Fitting the STIS data with magnetic white dwarf model spectra, we derive a field strength of B~144MG and an effective temperature of 17000K<Teff<23000K. This measurement makes RX J1554.2+2721 only the third cataclysmic variable containing a white dwarf with a field exceeding 100MG. Similar to the other high-field polar AR UMa, RX J1554.2+2721 is often found in a state of feeble mass transfer, which suggests that a considerable number of high-field polars may still remain undiscovered.Comment: 4 pages, accepted for ApJ Letter

A C-terminal Pfs48/45 malaria transmission-blocking vaccine candidate produced in the baculovirus expression system

This work is licensed under a Creative Commons Attribution 4.0 International License.The Plasmodium falciparum gametocyte surface protein, Pfs48/45, is a potential target for malaria transmission-blocking vaccines. However, due to its size and complexity, expression of the full-length protein has been difficult, leading to focus on the C-terminal six cysteine domain (6C) with the use of fusion proteins to facilitate expression and folding. In this study, we utilized the baculovirus system to evaluate the expression of three Pfs48/45 proteins including the full-length protein, the 6C domain fragment and the 6C domain mutant to prevent glycosylation. Expression of the recombinant Pfs48/45 proteins was conducted in super Sf9 cells combined with the use of tunicamycin to prevent N-glycosylation. The proteins were then evaluated as immunogens in mice to demonstrate the induction of functionally active polyclonal antibody responses as measured in the standard membrane feeding assay (SMFA). Only the 6C protein was found to exhibit significant transmission-reducing activity. Further characterization of the biologically active 6C protein demonstrated it was homogeneous in terms of size, charge, conformation, absence of glycosylation, and containing proper disulfide bond pairings. This study presents an alternative expression system, without the need of a fusion protein partner, for the Pfs48/45 6C protein fragment including further evaluation as a potential transmission-blocking vaccine candidate

Yeast Biological Networks Unfold the Interplay of Antioxidants, Genome and Phenotype, and Reveal a Novel Regulator of the Oxidative Stress Response

Background Identifying causative biological networks associated with relevant phenotypes is essential in the field of systems biology. We used ferulic acid (FA) as a model antioxidant to characterize the global expression programs triggered by this small molecule and decipher the transcriptional network controlling the phenotypic adaptation of the yeast Saccharomyces cerevisiae. Methodology/Principal Findings By employing a strict cut off value during gene expression data analysis, 106 genes were found to be involved in the cell response to FA, independent of aerobic or anaerobic conditions. Network analysis of the system guided us to a key target node, the FMP43 protein, that when deleted resulted in marked acceleration of cellular growth (~15% in both minimal and rich media). To extend our findings to human cells and identify proteins that could serve as drug targets, we replaced the yeast FMP43 protein with its human ortholog BRP44 in the genetic background of the yeast strain Δfmp43. The conservation of the two proteins was phenotypically evident, with BRP44 restoring the normal specific growth rate of the wild type. We also applied homology modeling to predict the 3D structure of the FMP43 and BRP44 proteins. The binding sites in the homology models of FMP43 and BRP44 were computationally predicted, and further docking studies were performed using FA as the ligand. The docking studies demonstrated the affinity of FA towards both FMP43 and BRP44. Conclusions This study proposes a hypothesis on the mechanisms yeast employs to respond to antioxidant molecules, while demonstrating how phenome and metabolome yeast data can serve as biomarkers for nutraceutical discovery and development. Additionally, we provide evidence for a putative therapeutic target, revealed by replacing the FMP43 protein with its human ortholog BRP44, a brain protein, and functionally characterizing the relevant mutant strain

The Pfs230 N-terminal fragment, Pfs230D1+: expression and characterization of a potential malaria transmission-blocking vaccine candidate

This work is licensed under a Creative Commons Attribution 4.0 International License.Background Control and elimination of malaria can be accelerated by transmission-blocking interventions such as vaccines. A surface antigen of Plasmodium falciparum gametocytes, Pfs230, is a leading vaccine target antigen, and has recently progressed to experimental clinical trials. To support vaccine product development, an N-terminal Pfs230 antigen was designed to increase yield, as well as to improve antigen quality, integrity, and homogeneity. Methods A scalable baculovirus expression system was used to express the Pfs230D1+ construct (aa 552–731), which was subsequently purified and analysed. Pfs230D1+ was designed to avoid glycosylation and protease digestion, thereby potentially increasing homogeneity and stability. The resulting Pfs230D1+ protein was compared to a previous iteration of the Pfs230 N-terminal domain, Pfs230C1 (aa 443–731), through physiochemical characterization and in vivo analysis. The induction of functional antibody responses was confirmed via the standard membrane feeding assay (SMFA). Results Pfs230D1+ was produced and purified to an overall yield of 23 mg/L culture supernatant, a twofold yield increase over Pfs230C1. The Pfs230D1+ protein migrated as a single band via SDS-PAGE and was detected by anti-Pfs230C1 monoclonal antibodies. Evaluation by SDS-PAGE, chromatography (size-exclusion and reversed phase) and capillary isoelectric focusing demonstrated the molecule had improved homogeneity in terms of size, conformation, and charge. Intact mass spectrometry confirmed its molecular weight and that it was free of glycosylation, a key difference to the prior Pfs230C1 protein. The correct formation of the two intramolecular disulfide bonds was initially inferred by binding of a conformation specific monoclonal antibody and directly confirmed by LC/MS and peptide mapping. When injected into mice the Pfs230D1+ protein elicited antibodies that demonstrated transmission-reducing activity, via SMFA, comparable to Pfs230C1. Conclusion By elimination of an O-glycosylation site, a potential N-glycosylation site, and two proteolytic cleavage sites, an improved N-terminal Pfs230 fragment was produced, termed D1+, which is non-glycosylated, homogeneous, and biologically active. An intact protein at higher yield than that previously observed for the Pfs230C1 fragment was achieved. The results indicate that Pfs230D1+ protein produced in the baculovirus expression system is an attractive antigen for transmission-blocking vaccine development

FUSE and HST/STIS far-ultraviolet observations of AM Herculis in an extended low state

We have obtained FUSE and HST/STIS time-resolved spectroscopy of the polar AM Herculis during a deep low state. The spectra are entirely dominated by the emission of the white dwarf. Both the far-ultraviolet (FUV) flux as well as the spectral shape vary substantially over the orbital period, with maximum flux occurring at the same phase as during the high state. The variations are due to the presence of a hot spot on the white dwarf, which we model quantitatively. The white dwarf parameters can be determined from a spectral fit to the faint phase data, when the hot spot is self-eclipsed. Adopting the distance of 79+8-6pc determined by Thorstensen, we find an effective temperature of 19800+-700K and a mass of Mwd=0.78+0.12-0.17Msun. The hot spot has a lower temperature than during the high state, ~34000-40000K, but covers a similar area, ~10% of the white dwarf surface. Low state FUSE and STIS spectra taken during four different epochs in 2002/3 show no variation of the FUV flux level or spectral shape, implying that the white dwarf temperature and the hot spot temperature, size, and location do not depend on the amount of time the system has spent in the low state. Possible explanations are ongoing accretion at a low level, or deep heating, both alternatives have some weaknesses that we discuss. No photospheric metal absorption lines are detected in the FUSE and STIS spectra, suggesting that the average metal abundances in the white dwarf atmosphere are lower than 1e-3 times their solar values.Comment: ApJ in press, 12 pages, 11 figure

The Freezeout Hypersurface at LHC from particle spectra: Flavor and Centrality Dependence

We extract the freezeout hypersurface in Pb-Pb collisions at $\sqrt{s_{\rm NN}}=$ 2760 GeV at the CERN Large Hadron Collider by analysing the data on transverse momentum spectra within a unified model for chemical and kinetic freezeout. The study has been done within two different schemes of freezeout, single freezeout where all the hadrons freezeout together versus double freezeout where those hadrons with non-zero strangeness content have different freezeout parameters compared to the non-strange ones. We demonstrate that the data is better described within the latter scenario. We obtain a strange freezeout hypersurface which is smaller in volume and hotter compared to the non-strange freezeout hypersurface for all centralities with a reduction in $\chi^2/N_{df}$ around $40\%$. We observe from the extracted parameters that the ratio of the transverse size to the freezeout proper time is invariant under expansion from the strange to the non-strange freezeout surfaces across all centralities. Moreover, except for the most peripheral bins, the ratio of the non-strange and strange freezeout proper times is close to $1.3$.Comment: Final version accepted for publicatio

The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents

Background:Many genomes contain a substantial number of transposable elements (TEs), a few of which are known to be involved in regulating gene expression. However, recent observations suggest that TEs may have played a very important role in the evolution of gene expression because many conserved non-genic sequences, some of which are know to be involved in gene regulation, resemble TEs. Results:Here we investigate whether new TE insertions affect gene expression profiles by testing whether gene expression divergence between mouse and rat is correlated to the numbers of new transposable elements inserted near genes. We show that expression divergence is significantly correlated to the number of new LTR and SINE elements, but not to the numbers of LINEs. We also show that expression divergence is not significantly correlated to the numbers of ancestral TEs in most cases, which suggests that the correlations between expression divergence and the numbers of new TEs are causal in nature. We quantify the effect and estimate that TE insertion has accounted for ~20% (95% confidence interval: 12% to 26%) of all expression profile divergence in rodents. Conclusions:We conclude that TE insertions may have had a major impact on the evolution of gene expression levels in rodents

The role of mutation rate variation and genetic diversity in the architecture of human disease

Background We have investigated the role that the mutation rate and the structure of genetic variation at a locus play in determining whether a gene is involved in disease. We predict that the mutation rate and its genetic diversity should be higher in genes associated with disease, unless all genes that could cause disease have already been identified. Results Consistent with our predictions we find that genes associated with Mendelian and complex disease are substantially longer than non-disease genes. However, we find that both Mendelian and complex disease genes are found in regions of the genome with relatively low mutation rates, as inferred from intron divergence between humans and chimpanzees, and they are predicted to have similar rates of non-synonymous mutation as other genes. Finally, we find that disease genes are in regions of significantly elevated genetic diversity, even when variation in the rate of mutation is controlled for. The effect is small nevertheless. Conclusions Our results suggest that gene length contributes to whether a gene is associated with disease. However, the mutation rate and the genetic architecture of the locus appear to play only a minor role in determining whether a gene is associated with disease

Sedimentation and subsidence history of the Lomonosov Ridge

During the first scientific ocean drilling expedition to the Arctic Ocean (Arctic Coring Expedition [ACEX]; Integrated Ocean Drilling Program Expedition 302), four sites were drilled and cored atop the central part of the Lomonosov Ridge in the Arctic Ocean at ~88°N, 140°E (see Fig. F18 in the "Sites M0001–M0004" chapter). The ridge was rifted from the Eurasian continental margin at ~57 Ma (Fig. F1) (Jokat et al., 1992, 1995). Since the rifting event and the concurrent tilting and erosion of this sliver of the outer continental margin, the Lomonosov Ridge subsided while hemipelagic and pelagic sediments were deposited above the angular rifting unconformity (see Fig. F7A in the "Sites M0001–M0004" chapter).The sections recovered from the four sites drilled during Expedition 302 can be correlated using their seismic signature, physical properties (porosity, magnetic susceptibility, resistivity, and P-wave velocity), chemostratigraphy (ammonia content of pore waters), lithostratigraphy, and biostratigraphy. The lithostratigraphy of the composite section combined with biostratigraphy provides an insight into the complex history of deposition, erosion, and preservation of the biogenic fraction. Eventually, the ridge subsided to its present water depth as it drifted from the Eurasian margin. In this chapter, we compare a simple model of subsidence history with the sedimentary record recovered from atop the ridge