LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint

Retrotransposons are genomic DNA sequences that copy themselves to new genomic locations via RNA intermediates; LINE-1 is the only active and autonomous retrotransposon in the human genome. The mobility of LINE-1 is largely repressed in somatic tissues but is derepressed in many cancers, where LINE-1 retrotransposition is correlated with p53 mutation and copy number alteration (CNA). In cell lines, inducing LINE-1 expression can cause double-strand breaks (DSBs) and replication stress. Reanalyzing multiomic data from breast, ovarian, endometrial, and colon cancers, we confirmed correlations between LINE-1 expression, p53 mutation status, and CNA. We observed a consistent correlation between LINE-1 expression and the abundance of DNA replication complex components, indicating that LINE-1 may also induce replication stress in human tumors. In endometrial cancer, high-quality phosphoproteomic data allowed us to identify the DSB-induced ATM-MRN-SMC S phase checkpoint pathway as the primary DNA damage response (DDR) pathway associated with LINE-1 expression. Induction of LINE-1 expression in an in vitro model led to increased phosphorylation of MRN complex member RAD50, suggesting that LINE-1 directly activates this pathway

LINE-1 ORF2p expression is nearly imperceptible in human cancers

Background Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines. Results We report mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743. Conclusions Although somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNVs without a detectable mRNA transcript were also observed, suggesting that transcriptome coverage was incomplete (∼80%). In contrast to germline variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than in the luminal tumor, raising the possibility of differential translation or protein degradation effects. In conclusion, this large-scale proteogenomic integration allowed us to determine the degree to which mutations are translated and identify gaps in sequence coverage, thereby benchmarking current technology and progress toward whole cancer proteome and transcriptome analysis

CTR2 and the nonsense-mediated mRNA decay pathway in Saccharomyces cerevisiae.

The nonsense-mediated mRNA decay (NMD) pathway recognizes and degrades mRNA with premature termination codon and some natural mRNA as well. CTR2 is a natural mRNA degraded by NMD in Saccharomyces cerevisiae. The goals of this research were to identify the sequence features that target the CTR2 mRNA for NMD and the physiological consequences resulting from this degradation. These goals were addressed by making fusion constructs and determining total cellular, cytoplasmic and vacuolar copper levels in wild-type and nmd mutant yeast cells. Features contribute to the NMD-mediated degradation of CTR2 were identified. When cultured in medium with excess copper, nmd mutants accumulated significantly higher vacuolar copper levels than wild-type yeast cells, however nmd mutants accumulated significantly less cytoplasmic copper levels than that in wild-type yeast cells. These results are consistent with the inference that nmd mutants tolerate excess copper as a result of ctr2p transporting excessive copper from cytoplasm into vacuole.M.S

State indicators of anaerobic digestion: A critical review on process monitoring and diagnosis

Anaerobic reactors in full-scale biogas plants often encounter process instability; thus, their operational efficiency and further promotion remain limited. Process monitoring can be used to ensure better process stability during anaerobic digestion, the key to which depends on the selection and quantitation of appropriate state indicators. The present review focuses on the recent progress related to state indicators in the field of process monitoring and discusses in detail the ability to identify process status and especially, provide early warning information on process instability, in addition to the current monitoring status at the industrial level. Results show that the explorations of effective state indicators have experienced vigorous development. Most of the proposed state indicators have mainly focused on the gas and liquid phases, and those commonly used are sufficient to achieve effective monitoring in different systems; however, their suitability for use as potential early warning indicators varies. A comprehensive interpretation of the process state requires a combination of different state indicators to supply complementary information. Moreover, the current mode based on setting threshold values to diagnose process stability remains primitive. To ensure that the early warning is more feasible and universal, improvements can be made in terms of establishing a plant-specific database and focusing on the response trends to process disturbance as a basis for diagnosis. On the other hand, monitoring of most key state indicators is limited to external laboratory tests and accordingly, the consequent additional monitoring costs can be reduced by creating a suitable schedule regarding their frequency

Influence of tropical Atlantic meridional dipole of sea surface temperature anomalies on Antarctic autumn sea ice

Antarctic sea ice plays an important role in polar ecosystems and global climate, while its variability is affected by many factors. Teleconnections between the tropical and high latitudes have profound impacts on Antarctic climate changes through the stationary Rossby wave mechanism. Recent studies have connected long-term Antarctic sea ice changes to multidecadal variabilities of the tropical ocean, including the Atlantic Multidecadal Oscillation and the Interdecadal Pacific Oscillation. On interannual timescales, whether an impact exists from teleconnection of the tropical Atlantic is not clear. Here we find an impact of sea surface temperature (SST) variability of the tropical Atlantic meridional dipole mode on Antarctic sea ice that is most prominent in austral autumn. The meridional dipole SST anomalies in the tropical Atlantic force deep convection anomalies locally and over the tropical Pacific, generating stationary Rossby wave trains propagating eastward and poleward, which induce atmospheric circulation anomalies affecting sea ice. Specifically, convective anomalies over the equatorial Atlantic and Pacific are opposite-signed, accompanied by anomalous wave sources over the subtropical Southern Hemisphere. The planetary-scale atmospheric response has significant impacts on sea ice concentration anomalies in the Ross Sea, near the Antarctic Peninsula, and east of the Weddell Sea

Thermodynamics of volatile fatty acid degradation during anaerobic digestion under organic overload stress: The potential to better identify process stability

Anaerobic digestion (AD) operating under organic overload stress usually increases the potential for process instability, leading to significant economic and ecological consequences. Volatile fatty acids (VFAs) accumulation is regularly considered a major factor during AD and their degradation is subject to thermodynamic constraints. To date, no study has systematically investigated the mechanisms of VFA degradation on process stability from the perspective of thermodynamics. Hence, increased substrate-to-inoculum ratio was applied in this study to simulate organic overload stress using batch tests with Hybrid Pennisetum. As a result, VFAs accumulation increased, accompanied by decreased methane yield, slower methane production kinetics and even severe process instability. Metagenomic analysis demonstrated that the accumulated propionate and butyrate were degraded by methyl-malonyl-CoA and the beta-oxidation pathway while syntrophic acetate oxidation was preferred during acetate degradation. The deviation of stability parameters to varying degrees from the recommended threshold values was observed. However, a subsequent thermodynamic analysis revealed that moderate organic overload stress merely retarded the syntrophic oxidation of propionate, butyrate, and acetate. As a result, the methanogenic activity decreased, and the lag phase of AD was extended, but no adverse thermodynamic effects actually occurred. Changes in the Gibbs free energy for syntrophic propionate and acetate oxidation have the potential to better identify process stability. This study provided novel insights into the underlying thermodynamic mechanisms of VFA degradation and may have important implications for improving the current diagnostic mode for AD process stability

Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China

Abstract Background Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises. Results The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study. Conclusions Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem

Melt-blended PLA/curcumin-cross-linked polyurethane film for enhanced UV-shielding ability

Schematic for the preparation of the PLA/CCPU blend films