ALBERT

Description: Drugs that reverse epigenetic silencing, such as the DNA methyltransferase inhibitor (DNMTi) 5-azacytidine (AZA), have profound effects on transcription and tumor cell survival. AZA is an approved drug for myelodysplastic syndromes and acute myeloid leukemia, and is under investigation for different solid malignant tumors. AZA treatment generates self, double-stranded RNA (dsRNA), transcribed from hypomethylated repetitive elements. Self dsRNA accumulation in DNMTi-treated cells leads to type I IFN production and IFN-stimulated gene expression. Here we report that cell death in response to AZA treatment occurs through the 2′,5′-oligoadenylate synthetase (OAS)-RNase L pathway. OASs are IFN-induced enzymes that synthesize the RNase L activator 2-5A in response to dsRNA. Cells deficient in RNase L or OAS1 to 3 are highly resistant to AZA, as are wild-type cells treated with a small-molecule inhibitor of RNase L. A small-molecule inhibitor of c-Jun NH2-terminal kinases (JNKs) also antagonizes RNase L-dependent cell death in response to AZA, consistent with a role for JNK in RNase L-induced apoptosis. In contrast, the rates of AZA-induced and RNase L-dependent cell death were increased by transfection of 2-5A, by deficiencies in ADAR1 (which edits and destabilizes dsRNA), PDE12 or AKAP7 (which degrade 2-5A), or by ionizing radiation (which induces IFN-dependent signaling). Finally, OAS1 expression correlates with AZA sensitivity in the NCI-60 set of tumor cell lines, suggesting that the level of OAS1 can be a biomarker for predicting AZA sensitivity of tumor cells. These studies may eventually lead to pharmacologic strategies for regulating the antitumor activity and toxicity of AZA and related drugs.

Description: The 2′,5′-oligoadenylate (2-5A) synthetase (OAS)–RNase L system is an IFN-induced antiviral pathway. RNase L activity depends on 2-5A, synthesized by OAS. Although all three enzymatically active OAS proteins in humans—OAS1, OAS2, and OAS3—synthesize 2-5A upon binding dsRNA, it is unclear which are responsible for RNase L activation during viral infection. We used clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein-9 nuclease (Cas9) technology to engineer human A549-derived cell lines in which each of the OAS genes or RNase L is knocked out. Upon transfection with poly(rI):poly(rC), a synthetic surrogate for viral dsRNA, or infection with each of four viruses from different groups (West Nile virus, Sindbis virus, influenza virus, or vaccinia virus), OAS1-KO and OAS2-KO cells synthesized amounts of 2-5A similar to those synthesized in parental wild-type cells, causing RNase L activation as assessed by rRNA degradation. In contrast, OAS3-KO cells synthesized minimal 2-5A, and rRNA remained intact, similar to infected RNase L-KO cells. All four viruses replicated to higher titers in OAS3-KO or RNase L-KO A549 cells than in parental, OAS1-KO, or OAS2-KO cells, demonstrating the antiviral effects of OAS3. OAS3 displayed a higher affinity for dsRNA in intact cells than either OAS1 or OAS2, consistent with its dominant role in RNase L activation. Finally, the requirement for OAS3 as the major OAS isoform responsible for RNase L activation was not restricted to A549 cells, because OAS3-KO cells derived from two other human cell lines also were deficient in RNase L activation.

Description: ABSTRACT Precipitation variability at inter- and intra-annual scales may influence land-use management decisions in semi-arid savannas worldwide, and in particular, over the Kavango-Zambezi Transfrontier Conservation Area (KAZA) in southern Africa. Over KAZA, spatiotemporal precipitation variability forced by the El Niño Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) is important to local and regional-scale decisions for planting, livestock grazing, and wildlife migration patterns. We investigate the annual water year (October–September) and early rainy season [October–November–December (OND)] precipitation patterns during 60 years before and after a 1970s shift in the global ocean–atmosphere system for this region in southern Africa. The coincidence of the number of wet (upper tercile) and dry (lower tercile) years and OND seasons during the various phases of ENSO and IOD are compared prior to (1950–1975) and after (1980–2008) the 1970s climate shift over KAZA. Since the 1970s climate shift, KAZA has been significantly drier and observed fewer wet years and OND seasons. ENSO is the dominant forcing of precipitation differences over southern Africa before and after the 1970s climate shift, with IOD playing a secondary role. However, when ENSO and IOD phases are analysed simultaneously, El Niño and positive IOD events are significantly related to dry periods. The forcing of atmospheric circulation over southern Africa before and after the 1970s climate shift during El Niño and La Niña events is significantly different. Prior to the 1970s climate shift, atmospheric circulation during El Niño (La Niña) favoured strong (weak) precipitation increases (decreases). Afterward the 1970s climate shift, atmospheric circulation during La Niña (El Niño) favoured strong (weak) precipitation decreases (increases). The shifting nature of climate modes, especially ENSO, and respective influence on rainfall variability for southern Africa is important to understand to better inform seasonal climate forecasts to improve operational decision-making for land-use and water management decisions in semi-arid savanna regions.

Description: Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, 〈i〉Eriocheir sinensis〈/i〉 Scientific Reports, Published online: 15 September 2015; doi:10.1038/srep14015

Description: The 2′,5′-oligoadenylate (2-5A) synthetase (OAS)–RNase L system is an IFN-induced antiviral pathway. RNase L activity depends on 2-5A, synthesized by OAS. Although all three enzymatically active OAS proteins in humans—OAS1, OAS2, and OAS3—synthesize 2-5A upon binding dsRNA, it is unclear which are responsible for RNase L activation during viral infection....

Description: Understanding how individuals, communities, and populations vary in their vulnerability requires defining and identifying vulnerability with respect to a condition, and then developing robust methods to reliably measure vulnerability. In this study, we illustrate how a conceptual model translated via simulation can guide the real-world implementation of data collection and measurement of a model system. We present a generalizable statistical framework that specifies linkages among interacting social and biophysical components in complex landscapes to examine vulnerability. We use the simulated data to present a case study in which households are vulnerable to conditions of land function, which we define as the provision of goods and services from the surrounding environment. We use an example of a transboundary region of Southern Africa and apply a set of hypothesized, simulated data to illustrate how one might use the framework to assess vulnerability based on empirical data. We define vulnerability as the predisposition of being adversely affected by environmental variation and its impacts on land uses and their outcomes as exposure (E), mediated by sensitivity (S), and mitigated by adaptive capacity (AC). We argue that these are latent, or hidden, characteristics that can be measured through a set of observable indicators. Those indicators and the linkages between latent variables require model specification prior to data collection, critical for applying the type of modeling framework presented. We discuss the strength and directional pathways between land function and vulnerability components, and assess their implications for identifying potential leverage points within the system for the benefit of future policy and management decisions.

Description: The scant literature on individual scientists collaboration dynamics is used to develop a provisional model of research collaboration effectiveness. It incorporates external, collaborator, and team management factors, forming the basis for our theoretically informed qualitative analysis. We use this provisional model to guide semi-structured interview themes, deriving data from 60 US academic researchers, selected from a range of scientific and engineering disciplines as well as one social sciences discipline (economics). We present our findings in the form of respondent quotations related to the provisional model. We then conduct a further content analysis on the organizing constructs of respondent-assessed good and bad collaboration responses. The results of this second thematic coding of the interview data form the basis for the refinement of our model to include additional indicators, and to discuss some preliminary expectations about the associative relationships among the external, collaborator, and team management factors that contribute to scientist collaboration.

Description: Bighead carp (Hypophthalmichthys nobilis ) and silver carp ( Hypophthalmichthys molitrix ), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F 1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F 1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor-joining distance tree constructed using over 2,500 one-to-one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression. We conducted de novo transcriptome assembly of pure and hybrid specimens of bigheaded carps collected from the Mississippi River Basin. We found 40,759–51,706 transcripts for pure, F 1 hybrid, and backcross bigheaded carps. Transcriptomic variation was detected between F1 hybrids, indicating certain F 1 hybrids may experience low fitness. The phylogenetic tree constructed using over 2,500 one-to-one orthologous sequences demonstrated the robustness of transcriptomes as a powerful tool to describe introgression and hybridization.

Description: Epi-illuminescence intravital fluorescence microscopy has been employed to study leukocyte-endothelial interactions in a number of brain pathologies. Historically, dyes such as Rhodamine 6G have been injected intravenously. However, intravenous injections can predispose experimental animals to a multitude of complications and requires a high degree of technical skill. Here, we study the efficacy of injecting Rhodamine 6G into the peritoneum (IP) for the purpose of analyzing leukocyte-endothelial interactions through a cranial window during real time intravital microscopy. After examining the number of rolling and adherent leukocytes through a cranial window, we found no advantage to the intravenous injection (IV). Additionally, we tested blood from both routes of injection by flow cytometry to gain a very precise picture of the two methods. The two routes of administration failed to show any difference in the ability to detect cells. The study supports the notion that IP Rhodamine 6G works as efficaciously as IV and should be considered a viable alternative in experimental design for investigations employing intravital microscopy. Facilitated intravital studies will allow for more exploration into cerebral pathologies and allow for more rapid translation from the laboratory to the patient with less chance of experimental error from failed IV access. Microsc. Res. Tech., 2015 . © 2015 Wiley Periodicals, Inc.