Site-specific and mRNA-specific control of accurate mRNA editing by a helicase complex in trypanosomes

Trypanosome U-insertion/deletion RNA editing in mitochondrial mRNAs involves guide RNAs (gRNAs) and the auxiliary RNA editing substrate binding complex (RESC) and RNA editing helicase 2 complex (REH2C). RESC and REH2C stably copurify with editing mRNAs but the functional interplay between these complexes remains unclear. Most steady-state mRNAs are partially edited and include misedited “junction” regions that match neither pre-mRNA nor fully edited transcripts. Editing specificity is central to mitochondrial RNA maturation and function, but its basic control mechanisms remain unclear. Here we applied a novel nucleotide-resolution RNA-seq approach to examine ribosomal protein subunit 12 (RPS12) and ATPase subunit 6 (A6) mRNA transcripts. We directly compared transcripts associated with RESC and REH2C to those found in total mitochondrial RNA. RESC-associated transcripts exhibited site-preferential enrichments in total and accurate edits. REH2C loss-of-function induced similar substrate-specific and site-specific editing effects in total and RESC-associated RNA. It decreased total editing primarily at RPS12 5′ positions but increased total editing at examined A6 3′ positions. REH2C loss-of-function caused site-preferential loss of accurate editing in both transcripts. However, changes in total or accurate edits did not necessarily involve common sites. A few 5′ nucleotides of the initiating gRNA (gRNA-1) directed accurate editing in both transcripts. However, in RPS12, two conserved 3′-terminal adenines in gRNA-1 could direct a noncanonical 2U-insertion that causes major pausing in 3′–5′ progression. In A6, a noncanonical sequence element that depends on REH2C in a region normally targeted by the 3′ half of gRNA-1 may hinder early editing progression. Overall, we defined transcript-specific effects of REH2C loss

The globalization of cultural eutrophication in the coastal ocean: causes and consequences

Coastal eutrophication caused by anthropogenic nutrient inputs is one of the greatest threats to the health of coastal estuarine and marine ecosystems worldwide. Globally, similar to 24% of the anthropogenic N released in coastal watersheds is estimated to reach coastal ecosystems. Seven contrasting coastal ecosystems subject to a range of riverine inputs of freshwater and nutrients are compared to better understand and manage this threat. The following are addressed: (i) impacts of anthropogenic nutrient inputs on ecosystem services; (ii) how ecosystem traits minimize or amplify these impacts; (iii) synergies among pressures (nutrient enrichment, over fishing, coastal development, and climate-driven pressures in particular); and (iv) management of nutrient inputs to coastal ecosystems. This comparative analysis shows that "trophic status," when defined in terms of the level of primary production, is not useful for relating anthropogenic nutrient loading to impacts. Ranked in terms of the impact of cultural eutrophication, Chesapeake Bay ranks number one followed by the Baltic Sea, Northern Adriatic Sea, Northern Gulf of Mexico, Santa Barbara Channel, East China Sea, and the Great Barrier Reef. The impacts of increases in anthropogenic nutrient loading (e.g., development of "dead zones," loss of biologically engineered habitats, and toxic phytoplankton events) are, and will continue to be, exacerbated by synergies with other pressures, including over fishing, coastal development and climate-driven increases in sea surface temperature, acidification and rainfall. With respect to management, reductions in point source inputs from sewage treatment plants are increasingly successful. However, controlling inputs from diffuse sources remains a challenging problem. The conclusion from this analysis is that the severity of coastal eutrophication will likely continue to increase in the absence of effectively enforced, ecosystem-based management of both point and diffuse sources of nitrogen and phosphorus. This requires sustained, integrated research and monitoring, as well as repeated assessments of nutrient loading and impacts. These must be informed and guided by ongoing collaborations among scientists, politicians, managers and the public.info:eu-repo/semantics/publishedVersio

Changes of temperature and bio-optical properties in the South China Sea in response to Typhoon Lingling, 2001

A large patch of enhanced chlorophyll a concentration (Chla), lower sea surface temperature (SST), and lower sea surface height (SSH) was revealed in the central South China Sea (SCS) in November 2001 after the passage of typhoon Lingling. Maximum SST reduction of 11 degrees C occurred one day after Lingling's passage on 11/11. Subsequently, against a background level of 0.08 mg/m(3), average Chla within the area of 12.60-16.49 degrees N, 112.17-117.05 degrees E increased to 0.14 mg/m(3) on 11/12 and then to 0.37 mg/m(3) on 11/14. Dissolved organic matter and detritus were differentiated from Chla using a recent bio-optical algorithm. They contributed 64% to the increase of total absorption immediately after Lingling, while most of the changes later (74%) were due to phytoplankton. The area under Lingling's impact covered ca. 3 degrees latitude and 4 degrees longitude, which is much greater than the two summer cases previously observed in the northern SCS. This event lasted for ca. 15 days, and resulted in carbon fixation in the order of 0.4 Mt. Such a drastic response was attributed to the coupling of typhoon-induced nutrient pumping with the pre-established cyclonic gyre in the central SCS driven by the prevailing northeast monsoon

Soil-tunnel Interaction under Medium Internal Blast Loading

AbstractA series of numerical simulations were carried out to study the interaction between subway tunnels and soils subjected to medium internal blast loading (< 200kg of TNT equivalent). The excess pore-water pressure was studied with an existing soil model (FHWA) that can simulate pore-water pressure and effective soil pressure. A recently developed blast loading scheme that removes the necessity of modeling the explosive in the numerical models but still maintains the advantages of nonlinear fluid-structure interaction was used to study the process of blast wave propagation in the air domain inside the tunnel

The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation

The phytohormone abscisic acid (ABA) mediates many complex aspects of plant development including seed maturation, dormancy, and germination as well as root growth. The B3-domain transcription factor abscisic acid-insensitive 3 (ABI3) is a central regulator in ABA signaling, but little is known of how this factor is regulated. Here, we show that ABI3 is an unstable protein and that an ABI3-interacting protein (AIP2), which contains a RING motif, can polyubiquitinate ABI3 in vitro. The AIP2 E3 ligase activity is abolished by mutations (C230S; C231S) in the RING motif and the AIP2 (C/S) mutant functions in a dominant-negative manner. AIP2 has a stronger binding affinity for the B2 + B3 domain of ABI3 than the A1 + B1 domain, but only ubiquitinates the latter. In double-transgenic plants, induced AIP2 expression leads to a decrease in ABI3 protein levels. In contrast, ABI3 levels are elevated upon induced expression of the AIP2 RING mutant, which interferes with the endogenous AIP2 E3 activity. An aip2-1-null mutant shows higher ABI3 protein levels compared with wild type after seed stratification, and is hypersensitive to ABA, mimicking the ABI3-overexpression phenotype, whereas AIP2-overexpression plants contain lower levels of ABI3 protein than wild type and are more resistant to ABA, phenocopying abi3. Our results indicate that AIP2 negatively regulates ABA signaling by targeting ABI3 for post-translational destruction

Small RNA-Sequencing Links Physiological Changes and RdDM Process to Vegetative-to-Floral Transition in Apple

Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined. Here, we performed Illumina sequencing of sRNA libraries prepared from vegetative and floral bud during flower induction of the apple trees. A large number of sRNAs exemplified by 33 previously annotated miRNAs and six novel members display significant differential expression (DE) patterns. Notably, most of these DE-miRNAs in floral transition displayed opposite expression changes in reported phase transition in apple trees. Bioinformatics analysis suggests most of the DE-miRNAs targeted transcripts involved in SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene regulation, stress responses, and auxin and gibberellin (GA) pathways, with further suggestion that there is an inherent link between physiological stress response and metabolism reprogramming during floral transition. We also observed significant changes in 24 nucleotide (nt) sRNAs that are hallmarks for RNA-dependent DNA methylation (RdDM) pathway, suggestive of the correlation between epigenetic modifications and the floral transition. The study not only provides new insight into our understanding of fundamental mechanism of poorly studied floral transition in apple and other woody plants, but also presents important sRNA resource for future in-depth research in the apple flowering physiology

Research Characteristics on Cyanotoxins in Inland Water: Insights from Bibliometrics

Eutrophication is a long-standing ecological and environmental problem, and the severity of harmful algal blooms continues to increase, causing large economic losses globally. One of the most important hazards created by harmful algal blooms is the production of cyanotoxins. This study aimed to analyze the characteristics and development trends of cyanotoxin research through bibliometric analysis. A total of 3265 publications from 1990 to 2020 on cyanotoxins were retrieved from the Science Citation Index (SCI) Expanded database, Web of Science. Over the past 30 years, most research has been concentrated in China (21.4%) and the USA (21.3%). Throughout the study period, microcystin was the focus of the research, accounting for 86% of the total number of publications. A word frequency analysis revealed that as people became more aware of drinking water safety and the construction of large-scale water conservation facilities, &ldquo;reservoirs&rdquo; and &ldquo;rivers&rdquo; became hot words for researchers, while &ldquo;lakes&rdquo; have always been important research objects. Nonmetric multidimensional scaling (NMDS) analysis of studies from the five countries with the largest numbers of publications showed that Chinese researchers typically associate eutrophication with Microcystis, while research subjects in other countries are more extensive and balanced. The development of cyanotoxin research around the world is not even, and we need to push for more research on major lakes that are outside of North America, Europe and China

Research Characteristics on Cyanotoxins in Inland Water: Insights from Bibliometrics

Eutrophication is a long-standing ecological and environmental problem, and the severity of harmful algal blooms continues to increase, causing large economic losses globally. One of the most important hazards created by harmful algal blooms is the production of cyanotoxins. This study aimed to analyze the characteristics and development trends of cyanotoxin research through bibliometric analysis. A total of 3265 publications from 1990 to 2020 on cyanotoxins were retrieved from the Science Citation Index (SCI) Expanded database, Web of Science. Over the past 30 years, most research has been concentrated in China (21.4%) and the USA (21.3%). Throughout the study period, microcystin was the focus of the research, accounting for 86% of the total number of publications. A word frequency analysis revealed that as people became more aware of drinking water safety and the construction of large-scale water conservation facilities, “reservoirs” and “rivers” became hot words for researchers, while “lakes” have always been important research objects. Nonmetric multidimensional scaling (NMDS) analysis of studies from the five countries with the largest numbers of publications showed that Chinese researchers typically associate eutrophication with Microcystis, while research subjects in other countries are more extensive and balanced. The development of cyanotoxin research around the world is not even, and we need to push for more research on major lakes that are outside of North America, Europe and China