Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control.

Readthrough into the 3' untranslated region (3' UTR) of the mRNA results in the production of aberrant proteins. Metazoans efficiently clear readthrough proteins, but the underlying mechanisms remain unknown. Here, we show in Caenorhabditis elegans and mammalian cells that readthrough proteins are targeted by a coupled, two-level quality control pathway involving the BAG6 chaperone complex and the ribosome-collision-sensing protein GCN1. Readthrough proteins with hydrophobic C-terminal extensions (CTEs) are recognized by SGTA-BAG6 and ubiquitylated by RNF126 for proteasomal degradation. Additionally, cotranslational mRNA decay initiated by GCN1 and CCR4/NOT limits the accumulation of readthrough products. Unexpectedly, selective ribosome profiling uncovered a general role of GCN1 in regulating translation dynamics when ribosomes collide at nonoptimal codons, enriched in 3' UTRs, transmembrane proteins, and collagens. GCN1 dysfunction increasingly perturbs these protein classes during aging, resulting in mRNA and proteome imbalance. Our results define GCN1 as a key factor acting during translation in maintaining protein homeostasis.

Experimental coral reef communities transform yet persist under mitigated future ocean warming and acidification.

Coral reefs are among the most sensitive ecosystems affected by ocean warming and acidification, and are predicted to collapse over the next few decades. Reefs are predicted to shift from net accreting calcifier-dominated systems with exceptionally high biodiversity to net eroding algal-dominated systems with dramatically reduced biodiversity. Here, we present a two-year experimental study examining the responses of entire mesocosm coral reef communities to warming (+2 °C), acidification (-0.2 pH units), and combined future ocean (+2 °C, -0.2 pH) treatments. Contrary to modeled projections, we show that under future ocean conditions, these communities shift structure and composition yet persist as novel calcifying ecosystems with high biodiversity. Our results suggest that if climate change is limited to Paris Climate Agreement targets, coral reefs could persist in an altered state rather than collapse.

The visual effect of wind turbines on property values is small and diminishing in space and time.

Renewable power generation is the key to decarbonizing the electricity system. Wind power is the fastest-growing renewable source of electricity in the United States. However, expanding wind capacity often faces local opposition, partly due to a perceived visual disamenity from large wind turbines. Here, we provide a US-wide assessment of the externality costs of wind power generation through the visibility impact on property values. To this end, we create a database on wind turbine visibility, combining information on the site and height of each utility-scale turbine having fed power into the U.S. grid, with a high-resolution elevation map to account for the underlying topography of the landscape. Building on hedonic valuation theory, we statistically estimate the impact of wind turbine visibility on home values, informed by data from the majority of home sales in the United States since 1997. We find that on average, wind turbine visibility negatively affects home values in an economically and statistically significant way in close proximity ([Formula: see text]5 miles/8 km). However, the effect diminishes over time and in distance and is indistinguishable from zero for larger distances and toward the end of our sample.

Optimizing restoration: A holistic spatial approach to deliver Nature's Contributions to People with minimal tradeoffs and maximal equity.

Ecosystem restoration is inherently a complex activity with inevitable tradeoffs in environmental and societal outcomes. These tradeoffs can potentially be large when policies and practices are focused on single outcomes versus joint achievement of multiple outcomes. Few studies have assessed the tradeoffs in Nature's Contributions to People (NCP) and the distributional equity of NCP from forest restoration strategies. Here, we optimized a defined forest restoration area across India with systematic conservation planning to assess the tradeoffs between three NCP: i) climate change mitigation NCP, ii) biodiversity value NCP (habitat created for forest-dependent mammals), and iii) societal NCP (human direct use of restored forests for livelihoods, housing construction material, and energy). We show that restoration plans aimed at a single-NCP tend not to deliver other NCP outcomes efficiently. In contrast, integrated spatial forest restoration plans aimed at achievement of multiple outcomes deliver on average 83.3% (43.2 to 100%) of climate change mitigation NCP, 89.9% (63.8 to 100%) of biodiversity value NCP, and 93.9% (64.5 to 100%) of societal NCP delivered by single-objective plans. Integrated plans deliver NCP more evenly across the restoration area when compared to other plans that identify certain regions such as the Western Ghats and north-eastern India. Last, 38 to 41% of the people impacted by integrated spatial plans belong to socioeconomically disadvantaged groups, greater than their overall representation in India's population. Moving ahead, effective policy design and evaluation integrating ecosystem protection and restoration strategies can benefit from the blueprint we provide in this study for India.

A bioenergy-focused versus a reforestation-focused mitigation pathway yields disparate carbon storage and climate responses.

Limiting global warming to 2 °C requires urgent action on land-based mitigation. This study evaluates the biogeochemical and biogeophysical implications of two alternative land-based mitigation scenarios that aim to achieve the same radiative forcing. One scenario is primarily driven by bioenergy expansion (SSP226Lu-BIOCROP), while the other involves re/afforestation (SSP126Lu-REFOREST). We find that overall, SSP126Lu-REFOREST is a more efficient strategy for removing CO2 from the atmosphere by 2100, resulting in a net carbon sink of 242 ~ 483 PgC with smaller uncertainties compared to SSP226Lu-BIOCROP, which exhibits a wider range of -78 ~ 621 PgC. However, SSP126Lu-REFOREST leads to a relatively warmer planetary climate than SSP226Lu-BIOCROP, and this relative warming can be intensified in certain re/afforested regions where local climates are not favorable for tree growth. Despite the cooling effect on a global scale, SSP226Lu-BIOCROP reshuffles regional warming hotspots, amplifying summer temperatures in vulnerable tropical regions such as Central Africa and Southeast Asia. Our findings highlight the need for strategic land use planning to identify suitable regions for re/afforestation and bioenergy expansion, thereby improving the likelihood of achieving the intended climate mitigation outcomes.

Health and equity implications of individual adaptation to air pollution in a changing climate.

Future climate change can cause more days with poor air quality. This could trigger more alerts telling people to stay inside to protect themselves, with potential consequences for health and health equity. Here, we study the change in US air quality alerts over this century due to fine particulate matter (PM2.5), who they may affect, and how they may respond. We find air quality alerts increase by over 1 mo per year in the eastern United States by 2100 and quadruple on average. They predominantly affect areas with high Black populations and leakier homes, exacerbating existing inequalities and impacting those less able to adapt. Reducing emissions can offer significant annual health benefits ($5,400 per person) by mitigating the effect of climate change on air pollution and its associated risks of early death. Relying on people to adapt, instead, would require them to stay inside, with doors and windows closed, for an extra 142 d per year, at an average cost of $11,000 per person. It appears likelier, however, that people will achieve minimal protection without policy to increase adaptation rates. Boosting adaptation can offer net benefits, even alongside deep emission cuts. New adaptation policies could, for example: reduce adaptation costs; reduce infiltration and improve indoor air quality; increase awareness of alerts and adaptation; and provide measures for those working or living outdoors. Reducing emissions, conversely, lowers everyone's need to adapt, and protects those who cannot adapt. Equitably protecting human health from air pollution under climate change requires both mitigation and adaptation.

US climate policy yields water quality cobenefits in the Mississippi Basin and Gulf of Mexico.

We utilize a coupled economy-agroecology-hydrology modeling framework to capture the cascading impacts of climate change mitigation policy on agriculture and the resulting water quality cobenefits. We analyze a policy that assigns a range of United States government's social cost of carbon estimates ($51, $76, and $152/ton of CO2-equivalents) to fossil fuel-based CO2 emissions. This policy raises energy costs and, importantly for agriculture, boosts the price of nitrogen fertilizer production. At the highest carbon price, US carbon emissions are reduced by about 50%, and nitrogen fertilizer prices rise by about 90%, leading to an approximate 15% reduction in fertilizer applications for corn production across the Mississippi River Basin. Corn and soybean production declines by about 7%, increasing crop prices by 6%, while nitrate leaching declines by about 10%. Simulated nitrate export to the Gulf of Mexico decreases by 8%, ultimately shrinking the average midsummer area of the Gulf of Mexico hypoxic area by 3% and hypoxic volume by 4%. We also consider the additional benefits of restored wetlands to mitigate nitrogen loading to reduce hypoxia in the Gulf of Mexico and find a targeted wetland restoration scenario approximately doubles the effect of a low to moderate social cost of carbon. Wetland restoration alone exhibited spillover effects that increased nitrate leaching in other parts of the basin which were mitigated with the inclusion of the carbon policy. We conclude that a national climate policy aimed at reducing greenhouse gas emissions in the United States would have important water quality cobenefits.

Investing in mini-livestock production for food security and carbon neutrality in China.

Future food farming technology faces challenges that must integrate the core goal of keeping the global temperature increase within 1.5 °C without reducing food security and nutrition. Here, we show that boosting the production of insects and earthworms based on food waste and livestock manure to provide food and feed in China will greatly contribute to meeting the country's food security and carbon neutrality pledges. By substituting domestic products with mini-livestock (defined as earthworms and insects produced for food or feed) protein and utilizing the recovered land for bioenergy production plus carbon capture and storage, China's agricultural sector could become carbon-neutral and reduce feed protein imports to near zero. This structural change may lead to reducing greenhouse gas emissions by 2,350 Tg CO2eq per year globally when both domestic and imported products are substituted. Overall, the success of mini-livestock protein production in achieving carbon neutrality and food security for China and its major trading partners depends on how the substitution strategies will be implemented and how the recovered agricultural land will be managed, e.g., free use for afforestation and bioenergy or by restricting this land to food crop use. Using China as an example, this study also demonstrates the potential of mini-livestock for decreasing the environmental burden of food production in general.

The weekly cycle of photosynthesis in Europe reveals the negative impact of particulate pollution on ecosystem productivity.

Aerosols can affect photosynthesis through radiative perturbations such as scattering and absorbing solar radiation. This biophysical impact has been widely studied using field measurements, but the sign and magnitude at continental scales remain uncertain. Solar-induced fluorescence (SIF), emitted by chlorophyll, strongly correlates with photosynthesis. With recent advancements in Earth observation satellites, we leverage SIF observations from the Tropospheric Monitoring Instrument (TROPOMI) with unprecedented spatial resolution and near-daily global coverage, to investigate the impact of aerosols on photosynthesis. Our analysis reveals that on weekends when there is more plant-available sunlight due to less particulate pollution, 64% of regions across Europe show increased SIF, indicating more photosynthesis. Moreover, we find a widespread negative relationship between SIF and aerosol loading across Europe. This suggests the possible reduction in photosynthesis as aerosol levels increase, particularly in ecosystems limited by light availability. By considering two plausible scenarios of improved air quality-reducing aerosol levels to the weekly minimum 3-d values and levels observed during the COVID-19 period-we estimate a potential of 41 to 50 Mt net additional annual CO2 uptake by terrestrial ecosystems in Europe. This work assesses human impacts on photosynthesis via aerosol pollution at continental scales using satellite observations. Our results highlight i) the use of spatiotemporal variations in satellite SIF to estimate the human impacts on photosynthesis and ii) the potential of reducing particulate pollution to enhance ecosystem productivity.

Field interventions for climate change mitigation behaviors: A second-order meta-analysis.

Behavioral change is essential to mitigate climate change. To advance current knowledge, we synthesize research on interventions aiming to promote climate change mitigation behaviors in field settings. In a preregistered second-order meta-analysis, we assess the overall effect of 10 meta-analyses, incorporating a total of 430 primary studies. In addition, we assess subgroup analyses for six types of interventions, five behaviors, and three publication bias adjustments. Results showed that climate change mitigation interventions were generally effective (dunadjusted = 0.31, 95% CI [0.30, 0.32]). A follow-up analysis using only unique primary studies, adjusted for publication bias, provides a more conservative overall estimate (d = 0.18, 95% CI [0.13, 0.24]). This translates into a mean treatment effect of 7 percentage points. Furthermore, in a subsample of adequately powered large-scale interventions (n > 9,000, k = 32), the effect was adjusted downward to approximately 2 percentage points. This discrepancy might be because large-scale interventions often target nonvoluntary participants by less direct techniques (e.g., "home energy reports") while small-scale interventions often target voluntary participants by more direct techniques (e.g., face-to-face interactions). Subgroup analyses showed that interventions based on social comparisons or financial incentives were the most effective, while education or feedback was the least effective. These results provide a comprehensive state-of-the-art summary of climate change mitigation interventions, guiding both future research and practice.

Transmission dynamics, complications and mitigation strategies of the current mpox outbreak: A comprehensive review with bibliometric study.

As the mankind counters the ongoing COVID-19 pandemic by the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), it simultaneously witnesses the emergence of mpox virus (MPXV) that signals at global spread and could potentially lead to another pandemic. Although MPXV has existed for more than 50 years now with most of the human cases being reported from the endemic West and Central African regions, the disease is recently being reported in non-endemic regions too that affect more than 50 countries. Controlling the spread of MPXV is important due to its potential danger of a global spread, causing severe morbidity and mortality. The article highlights the transmission dynamics, zoonosis potential, complication and mitigation strategies for MPXV infection, and concludes with suggested 'one health' approach for better management, control and prevention. Bibliometric analyses of the data extend the understanding and provide leads on the research trends, the global spread, and the need to revamp the critical research and healthcare interventions. Globally published mpox-related literature does not align well with endemic areas/regions of occurrence which should ideally have been the scenario. Such demographic and geographic gaps between the location of the research work and the endemic epicentres of the disease need to be bridged for greater and effective translation of the research outputs to pubic healthcare systems, it is suggested.

A weakened AMOC may prolong greenhouse gas-induced Mediterranean drying even with significant and rapid climate change mitigation.

The Mediterranean region has been identified as a climate hot spot, with models projecting a robust warming and rainfall decline in response to increasing greenhouse gases. The projected rainfall decline would have impacts on agriculture and water resources. Can such changes be reversed with significant reductions in greenhouse gases? To explore this, we examine large ensembles of a high-resolution climate model with various future radiative forcing scenarios, including a scenario with substantial reductions in greenhouse gas concentrations beginning in the mid-21st century. In response to greenhouse gas reductions, the Mediterranean summer rainfall decline is reversed, but the winter rainfall decline continues. This continued winter rainfall decline results from a persistent atmospheric anticyclone over the western Mediterranean. Using additional numerical experiments, we show that the anticyclone and continued winter rainfall decline are attributable to greenhouse gas-induced weakening of the Atlantic Meridional Overturning Circulation (AMOC) that continues throughout the 21st century. The persistently weak AMOC, in concert with greenhouse gas reductions, leads to rapid cooling and sea ice growth in the subpolar North Atlantic. This cooling leads to a strong cyclonic atmospheric circulation anomaly over the North Atlantic subpolar gyre and, via atmospheric teleconnections, to the anticyclonic circulation anomaly over the Mediterranean. The failure to reverse the winter rainfall decline, despite substantial climate change mitigation, is an example of a "surprise" in the climate system. In this case, a persistent AMOC change unexpectedly impedes the reversibility of Mediterranean climate change. Such surprises could complicate pathways toward full climate recovery.

Mitigation and adaptation emissions embedded in the broader climate transition.

Climate change necessitates a global effort to reduce greenhouse gas emissions while adapting to increased climate risks. This broader climate transition will involve large-scale global interventions including renewable energy deployment, coastal protection and retreat, and enhanced space cooling, all of which will result in CO2 emissions from energy and materials use. Yet, the magnitude of the emissions embedded in these interventions remains unconstrained, opening the potential for underaccounting of emissions and conflicts or synergies between mitigation and adaptation goals. Here, we use a suite of models to estimate the CO2 emissions embedded in the broader climate transition. For a gradual decarbonization pathway limiting warming to 2 °C, selected adaptation-related interventions will emit ∼1.3 GtCO2 through 2100, while emissions from energy used to deploy renewable capacity are much larger at ∼95 GtCO2. Together, these emissions are equivalent to over 2 y of current global emissions and 8.3% of the remaining carbon budget for 2 °C. Total embedded transition emissions are reduced by ∼80% to 21.2 GtCO2 under a rapid pathway limiting warming to 1.5 °C. However, they roughly double to 185 GtCO2 under a delayed pathway consistent with current policies (2.7 °C warming by 2100), mainly because a slower transition relies more on fossil fuel energy. Our results provide a holistic assessment of carbon emissions from the transition itself and suggest that these emissions can be minimized through more ambitious energy decarbonization. We argue that the emissions from mitigation, but likely much less so from adaptation, are of sufficient magnitude to merit greater consideration in climate science and policy.

Full adoption of the most effective strategies to mitigate methane emissions by ruminants can help meet the 1.5 °C target by 2030 but not 2050.

To meet the 1.5 °C target, methane (CH4) from ruminants must be reduced by 11 to 30% by 2030 and 24 to 47% by 2050 compared to 2010 levels. A meta-analysis identified strategies to decrease product-based (PB; CH4 per unit meat or milk) and absolute (ABS) enteric CH4 emissions while maintaining or increasing animal productivity (AP; weight gain or milk yield). Next, the potential of different adoption rates of one PB or one ABS strategy to contribute to the 1.5 °C target was estimated. The database included findings from 430 peer-reviewed studies, which reported 98 mitigation strategies that can be classified into three categories: animal and feed management, diet formulation, and rumen manipulation. A random-effects meta-analysis weighted by inverse variance was carried out. Three PB strategies­namely, increasing feeding level, decreasing grass maturity, and decreasing dietary forage-to-concentrate ratio­decreased CH4 per unit meat or milk by on average 12% and increased AP by a median of 17%. Five ABS strategies­namely CH4 inhibitors, tanniferous forages, electron sinks, oils and fats, and oilseeds­decreased daily methane by on average 21%. Globally, only 100% adoption of the most effective PB and ABS strategies can meet the 1.5 °C target by 2030 but not 2050, because mitigation effects are offset by projected increases in CH4 due to increasing milk and meat demand. Notably, by 2030 and 2050, low- and middle-income countries may not meet their contribution to the 1.5 °C target for this same reason, whereas high-income countries could meet their contributions due to only a minor projected increase in enteric CH4 emissions.

Potential for perceived failure of stratospheric aerosol injection deployment.

As anthropogenic activities warm the Earth, the fundamental solution of reducing greenhouse gas emissions remains elusive. Given this mitigation gap, global warming may lead to intolerable climate changes as adaptive capacity is exceeded. Thus, there is emerging interest in solar radiation modification, which is the process of deliberately increasing Earth's albedo to cool the planet. Stratospheric aerosol injection (SAI)-the theoretical deployment of particles in the stratosphere to enhance reflection of incoming solar radiation-is one strategy to slow, pause, or reverse global warming. If SAI is ever pursued, it will likely be for a specific aim, such as affording time to implement mitigation strategies, lessening extremes, or reducing the odds of reaching a biogeophysical tipping point. Using an ensemble climate model experiment that simulates the deployment of SAI in the context of an intermediate greenhouse gas trajectory, we quantified the probability that internal climate variability masks the effectiveness of SAI deployment on regional temperatures. We found that while global temperature was stabilized, substantial land areas continued to experience warming. For example, in the SAI scenario we explored, up to 55% of the global population experienced rising temperatures over the decade following SAI deployment and large areas exhibited high probability of extremely hot years. These conditions could cause SAI to be perceived as a failure. Countries with the largest economies experienced some of the largest probabilities of this perceived failure. The potential for perceived failure could therefore have major implications for policy decisions in the years immediately following SAI deployment.

Trade-offs between bycatch and target catches in static versus dynamic fishery closures.

While there have been recent improvements in reducing bycatch in many fisheries, bycatch remains a threat for numerous species around the globe. Static spatial and temporal closures are used in many places as a tool to reduce bycatch. However, their effectiveness in achieving this goal is uncertain, particularly for highly mobile species. We evaluated evidence for the effects of temporal, static, and dynamic area closures on the bycatch and target catch of 15 fisheries around the world. Assuming perfect knowledge of where the catch and bycatch occurs and a closure of 30% of the fishing area, we found that dynamic area closures could reduce bycatch by an average of 57% without sacrificing catch of target species, compared to 16% reductions in bycatch achievable by static closures. The degree of bycatch reduction achievable for a certain quantity of target catch was related to the correlation in space and time between target and bycatch species. If the correlation was high, it was harder to find an area to reduce bycatch without sacrificing catch of target species. If the goal of spatial closures is to reduce bycatch, our results suggest that dynamic management provides substantially better outcomes than classic static marine area closures. The use of dynamic ocean management might be difficult to implement and enforce in many regions. Nevertheless, dynamic approaches will be increasingly valuable as climate change drives species and fisheries into new habitats or extended ranges, altering species-fishery interactions and underscoring the need for more responsive and flexible regulatory mechanisms.

Mitigating climate disruption in time: A self-consistent approach for avoiding both near-term and long-term global warming.

The ongoing and projected impacts from human-induced climate change highlight the need for mitigation approaches to limit warming in both the near term (<2050) and the long term (>2050). We clarify the role of non-CO2 greenhouse gases and aerosols in the context of near-term and long-term climate mitigation, as well as the net effect of decarbonization strategies targeting fossil fuel (FF) phaseout by 2050. Relying on Intergovernmental Panel on Climate Change radiative forcing, we show that the net historical (2019 to 1750) radiative forcing effect of CO2 and non-CO2 climate forcers emitted by FF sources plus the CO2 emitted by land-use changes is comparable to the net from non-CO2 climate forcers emitted by non-FF sources. We find that mitigation measures that target only decarbonization are essential for strong long-term cooling but can result in weak near-term warming (due to unmasking the cooling effect of coemitted aerosols) and lead to temperatures exceeding 2 °C before 2050. In contrast, pairing decarbonization with additional mitigation measures targeting short-lived climate pollutants and N2O, slows the rate of warming a decade or two earlier than decarbonization alone and avoids the 2 °C threshold altogether. These non-CO2 targeted measures when combined with decarbonization can provide net cooling by 2030 and reduce the rate of warming from 2030 to 2050 by about 50%, roughly half of which comes from methane, significantly larger than decarbonization alone over this time frame. Our analysis demonstrates the need for a comprehensive CO2 and targeted non-CO2 mitigation approach to address both the near-term and long-term impacts of climate disruption.

Carbon mineralization with concurrent critical metal recovery from olivine.

Carbon dioxide utilization for enhanced metal recovery (EMR) during mineralization has been recently developed as part of CCUS (carbon capture, utilization, and storage). This paper describes fundamental studies on integrating CO2 mineralization and concurrent selective metal extraction from natural olivine. Nearly 90% of nickel and cobalt extraction and mineral carbonation efficiency are achieved in a highly selective, single-step process. Direct aqueous mineral carbonation releases Ni2+ and Co2+ into aqueous solution for subsequent recovery, while Mg2+ and Fe2+ simultaneously convert to stable mineral carbonates for permanent CO2 storage. This integrated process can be completed in neutral aqueous solution. Introduction of a metal-complexing ligand during mineral carbonation aids the highly selective extraction of Ni and Co over Fe and Mg. The ligand must have higher stability for Ni-/Co- complex ions compared with the Fe(II)-/Mg- complex ions and divalent metal carbonates. This single-step process with a suitable metal-complexing ligand is robust and utilizes carbonation processes under various kinetic regimes. This fundamental study provides a framework for further development and successful application of direct aqueous mineral carbonation with concurrent EMR. The enhanced metal extraction and CO2 mineralization process may have implications for the clean energy transition, CO2 storage and utilization, and development of new critical metal resources.

Preparing Patients for Oral Immunotherapy (PPOINT): International Delphi consensus for procedural preparation and consent.

BACKGROUND: Despite the promise of oral immunotherapy (OIT) to treat food allergies, this procedure is associated with potential risk. There is no current agreement about what elements should be included in the preparatory or consent process. OBJECTIVE: We developed consensus recommendations about the OIT process considerations and patient-specific factors that should be addressed before initiating OIT and developed a consensus OIT consent process and information form. METHODS: We convened a 36-member Preparing Patients for Oral Immunotherapy (PPOINT) panel of allergy experts to develop a consensus OIT patient preparation, informed consent process, and framework form. Consensus for themes and statements was reached using Delphi methodology, and the consent information form was developed. RESULTS: The expert panel reached consensus for 4 themes and 103 statements specific to OIT preparatory procedures, of which 76 statements reached consensus for inclusion specific to the following themes: general considerations for counseling patients about OIT; patient- and family-specific factors that should be addressed before initiating OIT and during OIT; indications for initiating OIT; and potential contraindications and precautions for OIT. The panel reached consensus on 9 OIT consent form themes: benefits, risks, outcomes, alternatives, risk mitigation, difficulties/challenges, discontinuation, office policies, and long-term management. From these themes, 219 statements were proposed, of which 189 reached consensus, and 71 were included on the consent information form. CONCLUSION: We developed consensus recommendations to prepare and counsel patients for safe and effective OIT in clinical practice with evidence-based risk mitigation. Adoption of these recommendations may help standardize clinical care and improve patient outcomes and quality of life.

Enhancing RNA-seq bias mitigation with the Gaussian self-benchmarking framework: towards unbiased sequencing data.

BACKGROUND: RNA sequencing is a vital technique for analyzing RNA behavior in cells, but it often suffers from various biases that distort the data. Traditional methods to address these biases are typically empirical and handle them individually, limiting their effectiveness. Our study introduces the Gaussian Self-Benchmarking (GSB) framework, a novel approach that leverages the natural distribution patterns of guanine (G) and cytosine (C) content in RNA to mitigate multiple biases simultaneously. This method is grounded in a theoretical model, organizing k-mers based on their GC content and applying a Gaussian model for alignment to ensure empirical sequencing data closely match their theoretical distribution. RESULTS: The GSB framework demonstrated superior performance in mitigating sequencing biases compared to existing methods. Testing with synthetic RNA constructs and real human samples showed that the GSB approach not only addresses individual biases more effectively but also manages co-existing biases jointly. The framework's reliance on accurately pre-determined parameters like mean and standard deviation of GC content distribution allows for a more precise representation of RNA samples. This results in improved accuracy and reliability of RNA sequencing data, enhancing our understanding of RNA behavior in health and disease. CONCLUSIONS: The GSB framework presents a significant advancement in RNA sequencing analysis by providing a well-validated, multi-bias mitigation strategy. It functions independently from previously identified dataset flaws and sets a new standard for unbiased RNA sequencing results. This development enhances the reliability of RNA studies, broadening the potential for scientific breakthroughs in medicine and biology, particularly in genetic disease research and the development of targeted treatments.