Sequence modeling and design from molecular to genome scale with Evo

Science, Год журнала: 2024, Номер 386(6723)

Опубликована: Ноя. 14, 2024

The genome is a sequence that encodes the DNA, RNA, and proteins orchestrate an organism’s function. We present Evo, long-context genomic foundation model with frontier architecture trained on millions of prokaryotic phage genomes, report scaling laws DNA to complement observations in language vision. Evo generalizes across proteins, enabling zero-shot function prediction competitive domain-specific models generation functional CRISPR-Cas transposon systems, representing first examples protein-RNA protein-DNA codesign model. also learns how small mutations affect whole-organism fitness generates megabase-scale sequences plausible architecture. These capabilities span molecular scales complexity, advancing our understanding control biology.

Язык: Английский

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Sequence modeling and design from molecular to genome scale with Evo

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 27, 2024

The genome is a sequence that completely encodes the DNA, RNA, and proteins orchestrate function of whole organism. Advances in machine learning combined with massive datasets genomes could enable biological foundation model accelerates mechanistic understanding generative design complex molecular interactions. We report Evo, genomic enables prediction generation tasks from to scale. Using an architecture based on advances deep signal processing, we scale Evo 7 billion parameters context length 131 kilobases (kb) at single-nucleotide, byte resolution. Trained prokaryotic genomes, can generalize across three fundamental modalities central dogma biology perform zero-shot competitive with, or outperforms, leading domain-specific language models. also excels multi-element tasks, which demonstrate by generating synthetic CRISPR-Cas complexes entire transposable systems for first time. information learned over predict gene essentiality nucleotide resolution generate coding-rich sequences up 650 kb length, orders magnitude longer than previous methods. multi-modal multi-scale provides promising path toward improving our control multiple levels complexity.

Язык: Английский

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Bending the curve of global freshwater biodiversity loss: what are the prospects?

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Год журнала: 2024, Номер unknown

Опубликована: Сен. 2, 2024

ABSTRACT Freshwater biodiversity conservation has received substantial attention in the scientific literature and is finally being recognized policy frameworks such as Global Biodiversity Framework its associated targets for 2030. This important progress. Nonetheless, freshwater species continue to be confronted with high levels of imperilment widespread ecosystem degradation. An Emergency Recovery Plan (ERP) proposed 2020 comprises six measures intended “bend curve” loss, if they are widely adopted adequately supported. We review evidence suggesting that combined intensity persistent emerging threats become so serious current projected efforts preserve, protect restore inland‐water ecosystems may insufficient avert losses coming decades. In particular, climate change, complex harmful impacts, will frustrate attempts prevent from already affected by multiple threats. Interactions among these limit recovery populations exacerbate declines resulting local or even global extinctions, especially low‐viability degraded fragmented ecosystems. addition impediments represented we identify several other areas where absolute scarcity fresh water, inadequate information predictive capacity, a failure mitigate anthropogenic stressors, liable set limits on biodiversity. Implementation ERP rapidly at scale through many dispersed actions focused regions intense threat, together an intensification ex‐situ efforts, necessary preserve native during increasingly uncertain climatic future which poorly understood, emergent interacting have more influential. But implementation must accompanied improve energy food security humans – without further compromising condition Unfortunately, political policies arrest environmental challenges change do not inspire confidence about possible success ERP. parts world, Anthropocene seems certain include extended periods uncontaminated surface runoff inevitably appropriated humans. Unless there step‐change societal awareness commitment biodiversity, established methods protecting bend curve enough continued degradation loss.

Язык: Английский

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The Nexus Between Innovation, Value Chains, and Social Sustainability in the Context of a Bioeconomy Upgrading

Business Strategy & Development, Год журнала: 2025, Номер 8(1)

Опубликована: Фев. 26, 2025

ABSTRACT The transition to a bio‐based economy promises path toward reducing greenhouse gas emissions while creating new business opportunities. However, sustainable implies shifting from high‐volume, low‐value biomass technologies advanced biotechnologies that minimize requirements and negative environmental impacts maximizing economic value‐added. This accelerated innovation process, which we define as bioeconomy upgrading, will likely reshape value chain structures affect benefits distribution. Yet, previous studies have ignored the relationship between chains technological change in bioeconomy. Using qualitative approach based on mapping, develop an overarching conceptual framework six representative models of study nexus innovation, chains, social sustainability is illustrated with up‐to‐date examples validated through expert survey. We find upgrading associated shorter more vertically coordinated leading role by big firms, higher levels research cooperation among firms. Finally, argue these changes organizational coming may expose most vulnerable actors risks thus propose some lines thought regarding potential distributional effects.

Язык: Английский

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Bionovelty and ecological restoration

Restoration Ecology, Год журнала: 2024, Номер 32(5)

Опубликована: Апрель 15, 2024

Anthropogenic activity has irreparably altered the ecological fabric of Earth. The emergence novelty from diverse drivers change is an increasingly challenging dimension ecosystem restoration. At same time, restorationist's tool kit continues to grow, including a variety powerful and prevalent technologies. Thus, restoration finds itself at center intersecting challenges. How should we respond common environmental system states with little or no historical precedent, whilst considering appropriate deployment potentially consequential largely untested interventions that may give rise organisms, states, and/or processes are likewise without precedent? We use term bionovelty encapsulate these themes examine implications for

Язык: Английский

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Antioxidant Capacity and Phenolics Profile of Portuguese Traditional Cultivars of Apples and Pears and Their By-Products: On the Way to Newer Applications

Foods, Год журнала: 2023, Номер 12(7), С. 1537 - 1537

Опубликована: Апрель 5, 2023

Pears (Pyrus communis L.) and apples (Malus domestica Borkh.) are two of the most popular fruits worldwide. The phenolic compounds they offer associated with human health benefits due to their antioxidant properties. Since these fruits' by-products not yet fully exploited, it is important characterize them, especially in terms aim this study was determine properties old traditional cultivars, six regional pear cultivars five apple grown Alcobaça region (Portugal). Antioxidant capacity assays were used evaluate Generally, capacity, total phenolics content (TPC), flavonoids (TFC) fruit byproducts (both seeds peels) higher than corresponding mesocarp, indicating potential as sources beneficial compounds. Moreover, a UHPLC-ToF-MS method optimized validated order quantify 21 distinct samples. analytical method's suitability for quantifying demonstrated by an evaluation linearity, limit detection, quantification, precision accuracy. This composition samples (local) cultivars. highest concentrations phlorizin chlorogenic acid. Principal component analysis (PCA) separate species while emphasizing similarities differences.

Язык: Английский

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Synthetic biology in Indonesia: Potential and projection in a country with mega biodiversity

Biotechnology Notes, Год журнала: 2023, Номер 4, С. 41 - 48

Опубликована: Янв. 1, 2023

Synthetic biology has gained many interest around the globe in last two decades, not only due to its rapid development but also potential provide addressable solutions using standardized design of biological systems. Considering huge population, biodiversity, and natural resources, Indonesia could play an important role shaping future synthetic towards a sustainable bio-circular economy. Here, we overview Indonesia, especially on exploring our biodiversity. We discuss some potentials solving national issues. Furthermore, projection landscape Indonesia. In addition, briefly explain challenges that may arise during development.

Язык: Английский

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A horizon scan of global biological conservation issues for 2024

Trends in Ecology & Evolution, Год журнала: 2023, Номер 39(1), С. 89 - 100

Опубликована: Дек. 18, 2023

We present the results of our 15th horizon scan novel issues that could influence biological conservation in future. From an initial list 96 issues, international panel scientists and practitioners identified 15 we consider important for societies worldwide to track potentially respond to. Issues are within or represent a substantial positive negative step-change with global regional extents. For example, new sources hydrogen fuel changes deep-sea currents may have profound impacts on marine terrestrial ecosystems. Technological advances be include benchtop DNA printers industrialisation approaches can create high-protein food from air, reducing pressure land production.

Язык: Английский

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The current status of the use of genetic modification and editing to improve biodiversity and ecological sustainability

All Life, Год журнала: 2024, Номер 17(1)

Опубликована: Окт. 25, 2024

Язык: Английский

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Horizon scanning of potential environmental applications of terrestrial animals, fish, algae and microorganisms produced by genetic modification, including the use of new genomic techniques

Frontiers in Genome Editing, Год журнала: 2024, Номер 6

Опубликована: Июнь 13, 2024

With scientific progress and the development of new genomic techniques (NGTs), spectrum organisms modified for various purposes is rapidly expanding includes a wide range taxonomic groups. An improved understanding which newly developed products may be introduced into market released environment in near more distant future particular interest policymakers, regulatory authorities, risk assessors. To address this information need, we conducted horizon scanning (HS) potential environmental applications four groups organisms: terrestrial animals (excluding insects with gene drives), fish, algae microorganisms. We applied formal scoping review methodology comprising structured search literature followed by eligibility screening, complemented survey grey literature, websites databases. In all identified broad stages basic as well advanced research, limited number are on, or ready to placed market. Research on GM including fish focused farmed primarily targets traits increase performance, influence reproduction, convey resistance against diseases. HS were unicellular, than half articles concerning biofuel production. use include biocontrol bioremediation, also main From assessor's perspective these entail multitude possible pathways harm. The current level experience amount available could constitute significant challenge future, assessors competent authorities urgently need prepare.

Язык: Английский

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