The Millennium Problems for Biology
The Millennium Problems for Biology
生物学的千年难题
01 Origins of life Demonstrate the emergence of life from chemical precursors in a laboratory setting. Specifically, demonstrate the unassisted emergence of self-replicating RNA- and protein-based cells from a plausible primordial soup with a plausible energy source. A “cell” may be any compartment with a defined boundary. To be considered successful, the following conditions must be met. Firstly, it must be shown that the emergent cells can increase their abundance by at least a factor of 10⁶ (roughly 20 generations), when provided with sufficient primordial soup and energy. Secondly, it must be plausible that division could continue indefinitely given sufficient energy and primordial soup. For example, solutions that involve the cells monotonically decreasing in size over successive divisions would not be accepted. Finally, the cells must have a clear way of encoding heritable genetic information, i.e., the molecular composition of the cells must be causally determined at least in part by information stored within the cell. Solutions that involve storing the information in the form of nucleic acids, polypeptides, or similar polymers are strongly preferred. Solutions in which the existence of heritable genetic information is ambiguous or controversial will be rejected by default.
01 生命起源 在实验室环境下证明生命从化学前体中涌现。具体而言，证明在合理的原始汤和能源条件下，能够自发产生基于 RNA 和蛋白质的自我复制细胞。所谓“细胞”可以是任何具有明确边界的区室。要被视为成功，必须满足以下条件：首先，必须证明当提供充足的原始汤和能量时，涌现出的细胞数量至少能增加 10⁶ 倍（约 20 代）。其次，必须证明在有充足能量和原始汤的情况下，细胞分裂能够无限持续。例如，那些在连续分裂过程中细胞体积单调递减的方案将不被接受。最后，细胞必须有一种明确的方式来编码可遗传的遗传信息，即细胞的分子组成必须至少部分由存储在细胞内的信息所决定。强烈建议采用以核酸、多肽或类似聚合物形式存储信息的方案。对于可遗传遗传信息存在与否模糊或具有争议的方案，将默认予以拒绝。
02 Cryopreservation Demonstrate the ability to cryopreserve and recover live wild-type mice with high viability. Specifically, demonstrate the reversible cryopreservation of live, intact, wild-type adult mice in a whole-body frozen or vitrified state. The mice must remain frozen or vitrified for at least 24 hours, must be recovered with >99% viability, and must not suffer any permanent organ damage or bodily harm. Somatic genetic engineering is discouraged but permitted. All experiments must be conducted with ethics approval.
02 低温保存 证明能够以高存活率对野生型活体小鼠进行低温保存并使其复苏。具体而言，证明能够对完整的野生型成年活体小鼠进行全身冷冻或玻璃化状态下的可逆低温保存。小鼠必须保持冷冻或玻璃化状态至少 24 小时，复苏后的存活率必须大于 99%，且不得遭受任何永久性的器官损伤或身体伤害。不鼓励但允许使用体细胞基因工程。所有实验必须在获得伦理批准的情况下进行。
03 The reverse translatase Create an enzyme that can “reverse translate” an arbitrary peptide sequence into RNA or DNA. Specifically, create a purified protein catalyst or fixed protein complex that processively reads an untagged polypeptide and synthesizes a covalent nucleic acid strand encoding its residue sequence under a preregistered codon convention, without a nucleic-acid template, preattached sequence barcode, residue-specific operator cycle, or database lookup. The resulting nucleic acid strand must be compatible with ordinary polymerases, ligases, and other similar enzymes, i.e., if nucleic acids other than RNA or DNA are used, they must be compatible with downstream amplification or sequencing reactions. For the challenge to be considered complete, at least 100 random peptide sequences of at least 50 amino acids each must be preregistered, synthesized, and pooled. It must then be shown that the sequences of these peptides can be inferred, without reference to a dictionary, by reverse translation and sequencing with at least 90% sequence accuracy. Moreover, the average read length must be at least 25 residues, and the average read quality score should be at least Q10.
03 反转录酶（蛋白质到核酸） 创造一种能够将任意多肽序列“反向翻译”为 RNA 或 DNA 的酶。具体而言，创造一种纯化的蛋白质催化剂或固定的蛋白质复合物，能够在无需核酸模板、预附序列条形码、残基特异性操作循环或数据库查询的情况下，根据预先注册的密码子约定，过程性地读取未标记的多肽并合成编码其残基序列的共价核酸链。所得核酸链必须与普通聚合酶、连接酶及其他类似酶兼容，即如果使用 RNA 或 DNA 以外的核酸，它们必须与下游的扩增或测序反应兼容。要完成此挑战，必须预先注册、合成并汇集至少 100 条随机多肽序列，每条序列至少包含 50 个氨基酸。随后必须证明，在不参考字典的情况下，通过反向翻译和测序，可以推断出这些多肽的序列，且序列准确率至少达到 90%。此外，平均读取长度必须至少为 25 个残基，平均读取质量分数应至少为 Q10。
04 Improve Rubisco Produce a Rubisco enzyme with specificity and enzymatic turnover beyond the naturally occurring pareto frontier. Specifically, produce an enzyme that catalyzes the carboxylation of ribulose-1,5-bisphosphate with a specificity for carbon dioxide over oxygen (Sc/o) at least as high as that of Galdieria Partita Rubisco, and with an enzymatic turnover (kcat) at least as high as that of maize Rubisco. To be considered successful, the specificity and enzymatic turnovers of the candidate enzyme must be measured in paired enzyme assays using G. Partita Rubisco and maize Rubisco as controls, respectively. The candidate enzyme may be designed de novo, discovered in nature, or engineered or evolved from naturally occurring starting points.
04 改进 Rubisco 生产一种在特异性和酶促转换率上超越自然界帕累托前沿的 Rubisco 酶。具体而言，生产一种催化核酮糖-1,5-二磷酸羧化反应的酶，其对二氧化碳相对于氧气的特异性（Sc/o）至少应达到 Galdieria Partita Rubisco 的水平，且其酶促转换率（kcat）至少应达到玉米 Rubisco 的水平。要被视为成功，候选酶的特异性和酶促转换率必须在配对酶测定中进行测量，并分别以 G. Partita Rubisco 和玉米 Rubisco 作为对照。候选酶可以通过从头设计、自然界发现，或从天然存在的起点进行工程化或进化而来。
05 The quadruplet cell Produce a living cell that uses a four-base codon code. Specifically, produce a living and replicating cell in which every protein-coding sequence, including the translation machinery itself, is encoded as uninterrupted nonoverlapping quadruplet codons, without detectable triplet decoding. The encoding scheme must be a bona fide quadruplet encoding, i.e., in the quadruplet encoding, the probability that a mutation is non-synonymous must be similar regardless of the index of the mutation in the codon. For example, quadruplet encodings in which the first three codon positions are always or almost always sufficient to specify the encoded amino acid will not be accepted. (Contributed by Erika Alden DeBenedictis)
05 四联体细胞 生产一种使用四碱基密码子的活细胞。具体而言，生产一种能够存活并复制的细胞，其中每一个蛋白质编码序列（包括翻译机器本身）都编码为不间断、非重叠的四联体密码子，且不存在可检测到的三联体解码。该编码方案必须是真正的四联体编码，即在四联体编码中，无论突变在密码子中的位置如何，突变导致非同义突变的概率必须相似。例如，如果前三个密码子位置总是或几乎总是足以指定所编码的氨基酸，则此类四联体编码将不被接受。（由 Erika Alden DeBenedictis 贡献）
06 Somatic limb regeneration Demonstrate the ability to regenerate lost limbs in adult wild-type mice. Specifically, demonstrate, in an adult wild type mouse, the reproducible ability to regrow limbs following amputation. Following regeneration, the mouse must perform indistinguishably from controls in a standard battery of motor function tests, must demonstrate indistinguishable sensory perception in the regrown limb, and blinded observers must not be capable of distinguishing which limb was regrown based on non-invasive observational data. All experiments must be conducted with ethics approval.
06 体细胞肢体再生 证明在成年野生型小鼠中再生缺失肢体的能力。具体而言，证明在成年野生型小鼠中，截肢后具有可重复的肢体再生能力。再生后，小鼠在标准运动功能测试中的表现必须与对照组无异，再生肢体必须表现出与正常肢体无异的感觉感知，且盲法观察者无法根据非侵入性观察数据区分出哪一肢是再生肢体。所有实验必须在获得伦理批准的情况下进行。
07 Bacterial production of gene therapies Demonstrate the ability to produce gene therapies in a bacterial host. Specifically, produce infectious replication-incompetent AAV and lentivirus in bacteria. The particles must contain a pre-specified viral genome; the ratio of physical capsids to viral genomes and the ratio of infectious units to viral genomes must be similar to the ratios obtained when purifying viruses from mammalian cell culture; and the viral genomes must be nuclease-resistant. It is anticipated that producing lentivirus in bacteria may be much more challenging than producing AAV, and thus demonstrating the ability to produce AAV on its own will be considered a partial success.
07 基因疗法的细菌生产 证明在细菌宿主中生产基因疗法的能力。具体而言，在细菌中生产具有感染性但无法复制的 AAV（腺相关病毒）和慢病毒。这些颗粒必须包含预先指定的病毒基因组；物理衣壳与病毒基因组的比率以及感染单位与病毒基因组的比率，必须与从哺乳动物细胞培养物中纯化病毒时获得的比率相似；且病毒基因组必须具有抗核酸酶能力。预计在细菌中生产慢病毒比生产 AAV 要困难得多，因此仅证明生产 AAV 的能力将被视为部分成功。
08 Programmable proteases Demonstrate the ability to produce enzymes on demand that will specifically and efficiently cut a specific protein sequence. Specifically, given a blinded, access…
08 可编程蛋白酶 证明能够按需生产能够特异性且高效切割特定蛋白质序列的酶的能力。具体而言，给定一个盲测的、访问……（注：原文此处中断）