公开(公告)号：US20240271122A1

公开(公告)日：2024-08-15

申请号：US18286611

申请日：2022-04-14

Applicant: Opentrons Labworks Inc.

Inventor： Joel S. BADER ,  Leslie MITCHELL

IPC: C12N15/10

CPC classification number: C12N15/1058 ,  C12N15/1082 ,  C12N15/1089

Abstract: Provided herein are methods and systems for codon rewriting and replacement. In some aspects, provided herein, is a method comprising: analyzing at least a portion of a genome of an organism to identify a first plurality of codons based on at least in part on a first local context of a codon-of-interest in the genome of the organism to be rewritten; and rewriting the first plurality of codons in the genome of the organism to a second codon. Also provided herein are methods and systems for producing a synthetic genome.

公开(公告)号：US20240175088A1

公开(公告)日：2024-05-30

申请号：US18435880

申请日：2024-02-07

Applicant: The Board of Trustees of the Leland Stanford Junior University

Inventor： David M. Kurtz ,  Maximilian Diehn ,  Arash Ash Alizadeh

IPC: C12Q1/6886 ,  C12N15/10 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B20/00 ,  G16B20/10 ,  G16B20/20 ,  G16B30/00 ,  G16B30/10 ,  G16B35/20 ,  G16B40/00 ,  G16H10/40 ,  G16H20/10 ,  G16H50/20 ,  G16H50/30 ,  G16H50/70 ,  G16H70/60 ,  G16H10/60

CPC classification number: C12Q1/6886 ,  C12N15/1089 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B20/00 ,  G16B20/10 ,  G16B20/20 ,  G16B30/00 ,  G16B30/10 ,  G16B35/20 ,  G16B40/00 ,  G16H10/40 ,  G16H20/10 ,  G16H50/20 ,  G16H50/30 ,  G16H50/70 ,  G16H70/60 ,  C12Q2600/112 ,  C12Q2600/156 ,  C12Q2600/158 ,  G01N2800/7028 ,  G16H10/60

Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

公开(公告)号：US20240145034A1

公开(公告)日：2024-05-02

申请号：US18279760

申请日：2022-03-01

Applicant: Dewpoint Therapeutics, Inc.

Inventor： William W. CHEN ,  John C. MANTEIGA ,  Violeta YU ,  Ann D. KWONG ,  Peter Jeffrey DANDLIKER ,  Bruce Aaron BEUTEL ,  Chi ZHANG ,  Lingyao ZENG ,  Andreas STEFFEN ,  Daniel Franz FREITAG

IPC: G16B20/20 ,  C12N15/10 ,  G16B40/20 ,  G16H70/40

CPC classification number: G16B20/20 ,  C12N15/1079 ,  C12N15/1089 ,  G16B40/20 ,  G16H70/40

Abstract: The present application provides, in some aspects, methods of identifying a condensate of interest associated with a el disease. Also provided are methods of identifying a marker for identifying a condensate of interest associated with a disease. In other aspects, provided herein are methods of identifying a therapeutic agent useful for treating a disease via the identified condensate of interest.

公开(公告)号：US20240124860A1

公开(公告)日：2024-04-18

申请号：US18488261

申请日：2023-10-17

Applicant: THE BROAD INSTITUTE, INC. ,  MASSACHUSETTS INSTITUTE OF TECHNOLOGY

Inventor： Feng Zhang ,  David Arthur Scott ,  Winston Xia Yan ,  Sourav Choudhury ,  Matthias Heidenreich

IPC: C12N9/22 ,  C12N15/10 ,  C12N15/86 ,  G16B20/00 ,  G16B30/10 ,  G16B30/20

CPC classification number: C12N9/22 ,  C12N15/102 ,  C12N15/1089 ,  C12N15/86 ,  G16B20/00 ,  G16B30/10 ,  G16B30/20 ,  C12N2310/20 ,  C12N2710/10343 ,  C12N2740/16043 ,  C12N2750/14143 ,  C12N2800/80

Abstract: In one aspect, embodiments disclosed herein are directed to engineered CRISPRCas effector proteins that comprise at least one modification compared to an unmodified CRISPR-Cas effector protein that enhances binding of the of the CRISPR complex to the binding site and/or alters editing preference as compared to wild type. In certain example embodiments, the CRISPR-Cas effector protein is a Type II effector protein. In certain other example embodiments, the Type V effector protein is Cas9 or an orthologs or engineered variant thereof. Example Cas9 proteins suitable for use in the embodiments disclosed herein are discussed in further detail below.

公开(公告)号：US11923045B2

公开(公告)日：2024-03-05

申请号：US18085269

申请日：2022-12-20

Applicant: TripleBar Bio, Inc.

Inventor： Jeremy Agresti ,  Andres Ornelas Vargas ,  Kevin Gregory Hoff

IPC: G01N33/48 ,  C12N15/10 ,  G01N33/50 ,  G16B20/00 ,  G16B20/50 ,  G16B35/10 ,  G16B40/00 ,  G16B99/00

CPC classification number: G16B20/00 ,  C12N15/1037 ,  C12N15/1058 ,  C12N15/1089 ,  G16B20/50 ,  G16B35/10 ,  G16B40/00 ,  G16B99/00

Abstract: Provided herein are systems and methods for screening desirable biological variants using a high-throughput integrated system. The integrated system may be configured to input a plurality of parameters from functional studies of biological variants under applied conditions, in conjunction with integrated libraries of biological variants, and filter the inputs to produce desirable biological variants based on an input performance requirement. The system may output optimized strains, molecules, or novel molecules expected to have a desirable functional characteristic. Accordingly, the methods and systems disclosed herein enable multi-parametric studies of biological diversity and conditional diversity in systems biology.

公开(公告)号：US20240055076A1

公开(公告)日：2024-02-15

申请号：US18266387

申请日：2021-12-09

Applicant: Cambridge Enterprise Limited ,  International Centre for Genetic Engineering and Biotechnology

Inventor： Sudhakaran PRABAKARAN

IPC: G16B35/00 ,  G16B20/20 ,  C12N15/10

CPC classification number: G16B35/00 ,  G16B20/20 ,  C12N15/1089

Abstract: The present application features methods of treating a disease associated with a genetic variant. The genetic variant is also present within a novel open reading frame (nORF) associated with the gene in which the variant encodes either the gain or loss of a stop codon.

公开(公告)号：US11845982B2

公开(公告)日：2023-12-19

申请号：US15855294

申请日：2017-12-27

Applicant: Anjali Chakradhar

Inventor： Anjali Chakradhar

IPC: C12Q1/6869 ,  C12Q1/6876 ,  C12N15/10 ,  G01N15/14 ,  G01N21/64 ,  G16B50/00

CPC classification number: C12Q1/6869 ,  C12N15/1086 ,  C12N15/1089 ,  C12Q1/6876 ,  G01N15/1429 ,  G01N15/1434 ,  G01N21/6428 ,  G01N2015/149 ,  G01N2021/6439 ,  G16B50/00

Abstract: A digital store comprising of a method to store digital data in live micro-organisms, and a method to selectively retrieve subsets of stored data, is disclosed. Digital data is represented as a plurality of key-value pairs. The proposed system stores copies of key-value pairs in a plurality of live micro-organisms. Upon presentation of a retrieval key, the proposed digital store retrieves the value associated with the retrieval key. Storage method for a key-value pair comprises of (a) mapping the key to a gene that expresses a unique fluorescent protein so that no two keys map to the same gene, (b) encoding the key-value pair as base-pair sequences, (c) synthesizing oligonucleotide chains from base-pairs for the key-value pair and the gene, (d) synthesizing recombinant DNA plasmids that have oligonucleotide chains for the key-value pair, the gene, and two primers, as foreign DNA inserts, (e) incorporation of recombinant DNA plasmids into live micro-organisms, (f) isolation of live micro-organisms that have absorbed the recombinant DNA plasmids, and (g) safe storage of population of live micro-organisms with embedded key-value pairs in a common pool. Retrieval of the value paired with a key comprises of (a) taking as input the retrieval key, and mapping the key to the specific gene for fluorescent protein, (b) taking a sample from the safe storage pool that contains live micro-organisms embedded with key-value pairs, (c) isolating the live micro-organisms that have expressed the gene by using high-speed fluorescence activated cell sorting or flow cytometry, (d) extracting DNA from the recombinant DNA plasmid in the isolated live micro-organisms, (d) selectively amplifying and sequencing only those DNA strands that contain the value for the key, and (e) decoding the base-pair sequence obtained after DNA sequencing to yield the value associated with the retrieval key.
We also disclose two important variations. The first variation relates to the storage step. The recombinant DNA plasmid is constructed to include additional non-fluorescent oligonucleotides and genes so that during the data retrieval step, the live micro-organisms that have absorbed the said plasmid can be sorted by cell sorters based on parameters of individual cells such as cell size, cell complexity, cell phenotype, cell structure, cell function, and magnetic or electrical properties. The second variation relates to both storage and retrieval of key-value pairs with large values. To store such a key-value pair, the large value is split into smaller blocks so that a block can fit into a recombinant DNA plasmid, and a distinct pair of primers is used for each block. A block's primer pair is used to selectively amplify and sequence only the DNA that encodes the data in the block, thereby enabling the retrieval of a specific block of the value, as opposed to retrieving the entire value associated with a key.

公开(公告)号：US11842798B2

公开(公告)日：2023-12-12

申请号：US16062075

申请日：2016-12-14

Applicant: Adapsyn Bioscience Inc.

Inventor： Nishanth Merwin ,  Chris DeJong ,  Chad Johnston ,  Gregory Chen ,  Haoxin Li ,  Michael Skinnider ,  McLean Edwards ,  Nathan Magarvey ,  Phil Rees

IPC: G16B5/20 ,  G16B5/00 ,  G16B15/00 ,  G16B20/00 ,  G16B40/00 ,  C12Q1/68 ,  C12N15/10 ,  G16B99/00 ,  G16B20/50 ,  G16B40/10 ,  G16B20/20 ,  G16B20/30

CPC classification number: G16B5/20 ,  C12N15/10 ,  C12N15/1089 ,  C12Q1/68 ,  G16B5/00 ,  G16B15/00 ,  G16B20/00 ,  G16B20/20 ,  G16B20/30 ,  G16B20/50 ,  G16B40/00 ,  G16B40/10 ,  G16B99/00

Abstract: A method for linking a natural product and gene cluster is disclosed. In some embodiments, monomers of natural products are predicted from a gene sequence. In other embodiments, monomers of natural products are predicted from a chemical structure of a natural product. In another embodiment, monomers predicted from gene sequences are aligned with monomers predicted from chemical structures.

公开(公告)号：US20230348893A1

公开(公告)日：2023-11-02

申请号：US18186118

申请日：2023-03-17

Applicant: ThinkCyte, Inc. ,  The University of Tokyo ,  RIKEN

Inventor： Asako TSUBOUCHI ,  Sadao OTA ,  Fumiko KAWASAKI

IPC: C12N15/10

CPC classification number: C12N15/1055 ,  C12N15/1065 ,  C12N15/1089 ,  C40B30/04

Abstract: The present disclosure provides a method for screening cells, the method including a step of preparing a plurality of cells which are tagged with a first barcode nucleic acid associated with a test target and treated with the test target, a step of sorting the plurality of cells based on cellular phenotype using an imaging cell sorter, and a step of identifying the test target used to treat each cell using the first barcode nucleic acid as an indicator.

公开(公告)号：US11749377B2

公开(公告)日：2023-09-05

申请号：US15565893

申请日：2016-04-14

Applicant: PEACCEL

Inventor： Nicolas Fontaine ,  Frédéric Cadet

IPC: G16B30/00 ,  G16B20/00 ,  G16B20/50 ,  C07K2/00 ,  G06F17/14 ,  C12N15/10 ,  C40B40/10

CPC classification number: G16B30/00 ,  C07K2/00 ,  G06F17/14 ,  G16B20/00 ,  G16B20/50 ,  C12N15/1089 ,  C40B40/10

Abstract: A method for predicting at least one fitness value of a protein is implemented on a computer and includes the following steps: encoding the amino acid sequence of the protein into a numerical sequence according to a protein database, the numerical sequence comprising a value for each amino acid of the sequence; calculating a protein spectrum according to the numerical sequence; and for each fitness: comparing the calculated protein spectrum with protein spectrum values of a predetermined database, said database containing protein spectrum values for different values of said fitness, predicting a value of said fitness according to the comparison step.