Disclosed herein are methods of identifying or engineering a polynucleotide sequence for directing tissue-specific gene expression. The methods may further include creating a regulatory element fragment library. Further disclosed are vectors comprising a tissue-specific regulatory element identified by the methods.

Disclosed herein are methods of identifying or engineering a polynucleotide sequence for directing tissue-specific gene expression. The methods may further include creating a regulatory element fragment library. Further disclosed are vectors comprising a tissue-specific regulatory element identified by the methods.

A biological library that includes a plurality of cryo-silicified cells, a plurality of dehydrated cryo-silicified cells, or both, where the cryo-silicified cells and/or the dehydrated cryo-silicified cells contain accessible biological information. In some embodiments, the biological information includes genetic information, proteomic information, or transcriptomic information. Members of the library may be analyzed to identify changes in the biological information associated with a medical condition or response to treatment. When the library includes B lymphocytes, cellular material from the B lymphocytes may be used to produce an antibody.

mRNAs containing an exogenous open reading frame (ORF) flanked by a 5′ untranslated region (UTR) and a 3′ UTR is provided, wherein the 5′ and 3′ UTRs are derived from a naturally abundant mRNA in a tissue. Also provided are methods for identifying the 5′ and 3′ UTRs, and methods for making and using the mRNAs.

The present invention is directed to a method for identifying a gene that regulates clostridial neurotoxin activity, the method comprising: a. providing a sample of human neuronal cells expressing a polypeptide that comprises a C-terminal detectable label, wherein the polypeptide is cleavable by a clostridial neurotoxin; b. altering expression of a target gene of the cells; c. contacting the cells with the clostridial neurotoxin; d. measuring an amount of C-terminal detectable label, thereby quantifying clostridial neurotoxin activity; and e. identifying the target gene as a regulator of clostridial neurotoxin activity when the quantified clostridial neurotoxin activity is different to the quantified clostridial neurotoxin activity when expression of the target gene is unaltered; or f. identifying that the target gene is not a regulator of clostridial neurotoxin activity when the quantified clostridial neurotoxin activity is equivalent to the quantified clostridial neurotoxin activity when expression of the target gene is unaltered. Also provided are related methods for identifying an agent that regulates clostridial neurotoxin activity, as well as human neuronal cells, nucleotides, vectors, polypeptides, kits, and compositions suitable for use in the methods of the invention.

The disclosure describes the effects of transcription mediated from a promoter on the transcription mediated by divergently coupled supercoiling-sensitive promoter. Transcription initiated from a promoter inhibits transcription mediated by a specific supercoiling-sensitive promoter that is divergently coupled to the promoter. A gyrase inhibitor relieves this inhibition and substantially increases the transcription mediated by the specific supercoiling-sensitive promoter that is divergently coupled to another promoter. Accordingly, the invention pertains to a method for identifying a compound as a gyrase inhibitor or not a gyrase inhibitor based on differential expression of genes under the control of divergently coupled promoters in the presence of the compound. Another embodiment of the invention provides an assay for identifying one or more compounds from a library of compounds as a gyrase inhibitor. Polynucleotides and cells containing such polynucleotides that are suitable for carrying out the methods described herein are also provided.

A method for developing capture agents for target proteins employs a compound library to find cyclic peptide sequences that bind the target protein. The target protein is also reacted with a clickable group-provider reagent to provide the protein with clickable groups. The compounds in the library are provided with complementary clickable groups that bind the clickable group on the target protein when the peptide sequences bind the target protein. In some embodiments, the cyclic peptide sequences that bind the target protein are incorporated into constructs having one or more arms that can serve as capture agents or potential treatments against the pathogens from which the target protein is derived. Some embodiments provide pharmaceutical compositions for immunoassays, diagnostics, therapeutics or the like, that employ the constructs.

Provided herein are methods for generating single-cell molecular analysis comprising a) delivering one or more proximity dependent probes to a cell population, wherein each proximity dependent probe comprises a target binding region configured to bind a target RNA and a primer binding site region; b) linking bound proximity dependent probes; c) isolating single cells from the cell population in separate individual discrete volumes, the individual discrete volumes further comprising a primer pair and amplification reagents, wherein the primer pair binds to the primer binding sites of the ligation dependent probes, and wherein at least one primer comprises a barcode sequence that uniquely identifies the individual discrete volume; d) amplifying the ligated probes using the primer pair, wherein the barcode is incorporated into each resulting amplicon; and e) quantifying target RNAs in each individual cell based at least in part on sequencing the resulting amplicons.

The disclosure relates to compositions comprising PU.1 inhibitors as well as methods of making and using the same. In some embodiments, methods of screening compounds for PU.1 inhibition are disclosed. In some embodiments, methods of screening a plurality of compounds for PU.1 inhibition are disclosed. In some embodiments, lambda-beta binding (LBB) motifs are used to screen compounds for PU.1 inhibition. In some embodiments, methods of treating neurodegenerative disorders are disclosed. In some embodiments pharmaceutical compounds are provided. In some embodiments, methods of treating Alzheimer's disease, inflammation, or excessive myelin uptake with PU.1 inhibitors are disclosed.

Rabbit antigen binding protein nucleic acid libraries are provided (e.g., nucleic acid libraries encoding antigen binding proteins that specifically recognize a target peptide-MHC (pMHC)). Methods of producing the rabbit antigen binding protein nucleic acid libraries are also provided.