Abstract: Embodiments disclosed herein provide methods for identifying new CRISPR loci and effectors, as well as different CRISPR loci combinations found in various organisms. Class-II CRISPR systems contain single-gene effectors that have been engineered for transformative biological discovery and biomedical applications. Discovery of additional single-gene or multi-component CRISPR effectors may enhance existing CRISPR applications, such as precision genome engineering. Comprehensive characterization of CRISPR-loci may identify novel functional roles of CRISPR loci enabling new tools for biomedicine and biological discovery. CRISPR loci have enormous feature complexity, but classification of CRISPR loci has been focused on a small fraction of highly abundant features. Increased genome sequencing has enhanced the sampling of this feature complexity.

Abstract: The invention generally provides a sieve valve including: a substrate defining a channel; a flexible membrane adapted and configured for deployment at an intersection with the channel; and one or more protrusions extending into the channel from the substrate or the flexible membrane. The one or more protrusions define a plurality of recesses extending beyond the intersection between the channel and the flexible membrane; A microfluidic circuit including one or more sieve valves. In particular embodiments, the circuit comprises one or more input/output valves. The one or one or more input/output valves can include one or more input valves and one or more output valves. The microfluidic circuit can further include a mixing circuit. At least one of the sieve valves can be positioned between the one or more input/output valves and the mixing circuit. The invention further provides methods of using the device for the analysis of samples comprising cells.

Abstract: Provided are systems, kits, and methods for the quantitative detection of single nucleotide polymorphisms or variants to identify malignant neoplasms. The methods include use of modified oligonucleotide blockers with peptide nucleic acid backbones that hybridize to and block logarithmic amplification of the wild-type alleles of a target, and incorporation of locked nucleic acids into probes that are complementary to a mutant allele of the target sequence to increase specificity. The methods include detection of variants in sequences with high GC content and/or low complexity, such as the TERT promoter, IDH1, BRAF, NRAS, GNAQ, GNA11 and H3F3 A gene variants. The methods include sensitive detection and staging of cancers with low cellularity, and can be used intraoperatively such as for glioma, or to detect cell-free circulating tumor DNA, such as for melanoma.

Abstract: Provided herein are compounds of the formula (IV) as well as pharmaceutically acceptable salts thereof, wherein the substituents are as those disclosed in the specification. These compounds, and the pharmaceutical compositions containing them, are useful as MITF inhibitors, MITF pathway inhibitors and for the treatment of cancer.

Abstract: Provided herein are compositions and methods of treating muscular dystrophy (MD), such as administering an effective amount of a composition that increases the expression of JAG1, a composition comprising a JAG1 agonist, or a composition that promotes JAG1 signaling. Also provided are methods of prognosing MD or evaluating responsiveness to treatment for MD, e.g., by measuring an expression level of JAG1, and methods of identifying a compound for the treatment of MD.

Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.

Abstract: The invention provides for the use of radiation sensitizing agents in combination with radiation for the treatment of neoplasia, methods for the identification of genotype-specific radiation sensitizing agents, and methods of identifying patients who could benefit from therapy with a genotype-specific radiation sensitizing agent.

Abstract: The present invention features a knock-in mouse comprising a mutation in an endogenous CRBN locus and methods of use thereof.

Abstract: The invention provides markers indicative of pre-cachexia, compositions and methods for identifying patients with a molecular signature indicative of pre-cachexia; a culture system that reproduces the cachetic process in cells in vitro, which facilitates the screening and identification of therapeutic agents useful for disrupting (slowing, reducing, reversing, or preventing) the progression of pre-cachexia to refractory cachexia; as well as therapeutic agents identified using the culture system of the invention.

Abstract: Provided herein are compounds of the formula (I): as well as pharmaceutically acceptable salts thereof, wherein the substituents are as those disclosed in the specification. These compounds, and the pharmaceutical compositions containing them, are useful for the treatment of malaria.

Abstract: The present invention features compositions and methods for identifying a subject having a B cell neoplasia or related condition responsive to treatment with lenalidomide and lenalidoinide-related compounds.

Abstract: The invention generally provides a sieve valve including: a substrate defining a channel; a flexible membrane adapted and configured for deployment at an intersection with the channel; and one or more protrusions extending into the channel from the substrate or the flexible membrane. The one or more protrusions define a plurality of recesses extending beyond the intersection between the channel and the flexible membrane; A microfluidic circuit including one or more sieve valves. In particular embodiments, the circuit comprises one or more input/output valves. The one or one or more input/output valves can include one or more input valves and one or more output valves. The microfluidic circuit can further include a mixing circuit. At least one of the sieve valves can be positioned between the one or more input/output valves and the mixing circuit. The invention further provides methods of using the device for the analysis of samples comprising cells.

Abstract: Embodiments of the present disclosure present bioinformatic systems, methods, for allelic HLA typing (as well as and computer readable media having instructions for performing methods of HLA typing) using, for example, Illumina exome-sequencing data (e.g., 101 basepair, paired-end reads).

Abstract: The present invention provides compositions and methods for the diagnosis and treatment of glioblastoma, particularly tumor propagating cells within the glioblastoma.

Abstract: The invention provides methods of detecting an EZH2 mutation and associated epigenetic markers in a cancer cell, methods cancer diagnosis and methods of screening for EZH2 inhibitors.

Abstract: Novel solid forms of tacedinaline (4-(acetylamino)-N-(2-aminophenyl)benzamide), including crystalline tacedinaline Form B, a novel crystalline tacedinaline TFA salt, and amorphous tacedinaline, are disclosed. Pharmaceutical compositions comprising crystalline tacedinaline Form B, the novel crystalline tacedinaline TFA salt, and/or amorphous tacedinaline, and methods of treating various conditions by administering those novel solid forms, are also disclosed.

Abstract: Disclosed are compounds, such as pyridazinones, that can be, inter alia, used for treating cancer.

Abstract: The present invention relates to methods for assessing the risk of a dog to develop canine atopic dermatitis. The methods comprise detecting in a sample of DNA obtained from a dog the presence or absence of at least one genetic marker, wherein said at least one genetic marker is located on dog (Canis familiaris) chromosome 27, said marker being associated with an increased risk of developing canine atopic dermatitis.

Abstract: The present invention provides novel compounds (e.g., compounds of Formula (I)), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof. Also provided are methods and kits comprising the inventive compounds, or compositions thereof, for treating and/or preventing a fungal or protozoan infection, inhibiting the activity of a fungal or protozoan enzyme, killing a fungus or protozoon, or inhibiting the growth of a fungus or protozoon. The fungus may be a Candida species, Aspergillus species, or other pathogenic fungal species. The compounds of the invention may inhibit the activity of fungal or protozoan cytochrome b and/or fungal or protozoan Hsp90. The present invention also provides synthetic methods of the inventive compounds.

Abstract: Embodiments disclosed herein relate to treatment methods, diagnosis methods, drug efficacy evaluation methods and prognosis evaluation methods of lymphangioleiomyomatosis (LAM) and a disease associated with a mutation in a tuberous sclerosis complex (TSC) gene. The methods comprising analyses of the levels of lysophosphatidylcholine (LPC) in a biological sample of a subject, or comprising analyses of images of the location and signal intensity of isotope-labeled choline in the subject.