Showing papers by "Torrey Pines Institute for Molecular Studies published in 2022"

Chemical editing of proteoglycan architecture

Abstract: Proteoglycans are heterogeneous macromolecular glycoconjugates that orchestrate many important cellular processes. While much attention has focused on the poly-sulfated glycosaminoglycan chains that decorate proteoglycans, other important elements of their architecture, such as core proteins and membrane localization, have garnered less emphasis. Hence, comprehensive structure-function relationships that consider the replete proteoglycan architecture as glycoconjugates are limited. Here we present an extensive approach to study proteoglycan structure and biology by fabricating defined semisynthetic modular proteoglycans that can be tailored for cell surface display. The expression of proteoglycan core proteins with unnatural amino acids permits bioorthogonal click chemistry with functionalized glycosaminoglycans for methodical dissection of the parameters required for optimal binding and function of various proteoglycan-binding proteins. We demonstrate that these sophisticated materials can recapitulate the functions of native proteoglycan ectodomains in mouse embryonic stem cell differentiation and cancer cell spreading while permitting the analysis of the contributing architectural elements toward function.

Modular Access to Diverse Chemiluminescent Dioxetane‐Luminophores through Convergent Synthesis

Abstract: Adamantyl-dioxetane luminophores are an important class of chemiluminescent molecular probes for diagnostics and imaging. We have developed a new efficient synthetic route for preparation of adamantyl-enolether as precursors for dioxetane chemiluminescent luminophores. The synthesis is convergent, using an unusual Stille cross-coupling reaction employing a stannane-enolether, to directly afford adamantyl-enolether. In a following simple step, the dioxetane is obtained by oxidation of the enolether precursor with singlet-oxygen. The scope of this synthetic route is broad since a large number of haloaryl substrates are either commercially available or easily accessible. Such a late-stage derivatization strategy simplifies the rapid exploration of novel luminogenic molecular structures in a library format and simplifies the synthesis of known dioxetane luminophores. We expect that this new synthetic strategy will be particularly useful in the design and synthesis of yet unexplored dioxetane chemiluminescent luminophores.

Scalable, Chemoselective Nickel Electrocatalytic Sulfinylation of Aryl Halides with SO ₂

Abstract: Simple access to aryl sulfinates from aryl iodides and bromides is reported using an inexpensive Ni-electrocatalytic protocol. The reaction exhibits a broad scope, uses stock solution of simple SO2 as sulfur source, and can be scaled up in batch and recycle flow settings. The limitations of this reaction are clearly shown and put into context by benchmarking with state-of-the-art Pd-based methods.

Trace Embeddings from Zero Surgery Homeomorphisms

Abstract: Manolescu and Piccirillo recently initiated a program to construct an exotic $S^4$ or $\# n \mathbb{CP}^2$ by using zero surgery homeomorphisms and Rasmussen's $s$-invariant. They find five knots that if any were slice, one could construct an exotic $S^4$ and disprove the Smooth $4$-dimensional Poincar\'e conjecture. We rule out this exciting possibility and show that these knots are not slice. To do this, we use a zero surgery homeomorphism to relate slice properties of two knots \textit{stably} after a connected sum with some $4$-manifold. Furthermore, we show that our techniques will extend to the entire infinite family of zero surgery homeomorphisms constructed by Manolescu and Piccirillo. However, our methods do not completely rule out the possibility of constructing an exotic $S^4$ or $\# n \mathbb{CP}^2$ as Manolescu and Piccirillo proposed. We explain the limits of these methods hoping this will inform and invite new attempts to construct an exotic $S^4$ or $\# n \mathbb{CP}^2$. We also show a family of homotopy spheres constructed by Manolescu and Piccirillo using annulus twists of a ribbon knot are all standard.

Total Synthesis of Kibdelomycin

Abstract: A modular total synthesis of kibdelomycin is disclosed that should enable structure–activity relationship (SAR) studies of this interesting class of antibiotics. The route uses simple building blocks and addresses lingering questions about its structural assignment and relationship to amycolamicin, a recently described natural product reported to have a similar structure. Initial antibacterial assays reveal that both C-22 epimers (the N-glycosidic linkage) of the natural product have similar activity while structurally truncated analogs lose activity.

cDNA Library Preparation for scRNA-seq of Human Meniscus (10x Genomics) v1

Abstract: Samples are processed using V2 barcoding chemistry kits of 10x Genomics. For each run, 10,000 cells from individual donors arelabeled with distinct oligo-barcoded antibodies (cell hashing), enabling us to pool samples from both conditions on each 10X Genomics run and reduce batch effects.All samples from a given experiment areprocessed in parallel in the same thermal cycler. The 10x user guide can be found https://assets.ctfassets.net/an68im79xiti/1C16trEdzy1Folq5xbOijE/7e6fb1f504e130bd561d898384da99d9/CG000315_ChromiumNextGEMSingleCell3-_GeneExpression_v3.1_DualIndex__RevB.pdf and is also an attached document.

Human Knee Meniscus Collection Protocol for scRNA-seq v1

Abstract: Meniscus is taken from the medial knee compartment is collected for scRNA-seq processing. The attached image indicates where the meniscal tissue is collected from.

Overview of scRNA-seq of Human Knee Meniscus v1

Abstract: The overview provides sub-protocols for each step required to complete scRNA-seq from human knee meniscus.