PubMed Health⌕ Search

Biomedical subjects

Sarah Kim

Publications and source records attributed to Sarah Kim.

8 recordsLinked to original sources
PubMed2026

Spatial proximity sequencing maps developmental dynamics in the germinal center.

Spatial profiling of proteins and protein interactions facilitates understanding of cell functions within tissues and is essential for studies in signaling, immunity, and cancer. We present spatial proximity sequencing (Sprox-seq) for simultaneous profiling of surface proteins, protein complexes, and mRNAs, recording the tissue location of each molecule. Sprox-seq profiled 32 proteins, 528 pairwise interactions, and thousands of mRNAs with spatial resolution across human tonsils and germinal centers. Mapping tissue-wide protein interactions recapitulated RNA-defined tissue architecture but also revealed higher interaction complexity in the light zone. Protein-interaction trajectories uncovered a B cell state transition distinct from that inferred by RNA. Integrated protein-complex and mRNA analysis related spatially enriched complexes with mitotic pathways. Sprox-seq captured cell-cell interactions, such as B cell-follicular dendritic cell interactions mediated by the receptor complex VLA-4-VCAM1. Sprox-seq provides a spatially resolved multi-modal view of cell states and an integrated study of protein and cellular interactions across tissues.

Humans↗
PubMed2006

5'-Triphosphate RNA is the ligand for RIG-I.

The structural basis for the distinction of viral RNA from abundant self RNA in the cytoplasm of virally infected cells is largely unknown. We demonstrated that the 5'-triphosphate end of RNA generated by viral polymerases is responsible for retinoic acid-inducible protein I (RIG-I)-mediated detection of RNA molecules. Detection of 5'-triphosphate RNA is abrogated by capping of the 5'-triphosphate end or by nucleoside modification of RNA, both occurring during posttranscriptional RNA processing in eukaryotes. Genomic RNA prepared from a negative-strand RNA virus and RNA prepared from virus-infected cells (but not from noninfected cells) triggered a potent interferon-alpha response in a phosphatase-sensitive manner. 5'-triphosphate RNA directly binds to RIG-I. Thus, uncapped 5'-triphosphate RNA (now termed 3pRNA) present in viruses known to be recognized by RIG-I, but absent in viruses known to be detected by MDA-5 such as the picornaviruses, serves as the molecular signature for the detection of viral infection by RIG-I.

Animals↗
PubMed2006

Patterned arrays of au rings for localized surface plasmon resonance.

In this paper, we examined the characteristic behavior of localized surface plasmon resonances (LSPR) of Au dot and ring arrays in response to the selective binding of biomolecules. To do this, patterned arrays of Au rings and dots with various feature scales were fabricated over large areas by an imprint lithography technique. Our results showed that the LSPR spectra of the Au nanorings exhibited a blue shift with increase in the ring widths and asymptotically converged to those for Au nanodots. This clearly implies that the LSPR spectra can be tuned over an extended wavelength range by varying the ring width. For an illustrative purpose, the patterned Au structures were used to detect the binding of streptavidin to biotin. In doing this, the Au patterns were chemically modified with G4 dendrimers of amine terminated poly(amidoamine), which facilitated the tethering of biotin onto the Au pattern. Exposure of the biotinylated Au nanorings to aqueous streptavidin solution induced both red-shifts of the LSPR spectra and changes in the peak intensities. The sensitivity of the LSPR spectra to the binding of the biomolecules was enhanced as the ring width of Au rings was decreased.

Biotin↗
PubMed2006

Nanoscopic Pd line arrays using nanocontact printed dendrimers.

High-density Pd line arrays with 55 nm line-width were obtained using nanocontact-printed dendrimer monolayers. Elastomeric PDMS stamps for nanocontact printing were replicated from silicon master molds which were fabricated by UV nanoimprinting in combination with reactive ion etching. The fabrication method effectively controlled the aspect ratios of high-density lines for resolving the problems encountered in both replicating silicon masters to PDMS stamps and printing with the replicated PDMS stamps. Using the PDMS nanostamp with an optimized aspect ratio, a self-assembled monolayer of dendrimer was patterned on a Pd film via nanocontact printing, which was facilitated by the strong interaction between Pd and amine groups of the dendrimer. The patterned self-assembled monolayer was used as an etch-resist mask against the wet etchant of Pd, leaving behind a high-density Pd line array over large areas. The resulting functional Pd nanopattern is of practical significance in microelectronics and bio- or gas-sensing devices.

Journal Article↗
PubMed2006

Nanomachining by colloidal lithography.

Colloidal lithography is a recently emerging field; the evolution of this simple technique is still in progress. Recent advances in this area have developed a variety of practical routes of colloidal lithography, which have great potential to replace, at least partially, complex and high-cost advanced lithographic techniques. This Review presents the state of the art of colloidal lithography and consists of three main parts, beginning with synthetic routes to monodisperse colloids and their self-assembly with low defect concentrations, which are used as lithographic masks. Then, we will introduce the modification of the colloidal masks using reactive ion etching (RIE), which produces a variety of nanoscopic features and multifaceted particles. Finally, a few prospective applications of colloidal lithography will be discussed.

Colloids↗
PubMed2005

Particle arrays with patterned pores by nanomachining with colloidal masks.

In summary, we have developed a new strategy for the fabrication of arrayed colloidal particles well-ordered nanometric holes of three or four fold symmetry by anisotropic reactive ion (plasma) etching of self-organized layers of colloidal spheres. We demonstrated that a mesoporous silica matrix with regular open windows could be used as a lithographic mask and the resulting arrangement of pores on a particle was dependent on the orientation of the colloidal particle stacking. A variety of organic and inorganic materials such as metals for metal-polymer composites, DNA and proteins, semiconducting and ceramic materials, and other polymers and small chemicals can be incorporated via chemical and physical attachment. Particles with patterned pores and composite particles by our nanomachining process can be used as novel functional materials in the field of electronics, photonics, and biotech areas.

Journal Article↗
PubMed2004

Osteopontin modulates angiotensin II-induced fibrosis in the intact murine heart.

OBJECTIVES: Osteopontin (OPN) is upregulated in left ventricular hypertrophy and is stimulated by angiotensin II (AngII). Our objective was to determine whether mice deficient in OPN would be protected from AngII-induced cardiac fibrosis. BACKGROUND: Interstitial fibrosis can lead to myocardial dysfunction and ultimately heart failure. Osteopontin activates integrins that regulate cell adhesion, migration, and growth, thus implicating OPN in the process of cardiac fibrosis. METHODS: Osteopontin null (OPN(-/-)) mice (n = 18) and wild-type controls (n = 20) were infused with AngII (2.5 or 3.0 microg/kg/min) for four days or three weeks via osmotic mini-pumps. Hearts were assessed morphometrically and histologically, including quantitative assessment of fibrosis via optical microscopic imaging analysis. Cardiac fibroblasts derived from these mice were evaluated for adhesion and proliferation. Cardiac transcript expression for cytokines, extracellular matrix (ECM), integrin, and atrial natriuretic peptide were assessed. RESULTS: Osteopontin(-/-) mice exhibited less cardiac fibrosis (0.7%) than wild-type mice (8.0%) (p < 0.01) and lowered heart/body weight ratios (0.10% vs. 0.23%) (p < 0.01) after three weeks of AngII infusion. Expression of transforming growth factor-beta, fibronectin, and collagen was not different between OPN(-/-) and wild-type mice, despite the decrease in ECM accumulation in the OPN(-/-) mice. Adhesion to ECM substrates decreased by 30% to 50% in cardiac fibroblasts of OPN(-/-) mice but was restored in OPN(-/-) cells by the addition of recombinant osteopontin. CONCLUSIONS: Osteopontin mediates cardiac fibrosis, probably through the modulation of cellular adhesion and proliferation. Because OPN is increased in cardiac hypertrophy and its lack attenuates fibrosis, understanding of OPN function is essential to extend our knowledge about molecular determinants of cardiac hypertrophy and failure.

Angiotensin II↗