Learning and Predicting DNA Sequences in DNA-nanotube Conjugates with High Response to Serotonin

DNA-wrapped single walled carbon nanotube (SWNT) conjugates have emerged as promising optical tools for imaging and sensing important small biological molecules, such as neurotransmitters. In this presentation, I will describe how we use experimental near-infrared (nIR) fluorescence response datasets for ~100 DNA-SWNT conjugates, to train machine learning (ML) models to predict new unique DNA sequences with strong optical responses to the neurotransmitter serotonin. First, classifier models based on convolutional neural networks (CNN) are trained on sequence features to classify DNA ligands as either high response or low response to serotonin. Second, support vector machine (SVM) regression models are trained to predict relative optical response values for DNA sequences. Finally, we demonstrate with validation experiments that integrating the predictions of multiple highest quality CNN classifiers and SVM regression models leads to the best predictions of both high and low response sequences. With our ML approaches, we discovered five new DNA-SWNT sensors with higher fluorescence intensity response to serotonin than obtained previously. These new approaches for discovering functional DNA molecules could be applied to developing tools to detect other biological molecules of interest

Facile fabrication of two-dimensional inorganic nanostructures and their conjugation to nanocrystals

Nanocomposites of two-dimensional (2D) inorganic nanosheets and inorganic nanocrystals are fabricated. Freestanding atomically flat gamma-AlOOH nanosheets (thickness <1 nm) are synthesized from a one-pot hydrothermal reaction. The freestanding and binder-free film composed of the gamma-AlOOH nanosheets is fabricated by sedimentation. Because they have positive zeta potentials in the pH range below ca. 9.3, the gamma-AlOOH nanosheets can function as positively charged 2D inorganic matrices in a broad pH range. By solution phase (pH 7.0) mixing of the gamma-AlOOH nanosheets (zeta potential: 30.7 +/- 0.8 mV) and inorganic nanocrystals with negative surface charge, including Au nanoparticles, Au nanorods, CdSe quantum dots, CdSe/CdS/ZnS quantum dots and CdSe nanorods, the nanocomposites are self-assembled via electrostatic interactions. Negatively charged inorganic nanostructures with a wide range of chemical compositions, shapes, sizes, surface ligands and adsorbates can be used as building blocks for gamma-AlOOH nanocomposites. Adsorption densities of inorganic nanocrystals on the nanocomposites can be controlled by varying concentrations of nanocrystal solutions. Nanocomposite films containing alternating layers of gamma-AlOOH and nanocrystals are obtained by a simple drop casting method.close3

The Effects of Gymnema sylvestre in High-Fat Diet-Induced Metabolic Disorders

This study used an integrated approach to investigate the effects of Gymnema sylvestre (GS) extract as a functional dietary supplement with a high-fat diet. This approach examined insulin resistance, the dysfunction of adipose tissue, and liver steatosis. Male C57BL/6J mice were fed a normal chow or high-fat diet (HFD) for the acute and chronic study, in addition to GS in different doses (100, 250 and 500 mg/kg body weight). Their body composition changes, serum lipid and glucose parameters, adipose and liver tissue histology, and gene expression were measured. It was found that GS significantly suppressed the increase of body weight, serum levels of lipid, insulin and leptin, and adipose tissue, and liver inflammation. GS also demonstrated hypoglycemic effects due to the amylase inhibition activity. Our results support the existence of a relationship between the HFD induced insulin resistance, adipose dysfunction and liver steatosis. In conclusion, GS works as a functional dietary supplement with preventative effects against metabolic disorder.

Direct observation of DNA target searching and cleavage by CRISPR-Cas12a

Cas12a (also called Cpf1) is a representative type V-A CRISPR effector RNA-guided DNA endonuclease, which provides an alternative to type II CRISPR-Cas9 for genome editing. Previous studies have revealed that Cas12a has unique features distinct from Cas9, but the detailed mechanisms of target searching and DNA cleavage by Cas12a are still unclear. Here, we directly observe this entire process by using single-molecule fluorescence assays to study Cas12a from Acidaminococcus sp. (AsCas12a). We determine that AsCas12a ribonucleoproteins search for their on-target site by a one-dimensional diffusion along elongated DNA molecules and induce cleavage in the two DNA strands in a well-defined order, beginning with the non-target strand. Furthermore, the protospacer-adjacent motif (PAM) for AsCas12a makes only a limited contribution of DNA unwinding during R-loop formation and shows a negligible role in the process of DNA cleavage, in contrast to the Cas9 PAM.

Colloidal Second Near-infrared-emitting Mn-doped Ag2S Quantum Dots

Incorporation of transition metal dopants within a semiconductor nanocrystal has a tremendous effect on the optical and magnetic properties of the semiconductor nanocrystals. Herein, we report on a novel synthesis of second near-infrared-emitting photoluminescent Mn2+-doped Ag2S quantum dots via co-pyrolysis of silver and manganese single-source precursors. The Mn2+ doping level was flexibly tuned in Ag2S quantum dots, which was confirmed by elemental analysis and electron paramagnetic resonance spectroscopy. The Mn2+ doping induced negligible change in the pristine monoclinic acanthite Ag2S crystal structure but significantly decreased the photoluminescent intensity. Mn2+-doped Ag2S QDs exhibit second near-infrared emission and ferromagnetic ordering, which show the potential applicability for multimodal fluorescence/MRI probes.11Nsciescopu

Medically translatable quantum dots for biosensing and imaging

1186Nsciescopu

Controlled Sulfurization of Ag Nanorod into Ag-Ag2S Hetero-Nanorod

1

Controlled Sulfurization of Ag Nanorod into Ag-Ag2S Hetero-Nanorod

1

Compact quantum dot probes for multiplex in vivo imaging at short-wave infrared range

1