Reduced Graphene Oxide–Silver Nanoparticle Composite as an Active SERS Material

Selectivity and enhanced sensitivity for SERS measurements are highly desirable for environmental and analytical applications. Interaction of a target molecule with SERS substrate plays a pivotal role in determining the magnitude of enhancement and spectral profile of the SERS signal. A reduced graphene oxide–Ag nanoparticle (RGO-Ag NP) composite has been designed to boost SERRS sensitivity of a porphyrin derivative. Complexation between 5,10,15,20-tetrakis­(1-methyl-4-pyridinio)­porphyrin tetra­(<i>p</i>-toluenesulfonate) (TMPyP) porphyrin and the RGO-Ag NP composite is evidenced by a red-shifted porphyrin absorption band. Results indicate complexation is influential in improved surface-enhanced resonance Raman (SERRS) signal for TMPyP and thus offers an advantage for target molecule detection at low concentration levels. The combined effects of RGO and Ag NPs in the enhancement of SERS signal of TMPyP are discussed

MOESM2 of Defining rules of CD8+ T cell expansion against pre-erythrocytic Plasmodium antigens in sporozoite-immunized mice

Additional file 2. Title: Proteins subjected to bioinformatics analysis and listing of all syntenic orthologue pairs. This file provides multiple worksheets listing species-by-species protein identifiers (PlasmoDB gene ID) as well as worksheets listing the syntenic orthologue pairs for P. yoelii 17XNL/P. berghei ANKA and P. falciparum 3D7/P. vivax Sal1. These pairings were used as input pairings for Additional files 3 and 4

MOESM3 of Defining rules of CD8+ T cell expansion against pre-erythrocytic Plasmodium antigens in sporozoite-immunized mice

Additional file 3. Title: Common peptides from syntenic orthologues of P. yoelii 17XNL and P. berghei ANKA. This file provides multiple worksheets listing ≥8 amino acid contiguous stretches of homology for P. yoelii 17XNL/P. berghei ANKA syntenic orthologue pairs for all lifecycle stages, sporozoite stage and liver stage proteins

MOESM1 of Defining rules of CD8+ T cell expansion against pre-erythrocytic Plasmodium antigens in sporozoite-immunized mice

Additional file 1: Figure S1. PyCSP-specific T cells expand while PyL3-specific T cells do not following multiple P. yoelii RAS immunizations BALB/cj mice were immunized one or three times with 1-2x104 P. yoelii 17XNL RAS at 3-week intervals and monitored T cell responses by ex vivo IFNγ ELISPOT using H2-Kd-binding peptides from PyCSP (A, SYVPSAEQI) and PyL3 (PY05881) (B, GYKSGMSHI). Bars display mean value and error bars show the 95% confidence interval; *p <0.05, **p <0.01, ***p <0.001, ****p <0.0001, Student’s t-test

Electron Hopping Through Single-to-Few-Layer Graphene Oxide Films. Side-Selective Photocatalytic Deposition of Metal Nanoparticles

Single- to few-layer graphene oxide (GO) sheets have been successfully anchored onto TiO₂ films using electrophoretic deposition. Upon UV illumination of TiO₂–GO films, photogenerated electrons from TiO₂ are captured by GO. These electrons are initially used in GO’s reduction, while additional electron transfer results in storage across its sp² network. In the presence of silver ions, deposition of silver nanoparticles (NPs) is accomplished on the GO surface opposite the TiO₂, thus confirming the ability of GO to transport electrons through its plane. Illumination-controlled reduction of silver ions allows for simple selection of particle size and loading, making these semiconductor–graphene–metal (SGM) films ideal for custom catalysis and sensor applications. Initial testing of SGM films as surface-enhanced resonance Raman (SERRS) sensors produced significant target molecule signal enhancements, enabling detection of nanomolar concentrations

Yang_JEB_ESM_rawdata

Raw data file for input to the R markdown documen

Yang_JEB_ESM_StatAnalysis

R markdown document (.Rmd) of all analyses described in the manuscript. Necessary descriptions of the variables and statistical details are included in the comment

Laser Flash Photolysis of Au-PNIPAM Core–Shell Nanoparticles: Dynamics of the Shell Response

Hydrophobic forces play a key role in the processes of collapse and reswelling of thermoresponsive polymers. However, little is known about the dynamics of these processes. Here, thermoresponsive poly­(<i>N</i>-isopropylacrylamide)-encapsulated gold nanoparticles (Au-PNIPAM) are heated via nanosecond laser flash photolysis. Photothermal heating via excitation of the localized surface plasmon resonance of the Au nanoparticle cores results in rapid PNIPAM shell collapse within the 10 ns pulse width of the laser. Remarkably, reswelling of the polymer shell takes place in less than 100 ns. A clear pump fluence threshold for the collapse of the PNIPAM shell is demonstrated, below which collapse is not observed. Reswelling takes longer at higher laser intensities

Electron Hopping Through Single-to-Few-Layer Graphene Oxide Films. Side-Selective Photocatalytic Deposition of Metal Nanoparticles

Single- to few-layer graphene oxide (GO) sheets have been successfully anchored onto TiO₂ films using electrophoretic deposition. Upon UV illumination of TiO₂–GO films, photogenerated electrons from TiO₂ are captured by GO. These electrons are initially used in GO’s reduction, while additional electron transfer results in storage across its sp² network. In the presence of silver ions, deposition of silver nanoparticles (NPs) is accomplished on the GO surface opposite the TiO₂, thus confirming the ability of GO to transport electrons through its plane. Illumination-controlled reduction of silver ions allows for simple selection of particle size and loading, making these semiconductor–graphene–metal (SGM) films ideal for custom catalysis and sensor applications. Initial testing of SGM films as surface-enhanced resonance Raman (SERRS) sensors produced significant target molecule signal enhancements, enabling detection of nanomolar concentrations

Predicting the Functional Effect of Amino Acid Substitutions and Indels

<div><p>As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. Different classes of sequence variations at the nucleotide level are involved in human diseases, including substitutions, insertions, deletions, frameshifts, and non-sense mutations. Frameshifts and non-sense mutations are likely to cause a negative effect on protein function. Existing prediction tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid conservation at the position of interest among related sequences, an approach that is not directly applicable to insertions or deletions. Here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query sequence to a protein sequence homolog before and after the introduction of an amino acid variation to the query sequence. Our results showed that the scoring scheme performs well in separating disease-associated variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human protein variations, and also in separating deleterious variants (n = 15,179) from neutral variants (n = 17,891) for UniProt non-human protein variations. In our approach, the area under the receiver operating characteristic curve (AUC) for the human and non-human protein variation datasets is ∼0.85. We also observed that the alignment-based score correlates with the deleteriousness of a sequence variation. In summary, we have developed a new algorithm, PROVEAN (<b>Pro</b>tein <b>V</b>ariation <b>E</b>ffect <b>An</b>alyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. The PROVEAN tool is available online at <a href="http://provean.jcvi.org">http://provean.jcvi.org</a>.</p> </div