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Here, we describe a new technology, designed to accelerate peptide discovery by quick identification and optimization of the residues critical for protein–protein interactions or ligand binding. We called it PepFusion. It is based on ligation of short DNA sequences generated from known ligand‐binding regions. We tested it by selecting peptide antagonists of interleukin‐6 (IL‐6), a key mediator of inflammatory diseases such as rheumatoid arthritis (RA), Crohn's disease, and Castleman disease (CD). The PepFusion library demonstrated superiority over a random library by yielding a peptide with low micromolar affinity for IL‐6, whereas the random library failed. The affinity of the peptide from the PepFusion library was further enhanced by additional rounds of mutagenesis leading to peptide variants with low nanomolar IL‐6 affinity. In addition to generating high‐affinity peptides, our method opens the way to solve the problem of the false positive sequences, which are common with all display technologies. [ABSTRACT FROM AUTHOR]

Circular RNA (circRNA) is an important class of noncoding RNA. Current, protocols to detected circRNAs have utilized nonpolyadenylated RNAs, ribosomal RNA‐depleted RNA samples (rRNA− library), and rRNA‐depleted RNA that has been treated with RNase R to digest linear RNA (rRNA− RNase R+ library). Accumulating evidence suggests the participation of circRNAs in Alzheimer's disease (AD)‐associated pathophysiology, but the details remain largely unknown. Here, we elucidated the brain circRNAs profiles of AD‐model and WT mice using two methods of library construction (rRNA− RNase R+ libraries and rRNA− libraries). We focused on the construction of libraries that best allow the identification of circRNAs from next‐generation RNA sequencing data. We obtained a significantly higher abundance of circRNAs in the rRNA− RNase R+ libraries than in the rRNA− libraries. Additionally, the rRNA− RNase R+ libraries more clearly revealed differentially expressed circRNAs. We performed a correlation analysis between differentially expressed circRNAs and their parental genes and performed KEGG analysis of the parental genes to explore the role of circRNA in AD. Our results identified significantly dysregulated circRNAs and KEGG analysis revealed that the identified circRNAs are involved in regulating AD development from distinct origins, including cAMP signaling, MAPK signaling, insulin secretion, Axon guidance, Long‐term potentiation, dopaminergic synapse, and ErBb signaling pathways. Following rigorous selection, we identified several important circRNAs and mRNAs and propose the circRNAs regulate parental gene transcription or affect variable splicing, which were discovered to be mainly involved in Aβ production and cognitive performance (TRPC6) and neuronal differentiation and development (NME7). These newly identified circRNAs should serve as a valuable resource for the future development of potential biomarkers and therapeutic targets for AD. [ABSTRACT FROM AUTHOR]

Target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as microarthropods can be challenging. Here, we propose easy to set up optimizations for DNA extraction and library preparation prior to target enrichment. Prepared libraries were used to capture 1,432 ultraconserved elements (UCEs) from microhymenoptera (Chalcidoidea), which are among the tiniest insects on Earth and the most commercialized worldwide for biological control purposes. Results show no correlation between input DNA quantities (1.8–250 ng, 0.4 ng with an extra whole genome amplification step) and the number of sequenced UCEs on an Illumina MiSeq. Phylogenetic inferences highlight the potential of UCEs to solve relationships within the families of chalcid wasps, which has not been achieved so far. The protocol (library preparation + target enrichment) allows processing 96 specimens in five working days, by a single person, without requiring the use of expensive robotic molecular biology platforms, which could help to generalize the use of target enrichment for minute specimens. [ABSTRACT FROM AUTHOR]

The need for dynamic, elastomeric polymeric biomaterials remains high, with few options with tunable control of mechanical properties, and environmental responses. Yet the diversity of these types of protein polymers pursued for biomaterials-related needs remains limited. Robust high-throughput synthesis and characterization methods will address the need to expand options for protein-polymers for a range of applications. Here, a combinatorial library approach with high throughput screening is used to select specific examples of dynamic protein silk-elastin-like polypeptides (SELPs) with unique stimuli responsive features, including tensile strength and adhesion. Using this approach, 64 different SELPs with different sequences and molecular weights are selected out of over 2000 recombinant E. coli colonies. New understanding of sequence-function relationships with this family of proteins is gained through this combinatorial-screening approach and can provide a guide to future library designs. Further, this approach yields new families of SELPs to match specific material functions. [ABSTRACT FROM AUTHOR]