Optimization of capture protocols across species targeting up to 32000 genes and their extension to pooled DNA

In-solution based capture is becoming a method of choice for sequencing targeted sequence. We assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single hybridization and showed it was an efficient and cost-effective strategy. We also extended the use of capture to pools of 100 samples and proved the efficiency of the method to assess allele frequency. Using a set of various organisms with different genome sizes, we demonstrated a correlation between the percentage of on-target reads vs. the relative size of the targeted sequences. Altogether, we proposed methods, strategies, cost-efficient protocols and statistics to better evaluate and more effectively use hybridization capture.

Sensitivity, Optimal Control, and Cost-Effectiveness Analysis of Intervention Strategies of Filariasis

In this work, sensitivity, optimal control, and cost-effectiveness of several intervention strategies of filariasis are discussed. We study the intervention strategies that are related to bednet use, insecticide, and the combination of bed-net use and insecticide. We use Pontryagin’s maximum principle to characterize the optimal controls. The Average Cost-Effectiveness Ratio (ACER) and Infection Averted Ratio (IAR) are used to identify the most cost-effective strategy. We also determine the basic reproduction number and investigate the sensitivity of the basic reproduction number on the parameters that are related to bed-net use and insecticide. Based on the ACER values, the most cost-effective strategy to control filariasis is insecticide intervention. On the other hand, the IAR values indicates that bed-net use intervention is the most cost-effective strategy. Furthermore, it is also the most effective strategy to eliminate filariasis. The sensitivity analysis results show that the control parameter related to bed net use and treatment have a central role in reducing the basic reproduction number and filariasis spread.

Interleaving Retrieval Practice Promotes Science Learning

Can interleaved retrieval practice enhance learning in classrooms? Across a four-week period, students (N = 155) took a weekly quiz in their science courses testing half of the concepts taught in that week. Questions on each quiz were either blocked by concept or interleaved with different concepts. A month after the final quiz, students were tested on the concepts covered in the four-week period. Replicating the retrieval practice effect, participants performed better on concepts that had been on blocked quizzes (M = 54%, SD = 28%) than on concepts not been quizzed (M = 47%, SD = 20%, d = .30). Interleaved quizzes led to even greater benefits, revealing an interleaving benefit: participants performed better on concepts that had been on interleaved quizzes (M = 63%, SD = 26%), than concepts that had been on blocked quizzes (d = .35). These results demonstrate a cost-effective strategy to promote classroom learning.

FN3 Domain Displaying Double Epitopes: A Cost-Effective Strategy for Producing Substitute Antigens

Construction of substitute antigens based on alternative scaffold proteins is a promising strategy in bioassay technology. In this study, we proposed a strategy for constructing substitute antigens derived from 10th human fibronectin type III (FN3) using two peptide epitopes of terminal pro-brain natriuretic peptide (NT-proBNP) as an example. The base sequences encoding the two antigenic epitopes of NT-proBNP were recombined into the FG loop region and the C-terminus of FN3, fused by 4 GS or polyN linker. The fusion proteins (named FN3-epitopes-4GS and FN3-epitopes-polyN, respectively) were expressed and purified cost-effectively using an Escherichia coli expression system. The immunoreactivity of recombinant substitutes was preliminarily confirmed by western blot analysis using epitope-specific antibodies. The sandwich enzyme-linked immunosorbent assay demonstrated that either FN3-epitopes-polyN or FN3-epitopes-4GS was highly sensitive, and FN3-epitopes-polyN exhibited better kinetics to specific antibodies than FN3-epitopes-4GS, showing a linear dose-response relationship in the concentration range of 0.06–12.85 ng/ml, which suggest that the polyN linker was more suitable for constructing the FN3-based substitute antigens compared to the 4 GS linker. Furthermore, the serum stability test and differential scanning calorimetry analysis showed that the recombinant FN3-epitopes-polyN maintained the original stability of FN3. Therefore, it was confirmed that FN3 could be engineered to construct a stable biomacromolecular substitute for displaying double epitopes of antigen proteins, such as NT-proBNP. In summary, a cost-effective strategy to produce NT-proBNP substitute antigens with good immunoreactivity and physicochemical stability was established in this work, which may provide potential uses for the production of other substitute antigens in the future.