Approaches to link RNA secondary structures with splicing regulation

In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitating or by hindering the interaction with factors and small nuclear ribonucleoproteins (snRNPs) that regulate splicing. Moreover, the secondary structure could play a fundamental role in the splicing of yeast species, which lack many of the regulatory splicing factors present in metazoans. This review describes the steps in the analysis of the secondary structure of the pre-mRNA and its possible relation to splicing. As a working example, we use the case of yeast and the problem of the recognition of the 3-prime splice site.Comment: 21 pages, 7 figure

The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin

The 3′ splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions. Native gel analysis, enzymatic/chemical structure probing, and oligonucleotide binding studies of a 63 nt fragment, containing the 3′ splice site, key residues of an SF2/ASF splicing factor binding site, and a polypyrimidine tract, provide evidence for an equilibrium between pseudoknot and hairpin structures. This equilibrium is sensitive to multivalent cations, and can be forced towards the pseudoknot by addition of 5 mM cobalt hexammine. In the two conformations, the splice site and other functional elements exist in very different structural environments. In particular, the splice site is sequestered in the middle of a double helix in the pseudoknot conformation, while in the hairpin it resides in a two-by-two nucleotide internal loop. The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site

A Program for At-Risk High School Students Informed by Evolutionary Science

Improving the academic performance of at-risk high school students has proven difficult, often calling for an extended day, extended school year, and other expensive measures. Here we report the results of a program for at-risk 9th and 10th graders in Binghamton, New York, called the Regents Academy that takes place during the normal school day and year. The design of the program is informed by the evolutionary dynamics of cooperation and learning, in general and for our species as a unique product of biocultural evolution. Not only did the Regents Academy students outperform their comparison group in a randomized control design, but they performed on a par with the average high school student in Binghamton on state-mandated exams. All students can benefit from the social environment provided for at-risk students at the Regents Academy, which is within the reach of most public school districts

Improving PBL in Empowering Meta cognitive Skill of Students

Abstract Objective: Problem-Based Learning (PBL) is a potential constructivist learning strategy that empowers students’ Meta cognitive skill. PBL focuses on problem, involves thinking activity to solve problems, and correlates to cognitive function of students. Methods: The implementation of PBL reveals various benefits, but there are also some weaknesses in this learning strategy. Thus, it is necessary to implement a certain learning strategy that can cover the PBL weaknesses, such as Reading, Questioning, and Answering (RQA) learning strategy. RQA is a new learning strategy developed based on a fact that almost all students do not read the next lecture materials, causing failure of learning strategy planned and finally the students’ comprehension becomes low. RQA is also potential to empower students’ Meta cognitive skill. Findings: The integration of RQA and PBL learning strategy is called PBL-RQA learning strategy. This study was a quasi-experimental study designed to compare the effect of PBL, RQA, and PBL-RQA learning strategies on the students’ Meta cognitive skill of Faculty of Mathematics and Science, State University of Makassar. Application: The results of the study showed that the potency of PBL learning strategy in empowering the students’ Meta cognitive skill has been increased by integrating it to RQA learning strategy. The meta cognitive skill mean score of the students taught by PBL-RQA learning strategy was 21% higher than that of the students taught by PBL and 26.9% higher than that of the students taught by RQA learning strategy. Keywords: Answering, Meta Cognitive Skill, Problem-Based Learning, Questioning, Reading, PBL-RQ