The feasibility of using Hyperstodio generated applications to accelerate learning

The purposes of this study were to assess the feasibility of usingHyperStudio™ generated applications to help students with specific needs to overcome their weaknesses, and to determine the perceptions of students about the experience.HyperStudio™ is an authoring tool that can be used to create multimedia applications. Sounds graphics and color can be combined in the design of thestack, a series of cards connected by buttons.The data was collected at an inner city elementary school in EastTennessee. Participants were ten 4th grade students aged 9 to 10. Pretest, posttest and retention tests were administered to determine gains in knowledge. The three tests were the same test and they were ten point tests. A questionnaire was prepared to assess participants’ perceptions on the experience.The first and second research questions regarding students’ gain knowledge and retention of knowledge were analyzed quantitatively. Gains from pretest to posttest were computed by group and individually. Retention of knowledge was measured by comparison of posttest and retention tests scores.Students’ perceptions of this experience were assessed using a questionnaire. Responses to each question were summed. The basic data treatment was limited to arithmetic computation, and results were reported in “number of total responses” format.Results of the analysis of data answered the research questions. Findings From this study point to several conclusions related to the research questions. Thefollowing are conclusions from this study;(1)The value of HyperStudio™ applications as remedial instruction for some students in some content areas is still open to questions. Some gains are not considered substantial for remedial students who are being instructed in the same content for a second time.(2)No patterns were found in relation to students’ gains. Students gained from1 to 7 points in different contents and applications.(3)The students who interacted with the applications seemed to enjoy them.(4)Retention was limited to short-term memory. Accuracy of measurement is questionable since a few students demonstrated gains between posttest and retention test without additional instruction.Suggestion for further investigation where research can be productive are given

Loss of Editing Activity During the Evolution of Mitochondrial Phenylalanyl-tRNA Synthetase

Accurate selection of amino acids is essential for faithful translation of the genetic code. Errors during amino acid selection are usually corrected by the editing activity of aminoacyl-tRNA synthetases such as phenylalanyl-tRNA synthetases (PheRS), which edit misactivated tyrosine. Comparison of cytosolic and mitochondrial PheRS from the yeast Saccharomyces cerevisiae suggested that the organellar protein might lack the editing activity. Yeast cytosolic PheRS was found to contain an editing site, which upon disruption abolished both cis and trans editing of Tyr-tRNAPhe. Wild-type mitochondrial PheRS lacked cis and trans editing and could synthesize Tyr-tRNAPhe, an activity enhanced in active site variants with improved tyrosine recognition. Possible trans editing was investigated in isolated mitochondrial extracts, but no such activity was detected. These data indicate that the mitochondrial protein synthesis machinery lacks the tyrosine proofreading activity characteristic of cytosolic translation. This difference between the mitochondria and the cytosol suggests that either organellar protein synthesis quality control is focused on another step or that translation in this compartment is inherently less accurate than in the cytosol

Effects of Trypanosoma brucei tryptophanyl-tRNA synthetases silencing by RNA interference

The kinetoplast genetic code deviates from the universal code in that 90% of mitochondrial tryptophans are specified by UGA instead of UGG codons. A single nucleus-encoded tRNA Trp(CCA) is used by both nuclear and mitochondria genes, since all kinetoplast tRNAs are imported into the mitochondria from the cytoplasm. To allow decoding of the mitochondrial UGA codons as tryptophan, the tRNA Trp(CCA) anticodon is changed to UCA by an editing event. Two tryptophanyl tRNA synthetases (TrpRSs) have been identified in Trypanosoma brucei: TbTrpRS1 and TbTrpRS2 which localize to the cytoplasm and mitochondria respectively. We used inducible RNA interference (RNAi) to assess the role of TbTrpRSs. Our data validates previous observations of TrpRS as potential drug design targets and investigates the RNAi effect on the mitochondria of the parasite

C to U Editing Stimulates A to I Editing in the Anticodon Loop of a Cytoplasmic Threonyl tRNA in Trypanosoma brucei

Editing of tRNAs is widespread in nature and either changes the decoding properties or restores the folding of a tRNA. Unlike the phylogenetically disperse adenosine (A) to inosine (I) editing, cytosine (C) to uridine (U) editing has only been previously described in organellar tRNAs. We have shown that cytoplasmic tRNAThr(AGU) undergoes two distinct editing events in the anticodon loop: C to U and A to I. In vivo, every inosine-containing tRNAThr is also C to U edited at position 32. In vitro, C to U editing stimulates conversion of A to I at the wobble base. Although the in vivo and in vitro requirements differ, in both cases, the C to U change plays a key role in A to I editing. Due to an unusual abundance of A34-containing tRNAs, our results also suggest that the unedited and edited tRNAs are functional, each dedicated to decoding a specific threonine codon. C to U editing of cytoplasmic tRNA expands the editing repertoire in eukaryotic cells, and when coupled to A to I changes, leads to an interrelation between editing sites

Multi-Substrate Specificity and the Evolutionary Basis for Interdependence in tRNA Editing and Methylation Enzymes

Among tRNA modification enzymes there is a correlation between specificity for multiple tRNA substrates and heteromultimerization. In general, enzymes that modify a conserved residue in different tRNA sequences adopt a heterodimeric structure. Presumably, such changes in the oligomeric state of enzymes, to gain multi-substrate recognition, are driven by the need to accommodate and catalyze a particular reaction in different substrates while maintaining high specificity. This review focuses on two classes of enzymes where the case for multimerization as a way to diversify molecular recognition can be made. We will highlight several new themes with tRNA methyltransferases and will also discuss recent findings with tRNA editing deaminases. These topics will be discussed in the context of several mechanisms by which heterodimerization may have been achieved during evolution and how these mechanisms might impact modifications in different systems

C to U editing at position 32 of the anticodon loop precedes tRNA 5′ leader removal in trypanosomatids

In all organisms, precursor tRNAs are processed into mature functional units by post-transcriptional changes. These involve 5′ and 3′ end trimming as well as the addition of a significant number of chemical modifications, including RNA editing. The only known example of non-organellar C to U editing of tRNAs occurs in trypanosomatids. In this system, editing at position 32 of the anticodon loop of tRNAThr(AGU) stimulates, but is not required for, the subsequent formation of inosine at position 34. In the present work, we expand the number of C to U edited tRNAs to include all the threonyl tRNA isoacceptors. Notably, the absence of a naturally encoded adenosine, at position 34, in two of these isoacceptors demonstrates that A to I is not required for C to U editing. We also show that C to U editing is a nuclear event while A to I is cytoplasmic, where C to U editing at position 32 occurs in the precursor tRNA prior to 5′ leader removal. Our data supports the view that C to U editing is more widespread than previously thought and is part of a stepwise process in the maturation of tRNAs in these organisms

Tracking the transfer of antimicrobial resistance genes from raw materials to sourdough breads

The present study hypothesizes that raw materials used in bread making can transfer antibiotic resistance genes (ARGs) to processed breads. Four types of flour and four types of semolina were purchased from supermarkets and inoculated with a commercial dried sourdough starter to make breads. The microbiological characteristics of all raw materials and fermented doughs were investigated. The levels of yeasts and lactic acid bacteria (LAB) increased up to 107 CFU/g. The values of pH decreased to 4.54–4.86 while total titratable acidity increased inversely. All unprocessed and processed samples, including breads, were analyzed by a molecular approach to detect bacterial and fungal DNAs and 17 antibiotic resistance genes for penicillins, macrolides, tetracyclines, and chloramphenicol. Illumina technology showed that the operational taxonomy units (OTUs) identified from unprocessed wheat milling products, fermented doughs, and baked products mainly belonged to Acetobacteraceae. Enterococci were present in all doughs. After baking, the relative abundance (RA)% of Enterococcus and Acetobacteraceae decreased. The DNA analyzed for fungal composition showed that Kazachstania humilis dominated dried sourdough starter and doughs, and its OTUs were also detected at high RA% in baked products. The search for ARGs revealed that all samples analyzed did not show resistance to penicillins, chloramphenicol, and macrolides. However, three of the semolinas included in this study (S1, S3 and S4) and the corresponding doughs (SD1, SD3 and SD4) were positive for tet(A) and tet(B) resistance genes. This work indicated that breads have a limited role in the dissemination of ARG

Tracking the transfer of antimicrobial resistance genes from raw materials to sourdough breads

The present study hypothesizes that raw materials used in bread making can transfer antibiotic resistance genes (ARGs) to processed breads. Four types of flour and four types of semolina were purchased from supermarkets and inoculated with a commercial dried sourdough starter to make breads. The microbiological characteristics of all raw materials and fermented doughs were investigated. The levels of yeasts and lactic acid bacteria (LAB) increased up to 107 CFU/g. The values of pH decreased to 4.54–4.86 while total titratable acidity increased inversely. All unprocessed and processed samples, including breads, were analyzed by a molecular approach to detect bacterial and fungal DNAs and 17 antibiotic resistance genes for penicillins, macrolides, tetracyclines, and chloramphenicol. Illumina technology showed that the operational taxonomy units (OTUs) identified from unprocessed wheat milling products, fermented doughs, and baked products mainly belonged to Acetobacteraceae. Enterococci were present in all doughs. After baking, the relative abundance (RA)% of Enterococcus and Acetobacteraceae decreased. The DNA analyzed for fungal composition showed that Kazachstania humilis dominated dried sourdough starter and doughs, and its OTUs were also detected at high RA% in baked products. The search for ARGs revealed that all samples analyzed did not show resistance to penicillins, chloramphenicol, and macrolides. However, three of the semolinas included in this study (S1, S3 and S4) and the corresponding doughs (SD1, SD3 and SD4) were positive for tet(A) and tet(B) resistance genes. This work indicated that breads have a limited role in the dissemination of ARGs