Pengembangan Perangkat Pembelajaran Matematika Kelas Rendah Berorientasi Model Pembelajaran Diskusi

This development was aimed at creating learning device for low level mathematics to increase the students\u27 participation and achievement through discussion learning model in Class A of the second semester of the Elementary School Teacher Education Department of Muhammadiyah University of Purwokerto of the academic year 2008/2009. The 49 subject takers was divided into 15 groups of 3 to 4 people. The procedure of developing the device used classroom action research. The action consisted of two cycles and took three months. Each cycle was done depending on the obtained improvement, design and the factor to be developed. The instrument which was used to get the data of participation and students\u27 response towards the lecture and the learning device was questioner, while he instrument to get data on students learning achievement were essay quiz, mid term test, and the end term test. The result was the device for learning low level mathematics, early-class learning material, students work, and increased learning participation. The learning achievement was still low which was due to their low ability in solving mathematical problem. Key words: Discussion learning model, participation, and mathematics learning achievement

Additional file 1: Table S1. of SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions

Sensitivity and specificity of our approach to discriminate non-target sequences. (XLSX 34 kb)ďť

Droplet MDA of low-input lambda DNA.

<p>(a) Sequential fluorescent images of droplets encapsulating lambda DNA at a concentration of 265 ag/droplet (5 copies lambda DNA per droplet) with Evagreen dye. (b) Time-dependent appearance of the fluorescence signal during compartmentalized amplification of the denatured lambda DNA (input concentration 54 ag/droplet (1 copy lamda DNA per droplet) and 265 ag/droplet). All data are presented as averaged intensities of fluorescent positive droplets measured with SEM, and 100 droplets were analyzed at each time point.</p

Amplicon yields by in-tube MDA and droplet MDA.

<p>No template control (NTC), 1 and 10 <i>E</i>. <i>coli</i> cells were used as start material. In the droplet MDA, lysed cells were pumped into the droplet generators and genome DNA fragments were randomly encapsulated into picoliter droplets consist of MDA mixture (67 pL per droplet, total 1.5× 10⁵ droplets). After 180 min of MDA reaction, the yields were evaluated following droplet breaking and amplicon purification. A total of 10 μL of MDA mixture was used in both droplet MDA and in-tube MDA reactions.</p

Evaluation of amplification bias of droplet MDA.

<p>Distributions of sequencing coverage of MDA products from single <i>Escherichia coli</i> cells (n = 3) were compared between in-tube MDA (left column) and droplet MDA (right column). Each graph shows the results of independent reactions. The averaged sequencing coverages were calculated from raw sequencing reads that mapped to with <i>E</i>. <i>coli</i> reference genome within 1-kb windows. Sequencing reads were normalized to 60× sequencing effort in each experiment.</p

Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification

<div><p>Whole genome amplification (WGA) is essential for obtaining genome sequences from single bacterial cells because the quantity of template DNA contained in a single cell is very low. Multiple displacement amplification (MDA), using Phi29 DNA polymerase and random primers, is the most widely used method for single-cell WGA. However, single-cell MDA usually results in uneven genome coverage because of amplification bias, background amplification of contaminating DNA, and formation of chimeras by linking of non-contiguous chromosomal regions. Here, we present a novel MDA method, termed droplet MDA, that minimizes amplification bias and amplification of contaminants by using picoliter-sized droplets for compartmentalized WGA reactions. Extracted DNA fragments from a lysed cell in MDA mixture are divided into 10⁵ droplets (67 pL) within minutes via flow through simple microfluidic channels. Compartmentalized genome fragments can be individually amplified in these droplets without the risk of encounter with reagent-borne or environmental contaminants. Following quality assessment of WGA products from single <i>Escherichia coli</i> cells, we showed that droplet MDA minimized unexpected amplification and improved the percentage of genome recovery from 59% to 89%. Our results demonstrate that microfluidic-generated droplets show potential as an efficient tool for effective amplification of low-input DNA for single-cell genomics and greatly reduce the cost and labor investment required for determination of nearly complete genome sequences of uncultured bacteria from environmental samples.</p></div

Assembly statistics of MDA products obtained from single <i>Escherichia coli</i> cells.

<p>A total of 10 μL of MDA product was evaluated for both droplet MDA and in-tube MDA. Sequencing reads were normalized to 0.8 M reads (60× sequencing effort) in each experiment.</p><p>Assembly statistics of MDA products obtained from single <i>Escherichia coli</i> cells.</p

Genome recovery from row sequence reads and <i>de novo</i> assembled contigs obtained from droplet MDA products of single and 10 <i>E</i>. <i>coli</i> cells.

<p>(a) Comparison of genome recovery from raw sequence reads as a function of sequencing effort. Each plot shows the averaged percentage of genome recovery with SD from raw sequence reads for single (n = 3) and 10 (n = 3) <i>Escherichia coli</i> cells at >1× or >10× sequencing coverage. (b) Comparison of genome recovery from <i>de novo</i> assembled contigs as a function of sequencing effort. Each plot shows <i>de novo</i> assembly result in in-tube MDA and the droplet MDA.</p

Generation of monodisperse picoliter droplets for compartmentalized MDA reactions.

<p>(a) Microphotograph of droplet generation at the microfluidic cross-junction. The MDA mixtures containing single-cell genomes were introduced into the microfluidic device for encapsulation in droplets at the single molecule level. (b) Microphotograph of droplets collected from the microfluidic droplet generator. (c) Size distribution of droplets used for compartmentalized MDA reactions. Ratio of flow rates (water: oil): (1) 2:4, (2) 3:3, (3) 3:1, and (4) 6:1 μL/min. Junction width: (1): 8.5 μm, (2 and 3): 17 μm, and (4): 34 μm.</p

Assembly statistics of sequence reads obtained from MDA products of contaminants in no template control (NTC) samples.

<p>A total of 10 μL of MDA mixture was used in both droplet MDA and in-tube MDA reactions. In both droplet MDA and in-tube MDA, a total of 1 ng of MDA product was used for sequence library preparation. Row sequence reads were obtained at 100× sequencing effort.</p><p>Assembly statistics of sequence reads obtained from MDA products of contaminants in no template control (NTC) samples.</p