Analisis Kesalahan Siswa kelas IV dalam Menyelesaikan Soal cerita Materi Pecahan di SDN Kolursari 2 Bangil

Salah satu materi yang diajarkan di Sekolah Dasar adalah Pecahan. Pecahan adalah salah satu materi yang harus dipahami siswa. Banyak pula kendala yang harus dilakukan oleh siswa agar memahami materi pecahan. Salah satunya yang terjadi di SDN Kolursari 2 Bangil terdapat beberapa siswa yang melakukan kesalahan konsep maupun operasi hitung yang menyebabkan terjadinya hasil dari ujian tengah semesternya kurang baik. Apalagi dalam masalah menyelesaikan materi pecahan. Penelitian ini merupakan penelitian deskriptif kualitatif yang bertujuan untuk mendeksripsikan jenis dan faktor penyebab kesalahan yang dilakukan pada siswa SD kelas IV. Subjek penelitian ini terdiri dari 20 siswa kelas IV SDN Kolursari 2 Kecamatan Bangil Kabupaten Pasuruan. Teknik pengumpulan data diambil dari mengumpulkan soal UTS semester ganjil yang ditentukan berdasarkan banyaknya kesalahan yang diketahui melalui tiap butir soal.Dari hasil analisis data dapat diperoleh kesimpulan presentase jenis kesalahan yang dilakukan siswa dalam menyelesaikan soal pecahan yaitu kesalahan konsep sebesar 59% dan kesalahan operasi hitung sebesar 41%. Penyebab kesalahan diakibatkan karena (1) kurangnya siswa dalam memahami terhadap konsep dasar pecahan senilai (2) kurang teliti dalam menghitung (3) kurang teliti dalam menyelesaikan soal (4) belum begitu hafal perkalian dan pembagian bilangan (5) tidak memahami konsep dasar operasi penjumlahan, pengurangan

Novel Quantitative Autophagy Analysis by Organelle Flow Cytometry after Cell Sonication

<div><p>Autophagy is a dynamic process of bulk degradation of cellular proteins and organelles in lysosomes. Current methods of autophagy measurement include microscopy-based counting of autophagic vacuoles (AVs) in cells. We have developed a novel method to quantitatively analyze individual AVs using flow cytometry. This method, OFACS (organelle flow after cell sonication), takes advantage of efficient cell disruption with a brief sonication, generating cell homogenates with fluorescently labeled AVs that retain their integrity as confirmed with light and electron microscopy analysis. These AVs could be detected directly in the sonicated cell homogenates on a flow cytometer as a distinct population of expected organelle size on a cytometry plot. Treatment of cells with inhibitors of autophagic flux, such as chloroquine or lysosomal protease inhibitors, increased the number of particles in this population under autophagy inducing conditions, while inhibition of autophagy induction with 3-methyladenine or knockdown of ATG proteins prevented this accumulation. This assay can be easily performed in a high-throughput format and opens up previously unexplored avenues for autophagy analysis.</p></div

Fate of the genes in pan-Overlaps in <i>Salmonella</i> strains.

<p>(A) Average of the percentages of the genes inside operons. (B) Average of the percentages of the genes outside of operons.</p

Evolutionary Dynamics of Overlapped Genes in <i>Salmonella</i>

<div><p>Presence of overlapping genes (OGs) is a common phenomenon in bacterial genomes. Most frequently, overlapping genes share coding regions with as few as one nucleotide to as many as thousands of nucleotides. Overlapping genes are often co-regulated, transcriptionally and translationally. Overlapping genes are also subject to the whims of evolution, as the gene overlap is known to be disrupted in some species/strains and participating genes are sometimes lost in independent lineages. Therefore, a better understanding of evolutionary patterns and rates of the disruption of overlapping genes is an important component of genome structure and evolution of gene function. In this study, we investigate the fate of ancestrally overlapping genes in complete genomes from 15 contemporary strains of <i>Salmonella</i> species. We find that the fates of overlapping genes inside and outside operons are distinctly different. A larger fraction of overlapping genes inside operons conserves their overlap as compared to gene pairs outside of the operons (average 0.89 vs. 0.83 per genome). However, when overlapping genes in the operons separate, one partner is lost more frequently than in those separated genes outside of operons (average 0.02 vs. 0.01 per genome). We also investigate the fate of a pan set of overlapping genes at the present and ancestral nodes over a phylogenetic tree based on genome sequence data, respectively. We propose that co-regulation plays important roles on the fates of genes. Furthermore, a vast majority of disruptions occurred prior to the common ancestor of all 15 <i>Salmonella</i> strains, which enables us to obtain an estimate of disruptions between <i>Salmonella</i> and <i>E. coli</i>.</p></div

Pharmacologically induced acidic vacuoles can be individually detected by OFACS from sonicated cells stained with AO.

<p><b>(A)</b> PC3 cells treated with 1 µM GDC-0941 and 10 µM CQ for 2 days analyzed by OFACS after staining with AO. FITC (green) vs. PerCP (red) channels of the organelle population are plotted. Percentage of the gated AO⁺ population is shown for each plot. <b>(B)</b> Quantification of the number of AO⁺ events as gated in <b>(A)</b> normalized to the number of cells used for sonication with each treatment. *, P<0.05. <b>(C)</b> Quantitative analysis by OFACS showing the normalized number of AO⁺ events under indicated treatments. PC3 cells transfected with Atg5 or Atg7 siRNA for 2 days were treated with 1 µM GDC-0941 or 5 µM GDC-0068 +/− 10 µM CQ for an additional day. *, P<0.05 vs. DMSO, CQ or GDC-0941/GDC-0068 alone with non-target siRNA; **, P<0.05 vs. non-target siRNA in the same treatment group. <b>(D,E)</b> Quantification of AO⁺ events obtained by OFACS analysis of PC3 cells treated with GDC-0941 or GDC-0068 +/− CQ or protease inhibitors for 2 days, showing the normalized number of AO⁺ events <b>(D)</b> and the total “red” signal intensity of AO⁺ events <b>(E)</b>, derived by multiplying the number of AO⁺ organelles by the mean value of the “red” AO signal. *, P<0.05 both vs. DMSO group treated with the same lysosomal inhibitor and vs. GDC-0941 or GDC-0068 alone. Error bars represent SEM (n = 3). P values are determined by Student's t-test. Representative data from one of three independent experiments are shown. All quantifications are normalized to the number of cells used for the sonication under each condition.</p

The ML phylogeny inferred from the four-fold degenerate sites of 474 genes.

<p>The internal nodes are labeled 19–35, with node 35 being the divergent point between <i>E. coli</i> and <i>Salmonella</i> and node 32 being the root node of the ingroup <i>Salmonella</i>.</p

Inhibition of autophagy by 3-MA at an early stage and by BafA1 at a later stage can be distinguished by individual AV analysis with OFACS.

<p>Untransfected PC3 cells <b>(A,B)</b> or PC3 cells expressing mCherry-eGFP-LC3B <b>(C)</b> treated with 1 µM GDC-0941 or 5 µM GDC-0068 +/− 10 µM CQ for 24 hours with the addition of: nothing (upper panels), 0–10 mM 3-MA (middle panels) or 0–100 nM Bafilomycin A1 (BafA1; bottom panels). AVs were analyzed by OFACS after staining with AO <b>(A,B)</b> or unstained <b>(C)</b>. Y axes represent the total “red” channel intensity of AO⁺ organelles normalized to cell number <b>(A,B)</b> or the percentage of mCherry⁺eGFP⁺ events of the total subcellular events <b>(C)</b>. Note the different scales of the y-axes in<b> (A)</b> vs.<b> (B).</b> Error bars represent standard deviations (SD), n = 3.</p

Completely sequenced genomes analyzed in this study.

*<p>Genomes with pre-identified orthlogous clusters in ATGC <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081016#pone.0081016-Novichkov1" target="_blank">[10]</a>.</p

Phylogenetic map of the overlapping gene pairs.

<p>(A) Phylogenetic map of the overlapping gene pair (<i>bcsC</i>, <i>bcsZ</i>). (B) Phylogenetic map of the overlapping gene pair (<i>ompR</i>, <i>envZ</i>).</p

mCherry-eGFP-LC3B, eGFP-p62, and Acridine Orange are co-localized with fluorescently-labeled chloroquine in AVs detected by OFACS.

<p><b>(A)</b> Representative microscopy images of PC3 cells stably expressing mCherry-eGFP-LC3B and treated with 1 µM GDC-0941 +/− 9 µM CQ and 1 µM LynxTag-CQ-blue for 24 hours. Images are shown in each fluorescence channel separately (top panels) or merged (bottom panels). Scale bar: 20 µm. <b>(B)</b> OFACS quantification of the experiment in <b>(A)</b> showing the normalized numbers of events with the indicated labels: total normalized number of “subcellular” events (black bars), CQblue⁺ (blue bars), eGFP⁺ (green bars) and dual positive (CQblue⁺eGFP⁺) (cyan bars). *, P<0.05 vs. DMSO, CQ or GDC-0941 only groups. <b>(C)</b> Representative microscopy images of PC3 cells transiently transfected with eGFP-p62 for 48 hours and treated with GDC-0941 (1 µM) +/− 9 µM CQ and 1 µM LynxTag-CQ-blue for 24 hours. Images are shown in green or blue channels separately or merged. Scale bar: 10 µm. <b>(D)</b> OFACS quantification of the experiment in <b>(C) </b>showing the normalized number of CQblue⁺eGFP⁺ events under each treatment. <b>(E)</b> “Red” (PerCP) vs. “blue” (DAPI) channel plots of PC3 cells treated with 1 µM GDC-0941 +/− 5uM LynxTag-CQ-blue for 24 hours, stained with AO, sonicated and analyzed by OFACS. Error bars represent SEM (n = 4). Representative data from 2 independent experiments are shown.</p