Models of classroom assessment for course-based research experiences

Course-based research pedagogy involves positioning students as contributors to authentic research projects as part of an engaging educational experience that promotes their learning and persistence in science. To develop a model for assessing and grading students engaged in this type of learning experience, the assessment aims and practices of a community of experienced course-based research instructors were collected and analyzed. This approach defines four aims of course-based research assessment—(1) Assessing Laboratory Work and Scientific Thinking; (2) Evaluating Mastery of Concepts, Quantitative Thinking and Skills; (3) Appraising Forms of Scientific Communication; and (4) Metacognition of Learning—along with a set of practices for each aim. These aims and practices of assessment were then integrated with previously developed models of course-based research instruction to reveal an assessment program in which instructors provide extensive feedback to support productive student engagement in research while grading those aspects of research that are necessary for the student to succeed. Assessment conducted in this way delicately balances the need to facilitate students’ ongoing research with the requirement of a final grade without undercutting the important aims of a CRE education

A novel cucumber gene associated with systemic acquired resistance

Several genes were isolated by differential display of mRNAs from cucumber leaves inoculated with the bacterium, Pseudomonas syringae pv. lachrymans. A full-length cDNA encoding a novel pathogen-induced gene, Cupi4, was cloned and characterized in detail. While Cupi4 did not share evident homology with known sequences in the database at the nucleotide level, the predicted amino acid sequence of Cupi4 shared homology with the pathogen-inducible proteins, pMB57-10G 5′ of Brassica napus (21%) and CXc750/ESC1 of Arabidopsis thaliana (16%). Cupi4 transcripts accumulated after 12 h in leaves inoculated with P. s. lachrymans and after 48 h in the systemic upper leaves of the inoculated plants. Treatment with the chemical inducers of systemic acquired resistance (SAR), salicylic acid, 2,6-dichloroisonicotinic acid and benzothiadiazole as well as inoculation with different pathogens, P. s. syringae, Colletotrichum lagenarium and tobacco necrosis virus also led to the accumulation of Cupi4 transcripts. The increase of Cupi4 transcripts in both the inoculated first leaf and in systemic upper leaves suggested that the Cupi4 gene product is associated with systemic acquired resistance in cucumber. Induced expression of CUPI4 in different host strains of a bacterium, Escherichia coli, led to death of bacterial host cells, suggesting that CUPI4 might have antibacterial properties

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which should be cited to refer to this work

Screening of lupine germplasm for resistance against Phytophthora sojae

Phytophthora sojae is a major pathogen in cultivated soybeans world-wide. Although incorporating resistance genes has been an effective management tool for soybean breeders, surveys of soybean fields in the Midwest US indicate that some P. sojae strains are capable of overcoming all known resistance genes. While P. sojae is known to have a very narrow host range, it can also infect Lupinus (lupine), varieties of which may provide potential sources for novel resistance genes that can be genetically engineered into soybean. The chemotactic behavior of zoospores and pathogenicity of P. sojae strain P6497 towards 17 lupine lines were explored. The two soybean varieties Williams and Williams 82 that are susceptible and resistant against P. sojae P6497, respectively, were used as controls. Chemotaxis assays showed that there was no coherent pattern between the number of zoospores colonizing the root surface and plant tolerance or resistance to phytophthora root rot. Pathogenicity tests identified two of 17 lupine lines tested (LAB 18 and LL 35) were resistant to P. sojae infection. Phylogenetic analysis of these two resistant lupine lines with Old World lupines of the Mediterranean and North African regions, and New World lupines of America, indicated that they originated from the Old World.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The Immunoreactive Exo-1,3-β-Glucanase from the Pathogenic Oomycete Pythium insidiosum Is Temperature Regulated and Exhibits Glycoside Hydrolase Activity.

The oomycete organism, Pythium insidiosum, is the etiologic agent of the life-threatening infectious disease called "pythiosis". Diagnosis and treatment of pythiosis is difficult and challenging. Novel methods for early diagnosis and effective treatment are urgently needed. Recently, we reported a 74-kDa immunodominant protein of P. insidiosum, which could be a diagnostic target, vaccine candidate, and virulence factor. The protein was identified as a putative exo-1,3-ß-glucanase (Exo1). This study reports on genetic, immunological, and biochemical characteristics of Exo1. The full-length exo1 coding sequence (2,229 bases) was cloned. Phylogenetic analysis showed that exo1 is grouped with glucanase-encoding genes of other oomycetes, and is far different from glucanase-encoding genes of fungi. exo1 was up-regulated upon exposure to body temperature, and its gene product is predicted to contain BglC and X8 domains, which are involved in carbohydrate transport, binding, and metabolism. Based on its sequence, Exo1 belongs to the Glycoside Hydrolase family 5 (GH5). Exo1, expressed in E. coli, exhibited ß-glucanase and cellulase activities. Exo1 is a major intracellular immunoreactive protein that can trigger host immune responses during infection. Since GH5 enzyme-encoding genes are not present in human genomes, Exo1 could be a useful target for drug and vaccine development against this pathogen

Protein structure of Exo1 and six transcriptome-derived homologous proteins.

<p>Protein domains of Exo1 and homologous proteins (UN05080, UN00475, UN03240, UN01457, UN24957 and UN22794; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135239#pone.0135239.t003" target="_blank">Table 3</a>) were predicted by SignalP, TMHMM, and NCBI’s conserved domain search programs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135239#sec002" target="_blank">Methods</a>). The DOG program was used to draw protein structures. Numbers indicate the first and last amino acid positions of each protein. Detailed characteristics of the homologous proteins are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135239#pone.0135239.t003" target="_blank">Table 3</a>. (Symbols: A, Peptide-A; B, Peptide-B; C/1, Peptide-C (the first half portion); C/2, Peptide-C (the second half portion); SP, signal peptide; BglC, BglC domain; X8, X8 domain; and TM, transmembrane region; The grey regions are sequences that do not match any protein domain defined by the NCBI’s conserved domain search program).</p

Expression of <i>exo1</i> in response to temperature, culture duration, and dextrose availability.

<p>Real-time PCR was used to measure <i>exo1</i> mRNA levels in <i>P</i>. <i>insidiosum</i> (strain Pi-S) at 5 culture conditions: (i) 28°C for 7 days (28c-7d-1x); (ii) 37°C for 7 days (37c-7d-1x); (iii) 28°C for 14 days (28c-14d-1x); and 28°C for 7 days with (iv) 2 mg/ml dextrose (28c-7d-0.1x), or (v) no dextrose (28c-7d-0x) supplement. <i>exo1</i> expression in each condition was normalized to the reference actin gene (<i>act1</i>). Asterisk indicates significant up- or down-regulation, relative to 28c-7d-1x.</p

Immunoreactivity of Exo1 peptides against rabbit anti-Exo1 peptide sera.

<p>ELISA result of rabbit pre-immune or anti-Exo1 peptide serum (raised against the combination of Peptide-A, -B, and -C) with the individual peptides (used to coat an ELISA plate).</p

Western blot analysis of <i>P</i>. <i>insidiosum</i>’s crude protein extracts using rabbit anti- Exo1 peptide serum.

<p>Crude proteins (SABH and CFA) extracted from <i>P</i>. <i>insidiosum</i> were separated in a SDS-PAGE gel, transferred to a Western blot membrane, and probed with the rabbit pre-immune or post-immune serum. The arrow and arrow head indicate the 82- and 78-kDa band, respectively. Protein molecular weight markers (7–175) are shown in kDa. (SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis; CFA, culture filtrate antigen; SABH, soluble antigen from broken hyphae; Pre-immune, rabbit pre-immune serum; Post-immune, rabbit anti-Exo1 peptide serum).</p

Phylogenetic analysis of glucanase genes from oomycetes and fungi.

<p><i>exo1</i> gene sequences from 6 strains of <i>P</i>. <i>insidiosum</i> (accession number: LC033486 to LC033491), and glucanase-encoding genes (top <i>exo1</i>-BLAST hit sequences) from 9 other oomycetes and 26 fungi (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135239#pone.0135239.t002" target="_blank">Table 2</a>) were included for phylogenetic analysis. Phylogenetic reconstruction was performed using the PhyML program (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135239#sec002" target="_blank">Methods</a>). Reliability for internal branch was analyzed using the aLRT test (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135239#sec002" target="_blank">Methods</a>).</p