Using journals to assess non-STEM student learning in STEM courses: A case study in cybersecurity education

Embry-Riddle Aeronautical University offers a minor course of study in cybersecurity as an option in our undergraduate Homeland Security program. Since the students are, by and large, social scientists, the focus of the program is to build hyper-awareness of how cybersecurity integrates within their professional aspirations rather than to provide cybersecurity career-level proficiency. Assessing student learning of the technical aspects cannot be performed using traditional tests, as they would not properly measure what the students are learning in a practical sense. Instead, we employ journals and self-reflection to ask the students to express and demonstrate their learning. Although somewhat harder to grade, the journals have huge benefits to the learning environment as well as to actual learning

Hairpin Plum pox virus coat protein (hpPPV-CP) structure in ‘HoneySweet’ C5 plum provides PPV resistance when genetically engineered into plum (Prunus domestica) seedlings

The genetically engineered plum ‘HoneySweet’ (aka C5) has proven to be highly resistant to Plum pox virus (PPV) for over 10 years in field trials. The original vector used for transformation to develop ‘HoneySweet’ carried a single sense sequence of the full length PPV coat protein (ppv-cp) gene, yet DNA blot analyses indicated that there was an inserted copy of the ppv-cp that appeared to be an inverted repeat structure. Since the resistance mechanism of ‘HoneySweet’ was found to be based on post-transcriptional gene silencing (PTGS), it was hypothesized that the inverted repeat structure conferred the resistance to PPV in ‘HoneySweet’. Sequencing of the transgene insertions confirmed the presence of an inverted repeat of the PPV-CP sequence. We hypothesized that transcription from this structure produced a hairpin (hp) RNA that was responsible for PTGS of the transgene and the destruction of PPV viral RNA resulting in the high level of resistance to PPV infection. In order to confirm this hypothesis the hpPPV-CP insert was cloned from ‘HoneySweet’ and transferred into ‘Bluebyrd’ plum seedlings through Agrobacterium tumefaciens transformation of hypocotyl slices. The introduced DNA contained the CP inverted repeat flanked by 35S promoters on either end. Transgenic plum plants containing single or multiple copies of this hp insert were inoculated with PPV D isolated from Pennsylvania, USA. PPV infection was evaluated through three cycles of cold-induced dormancy (CID) by symptom expression and by two or more ELISA and PCR tests. Of the 18 plants evaluated, eight were always virusfree, five occasionally had weak or moderate infections, and five plants were clearly infected in multiple tests. While all plants of some clones were virus-free others had a mix of uninfected and mildly infected plants of the same clone. Most of the resistant plants contained a single copy of the hp construct. These data strongly support the hypothesis that the hp structure of the ppv-cp insert in ‘HoneySweet’ plum can confer PPV resistance.Keywords: Breeding, gene silencing, Rosaceae, shark

Correction: Rice XB15, a Protein Phosphatase 2C, Negatively Regulates Cell Death and XA21-Mediated Innate Immunity

Perception of extracellular signals by cell surface receptors is of central importance to eukaryotic development and immunity. Kinases that are associated with the receptors or are part of the receptors themselves modulate signaling through phosphorylation events. The rice (Oryza sativa L.) XA21 receptor kinase is a key recognition and signaling determinant in the innate immune response. A yeast two-hybrid screen using the intracellular portion of XA21, including the juxtamembrane (JM) and kinase domain as bait, identified a protein phosphatase 2C (PP2C), called XA21 binding protein 15 (XB15). The interaction of XA21 and XB15 was confirmed in vitro and in vivo by glutathione-S-transferase (GST) pull-down and co-immunoprecipitation assays, respectively. XB15 fusion proteins purified from Escherichia coli and from transgenic rice carry PP2C activity. Autophosphorylated XA21 can be dephosphorylated by XB15 in a temporal- and dosage-dependent manner. A serine residue in the XA21 JM domain is required for XB15 binding. Xb15 mutants display a severe cell death phenotype, induction of pathogenesis-related genes, and enhanced XA21-mediated resistance. Overexpression of Xb15 in an XA21 rice line compromises resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae. These results demonstrate that Xb15 encodes a PP2C that negatively regulates the XA21-mediated innate immune response

Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes

Rice kinases with biotic stress responses. (XLSX 28 kb

ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome

<p>Abstract</p> <p>Background</p> <p>Maize (<it>Zea mays </it>ssp. <it>mays </it>L.) is an important model for plant basic and applied research. In 2009, the B73 maize genome sequencing made a great step forward, using clone by clone strategy; however, functional annotation and gene classification of the maize genome are still limited. Thus, a well-annotated datasets and informative database will be important for further research discoveries. Signal transduction is a fundamental biological process in living cells, and many protein families participate in this process in sensing, amplifying and responding to various extracellular or internal stimuli. Therefore, it is a good starting point to integrate information on the maize functional genes involved in signal transduction.</p> <p>Results</p> <p>Here we introduce a comprehensive database 'ProFITS' (Protein Families Involved in the Transduction of Signalling), which endeavours to identify and classify protein kinases/phosphatases, transcription factors and ubiquitin-proteasome-system related genes in the B73 maize genome. Users can explore gene models, corresponding transcripts and FLcDNAs using the three abovementioned protein hierarchical categories, and visualize them using an AJAX-based genome browser (JBrowse) or Generic Genome Browser (GBrowse). Functional annotations such as GO annotation, protein signatures, protein best-hits in the <it>Arabidopsis </it>and rice genome are provided. In addition, pre-calculated transcription factor binding sites of each gene are generated and mutant information is incorporated into ProFITS. In short, ProFITS provides a user-friendly web interface for studies in signal transduction process in maize.</p> <p>Conclusion</p> <p>ProFITS, which utilizes both the B73 maize genome and full length cDNA (FLcDNA) datasets, provides users a comprehensive platform of maize annotation with specific focus on the categorization of families involved in the signal transduction process. ProFITS is designed as a user-friendly web interface and it is valuable for experimental researchers. It is freely available now to all users at <url>http://bioinfo.cau.edu.cn/ProFITS</url>.</p

Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence

<p>Abstract</p> <p>Background</p> <p>Lignification of the fruit endocarp layer occurs in many angiosperms and plays a critical role in seed protection and dispersal. This process has been extensively studied with relationship to pod shatter or dehiscence in <it>Arabidopsis</it>. Dehiscence is controlled by a set of transcription factors that define the fruit tissue layers and whether or not they lignify. In contrast, relatively little is known about similar processes in other plants such as stone fruits which contain an extremely hard lignified endocarp or stone surrounding a single seed.</p> <p>Results</p> <p>Here we show that lignin deposition in peach initiates near the blossom end within the endocarp layer and proceeds in a distinct spatial-temporal pattern. Microarray studies using a developmental series from young fruits identified a sharp and transient induction of phenylpropanoid, lignin and flavonoid pathway genes concurrent with lignification and subsequent stone hardening. Quantitative polymerase chain reaction studies revealed that specific phenylpropanoid (phenylalanine ammonia-lyase and cinnamate 4-hydroxylase) and lignin (caffeoyl-CoA O-methyltransferase, peroxidase and laccase) pathway genes were induced in the endocarp layer over a 10 day time period, while two lignin genes (<it>p-</it>coumarate 3-hydroxylase and cinnamoyl CoA reductase) were co-regulated with flavonoid pathway genes (chalcone synthase, dihydroflavanol 4-reductase, leucoanthocyanidin dioxygen-ase and flavanone-3-hydrosylase) which were mesocarp and exocarp specific. Analysis of other fruit development expression studies revealed that flavonoid pathway induction is conserved in the related Rosaceae species apple while lignin pathway induction is not. The transcription factor expression of peach genes homologous to known endocarp determinant genes in <it>Arabidopsis </it>including <it>SHATTERPROOF</it>, <it>SEEDSTCK </it>and <it>NAC SECONDARY WALL THICENING PROMOTING FACTOR 1 </it>were found to be specifically expressed in the endocarp while the negative regulator <it>FRUITFU</it>L predominated in exocarp and mesocarp.</p> <p>Conclusions</p> <p>Collectively, the data suggests, first, that the process of endocarp determination and differentiation in peach and <it>Arabidopsis </it>share common regulators and, secondly, reveals a previously unknown coordination of competing lignin and flavonoid biosynthetic pathways during early fruit development.</p

The Peach v2.0 Release : An Improved Genome Sequence for Bridging the Gap Between Genomics and Breeding in Prunus

Since its release the high quality peach genome sequence (Peach v1.0) has fostered studies on comparative genomics as well as on genetic diversity, domestication and crop improvement in Prunus and related species. To improve the chromosome-scale assembly and genome annotation we performed further analyses. Extensive mapping data allowed the improvement of Peach v2.0 assembly in terms of fraction of mapped (99.2%) and orientated (97.9%) sequences and correction of misassembly issues (about 12.2 Mb of incorrectly positioned sequences). Assembled resequencing data (42x) improved base accuracy and contiguity: 859 SNPs and 1,347 Indels were corrected and 212 gaps were closed. As a result the contiguity of Peach v2.0 improved with a contig L50 of 255.4 kb (previously 214.2 kb) and a contig N50 of 250 (previously 294). Repeat annotation was enhanced including low copy repeats and the complete sequence and location of 1,157 non autonomous Helitrons. Gene prediction and annotation were improved using transcript assemblies obtained from 2.2 billion of RNA seq reads from different peach tissues and organs. In total, after masking with the improved repeat annotation, 26,873 protein-coding genes were predicted in Peach v2.1 annotation, 991 less than those predicted in Peach v1.0. Gene annotation was highly enhanced with the prediction of almost 20,000 new isoforms. The new peach release with improved assembly and annotation will be a pivotal resource for comparative genomics in the plant kingdom and will serve as a foundation for studies bridging the gap between genomics and breeding in Prunus and related species

LRR-RLK family from two Citrus species: Genome-wide identification and evolutionary aspects

Background: Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (sweet orange). In addition, we used large-scale phylogenetic approaches to elucidate the evolutionary relationships of the LRR-RLKs and further narrowed the analysis to the LRR-XII group, which contains several previously described cell surface immune receptors. Results: We built integrative protein signature databases for Citrus clementina and Citrus sinensis using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in C. clementina and C. sinensis, respectively. Maximum-likelihood phylogenetic trees were estimated using Arabidopsis LRR-RLK as a template and they allowed us to classify Citrus LRR- 34 RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each Citrus genome. Phylogenetic analysis also demonstrated the existence of two distinct LRR-XII clades, each one constituted mainly by RD and non-RD kinases. We identified 68 orthologous pairs from the C. clementina and C. sinensis LRR-XII genes. In addition, among the paralogs, we identified a subset of 78 and 62 clustered genes probably derived from tandem duplication events in the genomes of C. clementina and C. sinensis, respectively. Conclusions: This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. A large expansion of LRR-XII in Citrus genomes suggests that it might play a key role in adaptive responses in host-pathogen co-evolution, related to the perennial life cycle and domestication of the citrus crop species

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

BACKGROUND: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multi-domain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. METHODOLOGY: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. CONCLUSIONS: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multi-domain architecture