Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii.

BACKGROUND: Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms. RESULTS: In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class. CONCLUSIONS: Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes.published_or_final_versio

An ab initio investigation of boron nanotube in ringlike cluster form

Author name used in this publication: Yuan-Xu WangAuthor name used in this publication: V. C. Lo2009-2010 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Towards a model of effective use of video for teacher professional development

Based on previous research, this paper proposes an emerging model to outline the learning outcomes that teacher education programmes using video should consider. Besides cognitive and psychomotor learning, the affective and social needs of teachers are also highlighted in the model to inform the development of video-mediated teacher professional activities. Three broad strategies are identified in the model for bringing forth the learning outcomes, namely, critical reflection, meaningful comparison and productive discussion. These interact to shape the landscape of teacher professional learning. The model also identifies the key role of facilitators and the importance of video selection in enhancing teacher learning via video-mediated activities. It is suggested that the emergent model can serve as a heuristic guide on effective use of video for teacher professional development.postprintThe International Seminar, hosted by the national network of Science Learning Centres and University of York Science Education Group (UYSEG), York, U.K., February 2010

Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction

© 2014 Ashworth et al. Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of nonmodel organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins

BACKGROUND: Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how the expansion of the Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family in Halobacterium salinarum NRC-1 has aided in niche-adaptation of this archaeon to a complex and dynamically changing hypersaline environment.RESULTS: We mapped genome-wide binding locations for all eight FFRPs, investigated their preference for binding different effector molecules, and identified the contexts in which they act by analyzing transcriptional responses across 35 growth conditions that mimic different environmental and nutritional conditions this organism is likely to encounter in the wild. Integrative analysis of these data constructed an FFRP regulatory network with conditionally active states that reveal how interrelated variations in DNA-binding domains, effector-molecule preferences, and binding sites in target gene promoters have tuned the functions of each FFRP to the environments in which they act. We demonstrate how conditional regulation of similar genes by two FFRPs, AsnC (an activator) and VNG1237C (a repressor), have striking environment-specific fitness consequences for oxidative stress management and growth, respectively.CONCLUSIONS: This study provides a systems perspective into the evolutionary process by which gene duplication within a transcription factor family contributes to environment-specific adaptation of an organism

Oral health and breastfeeding promotion program for pregnant women

The aim of this project was to promote the awareness and knowledge of pregnant women and infant oral health as well as the oral benefits of breastfeeding through a multi-disciplinary approach. This pilot oral health promotion program was developed to promote oral health knowledge related to the common dental problems among pregnant women and infants, and the oral health advantages of breastfeeding for infants. The program was conducted twice during March to April 2016 at the Queen Elizabeth Hospital. It consisted of a 15-minute PowerPoint presentation and a 15-minute small-group interactive workshop on Oral Hygiene Instructions. Evaluation forms were used to collect the feedbacks of the participants. The feedbacks for both the PowerPoint presentation and the interactive workshop were positive. Over 70% of the participants found that the contents were well-presented and the dental students were able to answer their questions. Furthermore, the participants agreed that the stated objectives of the program were met and the content of the program could be applicable in the coming future. Over 80% of the participants expressed that they understood the oral health advantages of breastfeeding after this program. To conclude, this program can effectively promote the key oral health messages about the common oral health problems of pregnant women and infants as well as the oral health advantages of breastfeeding. Also, this program can be effectively incorporated into the existing ante-natal classes. Further research can be performed to quantify the effectiveness by comparing the dental knowledge of pregnant women before and after this program. Further cooperation with a wider range of organizations, such as midwifery and nursing schools should also be explored.published_or_final_versio

SWATH-MS Quantitative analysis of proteins in the rice inferior and superior spikelets during grain filling

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