Isolation of Thylakoid Membrane Complexes from Rice by a New Double-Strips BN/SDS-PAGE and Bioinformatics Prediction of Stromal Ridge Subunits Interaction

Thylakoid membrane complexes of rice (Oryza sativa L.) play crucial roles in growth and crop production. Understanding of protein interactions within the complex would provide new insights into photosynthesis. Here, a new “Double-Strips BN/SDS-PAGE” method was employed to separate thylakoid membrane complexes in order to increase the protein abundance on 2D-gels and to facilitate the identification of hydrophobic transmembrane proteins. A total of 58 protein spots could be observed and subunit constitution of these complexes exhibited on 2D-gels. The generality of this new approach was confirmed using thylakoid membrane from spinach (Spinacia oleracea) and pumpkin (Cucurita spp). Furthermore, the proteins separated from rice thylakoid membrane were identified by the mass spectrometry (MS). The stromal ridge proteins PsaD and PsaE were identified both in the holo- and core- PSI complexes of rice. Using molecular dynamics simulation to explore the recognition mechanism of these subunits, we showed that salt bridge interactions between residues R19 of PsaC and E168 of PasD as well as R75 of PsaC and E91 of PsaD played important roles in the stability of the complex. This stromal ridge subunits interaction was also supported by the subsequent analysis of the binding free energy, the intramolecular distances and the intramolecular energy

Toward Understanding the Mechanism of Protein Targeting in the Chloroplast Signal Recognition Particle Pathway

Protein targeting is a vital cellular function. The signal recognition particle (SRP) pathway is a universally conserved targeting system present in the cytosol and used to co-translationally target many proteins to the inner membrane of prokaryotes and the endoplasmic reticulum of eukaryotes. The chloroplast has a homologous SRP system which post-translationally targets light harvesting chlorophyll binding proteins (LHCPs) to the thylakoid membrane for integration. The chloroplast SRP (cpSRP) is a heterodimer with a 54 kDa subunit equivalent to SRP54 in the canonical pathway. In addition, cpSRP contains a novel 43 kDa subunit which is a unique and irreplaceable component. cpSRP43 is central to targeting the highly hydrophobic LHCPs to the Albino3 translocase at the thylakoid membrane by operating as a chaperone capable even of disaggregating LHCPs without any external energy input. cpSRP43 has multiple binding partners in the cpSRP pathway. Many details about these binding interactions have been discovered however exact residual details regarding these interactions still requires elucidation. A structure for cpSRP43 bound to cpSRP54 was determined by X-Ray crystallography although cpSRP43 also functions in free form in the chloroplast. The results of this study demonstrate the significant amount of structural flexibility and thermal stability cpSRP43 as well as its potential use as a generic chaperone for proteins outside of the chloroplast. The structure of the c-terminal end of Albino3 (cAlb) was also investigated here since the exact binding interface between cpSRP43 and cAlb is still under debate. The results here reveal a region in cAlb which has a high propensity toward structure. This region may prove to be important in binding to cpSRP43 and could lead toward a better understanding of the process of integration for LHCP

Biological Networks

Networks of coordinated interactions among biological entities govern a myriad of biological functions that span a wide range of both length and time scales—from ecosystems to individual cells and from years to milliseconds. For these networks, the concept “the whole is greater than the sum of its parts” applies as a norm rather than an exception. Meanwhile, continued advances in molecular biology and high-throughput technology have enabled a broad and systematic interrogation of whole-cell networks, allowing the investigation of biological processes and functions at unprecedented breadth and resolution—even down to the single-cell level. The explosion of biological data, especially molecular-level intracellular data, necessitates new paradigms for unraveling the complexity of biological networks and for understanding how biological functions emerge from such networks. These paradigms introduce new challenges related to the analysis of networks in which quantitative approaches such as machine learning and mathematical modeling play an indispensable role. The Special Issue on “Biological Networks” showcases advances in the development and application of in silico network modeling and analysis of biological systems

Applied Photosynthesis

Using the energy from sunlight, photosynthesis usually converts carbon dioxide into organic compounds, which are important for all living creatures. Photosynthesis is one of the most important reactions on Earth, and it is a scientific field that is intrinsically interdisciplinary, and many research groups have considered photosynthesis. The aim of this book is to provide new progresses on applied aspects of photosynthesis, and different research groups collected their voluble results from study of this interesting process. All sections have been written by experts in their fields, and book chapters present different and new subjects on photosynthesis

Vegetation Index and Dynamics

The book contemplates different ways of approaching the study of vegetation as well as the type of indices to be used. However, all the works pursue the same objective: to know and interpret nature from different points of view, either through knowledge of nature in situ or the use of technology and mapping using satellite images. Chapters analyze the ecological parameters that affect vegetation, the species that make up plant communities, and the influence of humans on vegetation

Forest genomics and biotechnology

This Research Topic addresses research in genomics and biotechnology to improve the growth and quality of forest trees for wood, pulp, biorefineries and carbon capture. Forests are the world’s greatest repository of terrestrial biomass and biodiversity. Forests serve critical ecological services, supporting the preservation of fauna and flora, and water resources. Planted forests also offer a renewable source of timber, for pulp and paper production, and the biorefinery. Despite their fundamental role for society, thousands of hectares of forests are lost annually due to deforestation, pests and pathogens and urban development. As a consequence, there is an increasing need to develop trees that are more productive under lower inputs, while understanding how they adapt to the environment and respond to biotic and abiotic stress. Forest genomics and biotechnology, disciplines that study the genetic composition of trees and the methods required to modify them, began over a quarter of a century ago with the development of the first genetic maps and establishment of early methods of genetic transformation. Since then, genomics and biotechnology have impacted all research areas of forestry. Genome analyses of tree populations have uncovered genes involved in adaptation and response to biotic and abiotic stress. Genes that regulate growth and development have been identified, and in many cases their mechanisms of action have been described. Genetic transformation is now widely used to understand the roles of genes and to develop germplasm that is more suitable for commercial tree plantations. However, in contrast to many annual crops that have benefited from centuries of domestication and extensive genomic and biotechnology research, in forestry the field is still in its infancy. Thus, tremendous opportunities remain unexplored. This Research Topic aims to briefly summarize recent findings, to discuss long-term goals and to think ahead about future developments and how this can be applied to improve growth and quality of forest trees. Mini-review articles are sought in forest genomics and biotechnology, with a focus on future directions applied to (1) genetic engineering, (2) adaptation, (3) genomics of conifers and hardwoods, (4) cell wall and wood formation, (5) development (6) metabolic engineering (7) biotic and abiotic resistance and (8) the biorefinery

Detection of loci associated with water-soluble carbohydrate accumulation and environmental adaptation in white clover (Trifolium repens L.) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Palmerston North, New Zealand

White clover (Trifolium repens L.) is an economically important forage legume in New Zealand/Aotearoa (NZ). It provides quality forage and a source of bioavailable nitrogen fixed through symbiosis with soil Rhizobium bacteria. This thesis investigated the genetic basis of two traits of significant agronomic interest in white clover. These were foliar water-soluble carbohydrate (WSC) accumulation and soil moisture deficit (SMD) tolerance. Previously generated divergent WSC lines of white clover were characterised for foliar WSC and leaf size. Significant (p < 0.05) divergence in foliar WSC content was observed between five breeding pools. Little correlation was observed between WSC and leaf size, indicating that breeding for increased WSC content could be achieved in large and small leaf size classes of white clover in as few as 2 – 3 generations. Genotyping by sequencing (GBS) data were obtained for 1,113 white clover individuals (approximately 47 individuals from each of 24 populations). Population structure was assessed using discriminant analysis of principal components (DAPC) and individuals were assigned to 11 genetic clusters. Divergent selection created a structure that differentiated high and low WSC populations. Outlier detection methodologies using PCAdapt, BayeScan and KGD-FST applied to the GBS data identified 33 SNPs in diverse gene families that discriminated high and low WSC populations. One SNP associated with the starch biosynthesis gene, glgC was identified in a genome-wide association study (GWAS) of 605 white clover individuals. Transcriptome and proteome analyses also provided evidence to suggest that high WSC levels in different breeding pools were achieved through sorting of allelic variants of carbohydrate metabolism pathway genes. Transcriptome and proteome analyses suggested 14 gene models from seven carbohydrate gene families (glgC, WAXY, glgA, glgB, BAM, AMY and ISA3) had responded to artificial selection. Patterns of SNP variation in the AMY, glgC and WAXY gene families separated low and high WSC individuals. Allelic variants in these gene families represent potential targets for assisted breeding of high WSC levels. Overall, multiple lines of evidence corroborate the importance of glgC for increasing foliar WSC accumulation in white clover. Soil moisture deficit (SMD) tolerance was investigated in naturalised populations of white clover collected from 17 sites representing contrasting SMD across the South Island/Te Waipounamu of NZ. Weak genetic differentiation of populations was detected in analyses of GBS data, with three genetic clusters identified by ADMIXTURE. Outlier detection and environmental association analyses identified 64 SNPs significantly (p < 0.05) associated with environmental variation. Mapping of these SNPs to the white clover reference genome, together with gene ontology analyses, suggested some SNPs were associated with genes involved in carbohydrate metabolism and root morphology. A common set of allelic variants in a subset of the populations from high SMD environments may also identify targets for selective breeding, but this variation needs further investigation

Unruptured brain arteriovenous malformations : primary ONYX embolization in ARUBA (A Randomized Trial of Unruptured Brain Arteriovenous Malformations)-eligible patients

Background and Purpose: In light of evidence from ARUBA (A Randomized Trial of Unruptured Brain Arteriovenous Malformations), neurovascular specialists had to reconsider deliberate treatment of unruptured brain arteriovenous malformations (uBAVMs). Our objective was to determine the outcomes of uBAVM treated with primary embolization using ethylene vinyl alcohol (ONYX). Methods: Patients with uBAVM who met the inclusion criteria of ARUBA and were treated with primary Onyx embolization were assigned to this retrospective study. The primary outcome was the modified Rankin Scale score. Secondary outcomes were stroke or death because of uBAVM or intervention and uBAVM obliteration. Results: Sixty-one patients (mean age, 38 years) were included. The median observation period was 60 months. Patients were treated by embolization alone (41.0%), embolization and radiosurgery (57.4%), or embolization and excision (1.6%). Occlusion was achieved in 44 of 57 patients with completed treatment (77.2%). Forty-seven patients (77.1%) had no clinical impairment at the end of observation (modified Rankin Scale score of <2). Twelve patients (19.7%) reached the outcome of stroke or death because of uBAVM or intervention. Treatment-related mortality was 6.6% (4 patients). Conclusions: In uBAVM, Onyx embolization alone or combined with stereotactic radiosurgery achieves a high occlusion rate. Morbidity remains a challenge, even if it seems lower than in the ARUBA trial