Abdul Baten

Inducing pluripotency in vitro: recent advances and highlights in induced pluripotent stem cells generation and pluripotency reprogramming.

Induced pluripotent stem cells (iPSCs) are considered patient‐specific counterparts of embryonic stem cells as they originate from somatic cells after forced expression of pluripotency reprogramming factors Oct4, Sox2, Klf4 and c‐Myc. iPSCs offer unprecedented opportunity for personalized cell therapies in regenerative medicine. In recent years, iPSC technology has undergone substantial improvement to overcome slow and inefficient reprogramming protocols, and to ensure clinical‐grade iPSCs and their functional derivatives. Recent developments in iPSC technology include better reprogramming methods employing novel delivery systems such as non‐integrating viral and non‐viral vectors, and characterization of alternative reprogramming factors. Concurrently, small chemical molecules (inhibitors of specific signalling or epigenetic regulators) have become crucial to iPSC reprogramming; they have the ability to replace putative reprogramming factors and boost reprogramming processes. Moreover, common dietary supplements, such as vitamin C and antioxidants, when introduced into reprogramming media, have been found to improve genomic and epigenomic profiles of iPSCs. In this article, we review the most recent advances in the iPSC field and potent application of iPSCs, in terms of cell therapy and tissue engineering.

Phosphorus remobilization from rice flag leaves during grain filling: an RNA-seq study.

Summary The physiology and molecular regulation of phosphorus (P) remobilization from vegetative tissues to grains during grain filling is poorly understood, despite the pivotal role it plays in the global P cycle. To test the hypothesis that a subset of genes involved in the P starvation response are involved in remobilization of P from flag leaves to developing grains, we conducted an RNA‐seq analysis of rice flag leaves during the preremobilization phase (6 DAA) and when the leaves were acting as a P source (15 DAA). Several genes that respond to phosphate starvation, including three purple acid phosphatases (OsPAP3, OsPAP9b and OsPAP10a), were significantly up‐regulated at 15 DAA, consistent with a role in remobilization of P from flag leaves during grain filling. A number of genes that have not been implicated in the phosphate starvation response, OsPAP26, SPX‐MFS1 (a putative P transporter) and SPX‐MFS2, also showed expression profiles consistent with involvement in P remobilization from senescing flag leaves. Metabolic pathway analysis using the KEGG system suggested plastid membrane lipid synthesis is a critical process during the P remobilization phase. In particular, the up‐regulation of OsPLDz2 and OsSQD2 at 15 DAA suggested phospholipids were being degraded and replaced by other lipids to enable continued cellular function while liberating P for export to developing grains. Three genes associated with RNA degradation that have not previously been implicated in the P starvation response also showed expression profiles consistent with a role in P mobilization from senescing flag leaves.

Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod.

Dicathais orbita is a marine mollusc recognised for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the diversity and identity of bacteria associated with the Tyrian purple producing hypobranchial gland, in comparison with foot tissue, using a high-throughput sequencing approach. Taxonomic and phylogenetic analysis of variable region V1-V3 of 16S rRNA bacterial gene amplicons in QIIME and MEGAN were carried out. This analysis revealed a highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The dominant bacterial phylum in the 16S rRNA bacterial profiling data set was Proteobacteria followed by Bacteroidetes, Tenericutes and Spirochaetes. In comparison to the foot, the hypobranchial gland had significantly lower bacterial diversity and a different community composition, based on taxonomic assignment at the genus level. A higher abundance of indole producing Vibrio spp. and the presence of bacteria with brominating capabilities in the hypobranchial gland suggest bacteria have a potential role in biosynthesis of Tyrian purple in D. orbita.

Indole-producing bacteria from the biosynthetic organs of a muricid mollusc could contribute to tyrian purple production

ABSTRACT The muricid mollusc Dicathais orbita produces Tyrian purple, which is a brominated derivative of the blue dye indigo. This study aimed to establish whether distinct bacterial communities occur in the organs of D. orbita associated with Tyrian purple production and to identify indole-producing bacteria using 16S rRNA sequencing. Biochemical profiles of microbial communities from different D. orbita tissues were investigated and the composition of aerobic heterotrophic bacterial populations from homogenates and swabs assessed. There were significant differences in biochemical activity profiles and bacterial communities cultured from different D. orbita tissues, but no significant differences between males and females. Bacterial communities derived from foot tissue and seawater samples were similar. The biochemical and molecular evidence from swabs and tissue homogenates suggest indole-producing isolates are Vibrio spp. This study suggests Tyrian purple indole precursors could be obtained from opportunistic ubiquitous bacteria.

Geospatial binding for transdisciplinary research in crop science: the GRASPgfs initiative

The paper retraces the GRASPgfs endeavor (Geospatial Resource for Agricultural Species and Pests with integrated workflow modelling to support Global Food Security) between multiple disciplines around a common objective of facilitating research and model simulations for sustainable food security. Within this endeavor, the geospatial media has been the enabler for multidisciplinary research in crop modelling. Geospatial genetic-trait variations and associations with environmental forecasting were the main focus of the GRASPgfs. Designing the platform achieving this objective generated a transdisciplinary vision of modelling and forecasting for sustainable agriculture. Based on interoperability principles, seamless access as well as sharing for data, metadata and processing models, the design is described in this paper. This geospatial binding facilitates and supports new types of hypotheses and analysis as illustrated in the paper with a landscape genetic case study (bambara groundnut) and a crop disease modelling (eyespot disease). The approach and the eGRASP platform are generic enough to accommodate further complexity into the integrated modelling that this geospatial binding enables.

Terpene synthase genes in Melaleuca alternifolia: comparativeanalysis of lineage‑specifc subfamily variation within Myrtaceae

Terpenes are a multifarious group of secondary compounds present throughout the living world that function primarily in defence, or otherwise in regulating interactions between an organism and its environment. Terpene synthases (TPS) are a mid-sized gene family whose diversity and make-up reflects a plant’s ecological requirements and unique adaptive history. Here we catalogue TPS in Melaleuca alternifolia and examine lineage-specific expansion in TPS relative to other sequenced Myrtaceae. Overall, far fewer (37) putative TPS genes were identified in M. alternifolia compared with Eucalyptus grandis (113) and E. globulus (106). The number of genes in clade TPS-b1 (12), which encode enzymes that produce cyclic monoterpenes, was proportionally larger in M. alternifolia than in any other well-characterised plant. Relative to E. grandis, the isoprene-/ocimene-producing TPS-b2 clade in M. alternifolia tended to be proportionally smaller. This suggested there may be lineage-specific subfamily change in Melaleuca relative to other sequenced Myrtaceae, perhaps as a consequence of its semi-aquatic evolutionary history.

Transcriptional response of rice flag leaves to restricted external phosphorus supply during grain filling in rice cv. IR64

Plant phosphorus (P) remobilisation during leaf senescence has fundamental implications for global P cycle fluxes. Hypothesising that genes involved in remobilisation of P from leaves during grain filling would show altered expression in response to P deprivation, we investigated gene expression in rice flag leaves at 8 days after anthesis (DAA) and 16 DAA in plants that received a continuous supply of P in the nutrient solution vs plants where P was omitted from the nutrient solution for 8 consecutive days prior to measurement. The transcriptional response to growth in the absence of P differed between the early stage (8 DAA) and the later stage (16 DAA) of grain filling. At 8 DAA, rice plants maintained production of energy substrates through upregulation of genes involved in photosynthesis. In contrast, at 16 DAA carbon substrates were produced by degradation of structural polysaccharides and over 50% of highly upregulated genes in P-deprived plants were associated with protein degradation and nitrogen/amino acid transport, suggesting withdrawal of P from the nutrient solution led to accelerated senescence. Genes involved in liberating inorganic P from the organic P compounds and vacuolar P transporters displayed differential expression depending on the stage of grain filling stage and timing of P withdrawal.

Brassica napus Genomic Resources

This chapter provides an overview of the various physical experimental and reference data resources available in the public domain to support evolutionary, comparative and functional analysis of Brassica napus genomes, and that underpin pre-breeding R&D and breeding activities for canola and related oilseed crops. Many of these resources have become available as a result of international cooperation through the Multinational Brassica Genome Project (MBGP). The role and establishment of nomenclature and other standards for Brassica species is outlined. Specific plant resources and their use in mutant screening, mapping and genome-wide association studies are described, along with genomic tools such as genetic marker and transcriptome platforms. The range of current genomic data, information resources, bioinformatics tools and analysis pipelines for B. napus are introduced, together with the available dedicated B. napus-specific genome browsers and related online sites. In addition, databases dedicated to managing phenotypic trait, trial and related data are described, and future requirements are identified for enabling greater integration of phenotypic and genotypic information and tools to collate and navigate increasingly complex data sets. Due to rapidly changing genomic technologies and funding support, the coverage of resources described here is unlikely to be comprehensive. However, many additional details are to be found either hosted at or linked from the http://www.brassica.info website on behalf of the MBGP. The Brassica database (BRAD) maintained at http://Brassicadb.org/brad/ also continues to provide a valuable set of reference information.

Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus

Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The plant family Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in terpene profiles. Many Myrtaceae are grown commercially for terpene products including the eucalypts Corymbia and Eucalyptus. Eucalyptus grandis has the largest TPS gene family of plants currently sequenced, which is largely conserved in the closely related E. globulus. However, the TPS gene family has been well studied only in these two eucalypt species. The recent assembly of two Corymbia citriodora subsp. variegata genomes presents an opportunity to examine the conservation of this important gene family across more divergent eucalypt lineages. Manual annotation of the TPS gene family in C. citriodora subsp. variegata revealed a similar overall number, and relative subfamily representation, to that previously reported in E. grandis and E. globulus. Many of the TPS genes were in physical clusters that varied considerably between Eucalyptus and Corymbia, with several instances of translocation, expansion/contraction and loss. Notably, there was greater conservation in the subfamilies involved in primary metabolism than those involved in secondary metabolism, likely reflecting different selective constraints. The variation in cluster size within subfamilies and the broad conservation between the eucalypts in the face of this variation are discussed, highlighting the potential contribution of selection, concerted evolution and stochastic processes. These findings provide the foundation to better understand terpene evolution within the ecologically and economically important Myrtaceae.

Maternal RNA-directed DNA methylation is required for seed development in Brassica rapa

Some organisms deploy small RNAs from accessory cells to maintain genome integrity in the zygote, a mechanism that has been proposed but not demonstrated in plants. Here we show that maternal mutations in the Pol IV-dependent small RNA pathway cause abortion of developing seeds in Brassica rapa. Surprisingly, small RNA production is required in maternal somatic tissues, but not in maternal gametes or the developing zygote. We propose that parental influence over zygotic genomes is a common strategy in eukaryotes and that outbreeding species such as B. rapa are key to understanding the role of small RNAs during reproduction.