King Abdullah University of Science and Technology

About: King Abdullah University of Science and Technology is a education organization based out in Jeddah, Saudi Arabia. It is known for research contribution in the topics: Catalysis & Membrane. The organization has 6221 authors who have published 22019 publications receiving 625706 citations. The organization is also known as: KAUST.

Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.

Abstract: Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts. Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.

Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis

Abstract: Crocus sativus stigmas are the source of the saffron spice and accumulate the apocarotenoids crocetin, crocins, picrocrocin, and safranal, responsible for its color, taste, and aroma. Through deep transcriptome sequencing, we identified a novel dioxygenase, carotenoid cleavage dioxygenase 2 (CCD2), expressed early during stigma development and closely related to, but distinct from, the CCD1 dioxygenase family. CCD2 is the only identified member of a novel CCD clade, presents the structural features of a bona fide CCD, and is able to cleave zeaxanthin, the presumed precursor of saffron apocarotenoids, both in Escherichia coli and in maize endosperm. The cleavage products, identified through high-resolution mass spectrometry and comigration with authentic standards, are crocetin dialdehyde and crocetin, respectively. In vitro assays show that CCD2 cleaves sequentially the 7,8 and 7′,8′ double bonds adjacent to a 3-OH-β-ionone ring and that the conversion of zeaxanthin to crocetin dialdehyde proceeds via the C30 intermediate 3-OH-β-apo-8′-carotenal. In contrast, zeaxanthin cleavage dioxygenase (ZCD), an enzyme previously claimed to mediate crocetin formation, did not cleave zeaxanthin or 3-OH-β-apo-8′-carotenal in the test systems used. Sequence comparison and structure prediction suggest that ZCD is an N-truncated CCD4 form, lacking one blade of the β-propeller structure conserved in all CCDs. These results constitute strong evidence that CCD2 catalyzes the first dedicated step in crocin biosynthesis. Similar to CCD1, CCD2 has a cytoplasmic localization, suggesting that it may cleave carotenoids localized in the chromoplast outer envelope.

Effects of cytosine methylation on transcription factor binding sites

Abstract: DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important. We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines “traffic lights”. We observed a strong selection against CpG “traffic lights” within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions. Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription.

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research.

Abstract: 'Speed breeding' (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

SRCMOD: An Online Database of Finite‐Fault Rupture Models

Abstract: This contribution to the Electronic Seismologist presents the online SRCMOD database of finite‐fault rupture models for past earthquakes, accessible at http://equake-rc.info/srcmod. Finite‐fault earthquake source inversions have become a standard tool in seismological research. Using seismic data, these inversions image the spatiotemporal rupture evolution on one or more assumed fault segments. If geodetic data are used, the source inversions put constraints on the fault geometry and the static slip distribution (i.e., final displacements over the fault surfaces). Joint inversions, using a combination of available seismic, geodetic, and potentially other data, try to match all observations to develop a more comprehensive image of the rupture process. Some joint inversions use all data simultaneously, whereas others take an iterative approach wherein one set of observations is utilized to construct an initial (prior) model for subsequent inversions using other available data. The field of finite‐fault inversion was pioneered in the early 1980s (Olson and Apsel, 1982; Hartzell and Heaton, 1983). Subsequently, their method has been applied to numerous earthquakes (e.g., Hartzell, 1989; Hartzell et al. , 1991; Wald et al. , 1991; Hartzell and Langer, 1993; Wald et al. , 1993; Wald and Somerville, 1995), while simultaneously additional source‐inversion strategies were developed and applied (e.g., Beroza and Spudich, 1988; Beroza, 1991; Hartzell and Lui, 1995; Hartzell et al. , 1996; Zeng and Anderson, 1996). It is beyond the scope of this article to provide a detailed review of source‐inversion methods, their theoretical bases, implementations, and parameterizations; instead, we refer to Ide (2007) for a more comprehensive summary. Finite‐fault source inversions help to shape our understanding of the complexity of the earthquake rupture process. These source images provide information, albeit at rather low spatial resolution, of earthquake slip at depth, and potentially also on the temporal rupture evolution. …