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Fig. 7 in Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps

Fig. 7. Stages in the biosynthesis of parent glucosinolates (GSLs) without (A) or with (B) chain elongation of the precursor standard amino acid. A CYP79 enzyme catalyzes the first reaction in the known (cytosolic) core structure biosynthesis pathways, followed by six enzymatic steps constituting the remaining core structure biosynthesis pathway, abbreviated "r. csb". For GSLs without chain elongation (A), the CYP79 catalyzed reaction is the committed step. For GSLs needing chain elongation (B), however, the chain elongation machinery as well as transport ("T") across the chloroplast membrane and reversible amino transferase reactions collectively constitute the committed step, illustrated as a box-like reaction arrow containing the individual reactions.

Fig. 4 in Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps

Fig. 4. All glucosinolates (GSLs) derived from aliphatic amino acids known from the tribe Cardamineae. The constant part of the GSLs is abbreviated GSL in most structures and exemplified in case of 107. Abbreviations of individual GSLs follow a comprehensive system explained in the text (Section 1.1.); spaces have occasionally been inserted in some long names and abbreviations for easier reading. BCAA; branched chain amino acid.

Fig. 1 in Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps

Fig. 1. An archetypic glucosinolate-myrosinase system, leading to an isothiocyanate (A) and an oxazolidine-2-thione (B) from myrosinase-catalyzed hydrolysis of two ancient glucosinolates, 11 and 31. The hydrolysis reactions are unbalanced; water is an additional reactant and glucose, sulfate and hydrogen ion are also released during the myrosinase-catalyzed hydrolysis. A rearrangement precedes the formation of isothiocyanate (Blaˇzevi´c et al., 2020).

Fig. 3 in Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps

Fig. 3. All glucosinolates (GSLs) derived from aromatic amino acids known from the tribe Cardamineae. The constant part of the GSLs is abbreviated GSL in most structures and exemplified in case of 11, a similar system is used for 6′-isoferuloylated GSLs as exemplified for 129. Abbreviations of individual GSLs follow a comprehensive system systematically explained in an accompanying paper (Agerbirk et al., 2021); spaces have occasionally been inserted in some long names and abbreviations for easier reading. The semisystematic name of "glucobarbarin" is (S)-2-hydroxy-2-phenylethylGSL, and for "epiglucobarbarin" it is (R)-2-hydroxy-2-phenylethylGSL.

Fig. 6 in Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps

Fig. 6. Aspects of glucosinolate (GSL) evolution in the order Brassicales with focus on the tribe Cardamineae. A. Phylogeny matched with GSL structural or biosynthetic features. Structural and biochemical features of GSL profiles of the respective species are indicated as deduced precursor amino acids and deduced modification of parent GSLs from the various precursors. Categories are based on GSL profiles as in Fig. 5C, but interpreted in a biosynthetic context. Presence of para- hydroxylated phenyl groups can potentially be due to either use of a specific precursor amino acid (Tyr or homoTyr) or a specific modification (para-hydroxylation), and is hence shown in an intermediate position, with the relevant backbones shown in B. Panel C shows the deduced modification steps. For the phylogeny in A, phylogenetic relationships based on Bayesian inference (MrBayes) of ITS regions were calculated for a subset of species from Brassicaceae and using Reseda (Resedaceae) as outgroup. Labels for B. vulgaris (group 3, group 7) refer to the ITS sequence pools listed in Agerbirk et al., (in review). Bootstrap values from 1000 replicates are shown for Bayesian and maximum-likelihood inference, respectively. Side-chain modification exclusively known from n-homoMet derived GSLs (Fig. 5B) is left out for space-considerations. For GSL profile data, group 7 of B. vulgaris was assumed to represent ssp. vulgaris.

Fig. 5 in Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps

Fig. 5. Structural redundancy and innovation in glucosinolate (GSL) biodiversity. A. Representative GSL structures categorized as ancient due to presence in nonBrassicaceae members of the order Brassicales. The poorly known status for a substituted Trp-derived is indicated (see text). B. Representative GSLs from three derived families (Capparaceae, Cleomaceae and Brassicaceae) with a simplified indication of the biosynthetic connections of n-homoMet derived GSLs. C. Distribution of three groups of GSLs in selected members of the tribes Cardamineae, Arabideae and Brassiceae. The first group, those illustrated in panel A, seem to be due to ancient or recapitulated biosynthesis. The second group seem to be of intermediate age, the n-homoMet derived are pooled for space considerations. Possibly, the 4-substituted Trp derived 4moIM (48) and homoIle derived 54 and 29 also belongs to this group. The third group is deduced to represent recently evolved biosyntheses, as discussed in text, and the GSLs are illustrated in panel D. The category "Present" in panel C indicates one or more conclusive demonstrations of the relevant GSL, while "Tested, not reported" means that relevant organs have been tested using relevant methods, yet the GSL was not reported, although explicit search for the GSL was not necessarily reported. Hence we could not conclude the GSL to be "not found", although this would be the simplest interpretation. The category "Circumstantial evidence" means that reasonable but not conclusive evidence for the relevant GSL has been published, while the category "Insufficent or missing data" means that relevant organs (roots for substituted Trp-derived and seeds for SGlc-acylated) have not been sufficiently investigated using methods with demonstrated ability to reveal the GSL in question.

opencc-by-4.0Aug 2023View details →

Repeatome turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

The present repository provides zipped archives containing the results of the RepeatExplorer2 runs of individual as well as comparative repeat analyses in beet genomes.   Sugar beet (Beta vulgaris subsp. vulgaris) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation. We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet genera Beta and Patellifolia. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the section Corollinae/Nanae. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia species to the formation of patchwork chromosomes in Corollinae/Nanae species.  We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.

Evaluation of Repetitive Transcranial Magnetic Stimulation as an Adjunct to Modified Constraint Induced Movement Therapy in Improving Upper Limb Function in Children With Hemiparetic Cerebral Palsy Ag

ClinicalTrials.gov study NCT03792789. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.

Low-Frequency REpetitive TRanscranial Magnetic Stimulation Combined With Endovascular Treatment in ACute Ischemic StrokE

ClinicalTrials.gov study NCT06064747. IPD Sharing: NO. Countries: 1. Publications: 1.

Repetitive Transcranial Magnetic Stimulation in Symptoms of Attention Deficit Hyperactivity Disorder and Cognitive Function In Cocaine Addicts

ClinicalTrials.gov study NCT01593982. IPD Sharing: Not stated. Countries: 1. Publications: 4.

Repetitive Transcranial Magnetic Stimulation and Multi-modality Aphasia Therapy for Post-stroke Non-fluent Aphasia

ClinicalTrials.gov study NCT04102228. IPD Sharing: NO. Countries: 1. Publications: 1.

Comparing Perceptual Motor Training and Repetitive Facilitation Exercises on UE in Stroke

ClinicalTrials.gov study NCT06688812. IPD Sharing: NO. Countries: 1. Publications: 7.

A Study of Repetitive Transcranial Magnetic Stimulation in Bipolar Patients

ClinicalTrials.gov study NCT03207048. IPD Sharing: Not stated. Countries: 1. Publications: 2.

Repetitive Arm Training + FES on Upper Extremity Motor Recovery in Sub-acute Stroke Survivors

ClinicalTrials.gov study NCT02267798. IPD Sharing: NO. Countries: 1. Publications: 1.

Deep High-Frequency Repetitive Transcranial Magnetic Stimulation for Smoking Cessation

ClinicalTrials.gov study NCT00951782. IPD Sharing: Not stated. Countries: 1. Publications: 1.

The Effect of a Brief Psychological Intervention on Reducing Self-harm Repetition: Feasibility Study

ClinicalTrials.gov study NCT03376113. IPD Sharing: Not stated. Countries: 1. Publications: 2.

This Study is About the Efficacy of Repetitive Peripheral Magnetic Stimulation on the Treatment of Shoulder Subluxation in Subacute Stroke Patients.

ClinicalTrials.gov study NCT06678425. IPD Sharing: UNDECIDED. Countries: 1. Publications: 20.

A Long-Term Prospective Randomized Controlled Study Using Repetitive Education at Six-Month Intervals and Monitoring for Adherence in Heart Failure Outpatients - The REMADHE Study

ClinicalTrials.gov study NCT00505050. IPD Sharing: Not stated. Countries: 1. Publications: 4.

Repetitive Transcranial Magnetic Stimulation in Patients With Opioid Use Disorders

ClinicalTrials.gov study NCT03229642. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Repetitive Versus Deep Transcranial Magnetic Stimulation for Major Depression

ClinicalTrials.gov study NCT05902312. IPD Sharing: NO. Countries: 1. Publications: 0.