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This document is a response to a critique of a scientific paper published in Nature Communications. The authors of the response address the criticisms made by Dr. Goldsmith and his colleagues regarding the enzyme activities described in their paper. They clarify that their results were measured using a different method than assumed by Dr. Goldsmith. The authors also present their own experiments that challenge the proposed substrate for one of the enzymes involved in the synthesis of β-ODAP, a compound found in grass peas that can cause a neurodegenerative disorder called lathyrism. They conclude that the synthesis of a key compound involved in β-ODAP synthesis is likely limited in the cytosol of grass pea plants. The article highlights the proposed mechanism for β-ODAP synthesis and provides experimental evidence to support it, while also addressing criticisms and emphasizing the importance of understanding this process for improving the crop. [Extracted from the article]

Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a changing climate. The lack of genetic resources and the crop’s association with the disease neurolathyrism have limited the cultivation of grass pea. Here, we present an annotated, long read-based assembly of the 6.5 Gbp L. sativus genome. Using this genome sequence, we have elucidated the biosynthetic pathway leading to the formation of the neurotoxin, β-L-oxalyl-2,3-diaminopropionic acid (β-L-ODAP). The final reaction of the pathway depends on an interaction between L. sativus acyl-activating enzyme 3 (LsAAE3) and a BAHD-acyltransferase (LsBOS) that form a metabolon activated by CoA to produce β-L-ODAP. This provides valuable insight into the best approaches for developing varieties which produce substantially less toxin.Grass pea is a multi-stress tolerant orphan crop and developing cultivars with decreased accumulation of the neurotoxin β-L-oxalyl-2,3-diaminopropionic acid (β-L-ODAP) is one of its breeding objectives. Here, the authors assemble its genome and reveal genes involved in the biosynthesis of β-L-ODAP. [ABSTRACT FROM AUTHOR]

Similarly, affiliation 12 was incorrectly given as "Department of Biology, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA 02142-1479, USA" but should be "Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA". Author Correction: Genomics and biochemical analyses reveal a metabolon key to -L-ODAP biosynthesis in Lathyrus sativus Affiliation 11 was incorrectly given as "Department of Biological Engineering, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA 02142-1479, USA" but should be "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA". [Extracted from the article]

Introduction: To design and run an effective pharmacovigilance system, one must understand potential hazards that may cause the system to fail. System-Theoretic Process Analysis (STPA) is a hazard analysis technique that has been successfully applied in domains including aviation, nuclear power, and defence systems; however, it has not yet been applied to a critical pharmacovigilance process. Objectives: The objective of this project was to assess the value of STPA in pharmacovigilance by using the example of signal management, in order to identify process risks, areas for improvement, and applicable process metrics. Methods: Hierarchical control structure (HCS) is the starting point for STPA. The HCS models a process as a set of interacting feedback control systems, which maintain the system in a 'safe state' where losses do not occur. 'Losses' can be defined as harm to patients, regulatory non-compliance, or other negative consequences. The HCS viewpoint is a considerable departure from the usual consideration of a pharmacovigilance process as a series of sequential steps carried out by responsible individuals. Following the definition of the HCS, a two-step STPA process was carried out, leading to a set of unsafe actions and scenarios by which process failures could lead to loss. Recommendations were then made to prevent those scenarios that were not already covered by existing features of the process. Results: The signal management process was successfully modelled as a feedback control system, which dynamically ensures that an incoming stream of safety data is accurately reflected in the reference safety information for the product. After creating the HCS, we conducted the STPA itself. This yielded 215 scenarios through which the process could end up in an unsafe state where losses could occur. The scenarios included 91 that were covered by existing measures, 28 related to existing or planned metrics, and 25 were scenarios considered implausible, inconsequential, undetectable, or out-of-scope. The remaining 71 scenarios were consolidated into 8 proposed recommendations for enhancements to metrics, 10 proposed recommendations for enhancements to the process itself, and 8 proposed recommendations regarding infrastructure or related processes, including the associated quality management system. STPA considers 'soft' factors such as cultural influences, and this was reflected in several recommendations, for instance regarding training. Conclusion: STPA is a labour-intensive and time-consuming process, most appropriate for high-risk, compliance-critical processes. STPA is a powerful technique for identification of risks in pharmacovigilance systems, and can contribute to process reliability with the potential to improve patient safety and the maintenance of regulatory compliance. [ABSTRACT FROM AUTHOR]

Extracellular β-glucosidases from Aspergillus oryzae (two strains), Fusarium oxysporum, Aspergillus terreus and Talaromyces flavus were either induced by cellobiose or 6-deoxyglucose, or produced without induction, i.e., either on casein acid hydrolyzate or on the Sabouraud medium. They were tested to catalyze a stereoselective synthesis of the cis- and trans-isomers of 2-(4-methoxybenzyl)-1-cyclohexyl β-d-glucopyranosides with either d-glucose or phenyl β-d-glucopyranoside as sources of the glucosyl unit. The enzymes also hydrolyzed (resolved) diastereoisomeric mixtures of alkyl β-d-glucopyranosides, which were prepared by the Koenigs–Knorr method from the respective cis- and trans-isomers of 2-(4-methoxybenzyl)-1-cyclohexanol. [ABSTRACT FROM AUTHOR]

Research results are summarized from a series of insect juvenile hormone analogs derived from 2-(4-hydroxybenzyl)-1-cycloalkanones, which have been investigated at the Institute of Organic Chemistry and Biochemistry in Prague during the past 20 years. At present, practical application of several prospective structures for insect control is under investigation. Biological activity values were determined to delineate the most important subseries of compounds and the most promising insect juvenile hormone analogs selected from the subseries. Carbamates, and in particular compound 47 proved to be highly active against aphids, cockroaches, flies, and many other insect species. [ABSTRACT FROM AUTHOR]

Lipase biocatalysis was investigated as a tool for the production of esters by two model reactions, esterification of 1-butanol with 2-methyl-1-pentanoic acid and irreversible transesterification between 2-methyl-1-pentanol and vinyl acetate. The reactions were carried out in hexane using lipases from Candida cylindracea and porcine pancreas. The initial water content influenced both the yield of the ester and the enantioselectivity of the reaction (esterifica-tions) or the ester formation only (transesterifications). [ABSTRACT FROM AUTHOR]

Iminosugars are carbohydrate mimics that are useful as molecular probes to dissect metabolism in plants. To analyse the effects of iminosugar derivatives on germination and seedling growth, we screened a library of 390 N-substituted iminosugar analogues against Arabidopsis and the small cereal Eragrostis tef (Tef). The most potent compound identified in both systems, N-5-(adamantane-1-yl-ethoxy)pentyl- L-ido-deoxynojirimycin (L-ido-AEP-DNJ), inhibited root growth in agar plate assays by 92% and 96% in Arabidopsis and Tef respectively, at 10 µM concentration. Phenocopying the effect of L-ido-AEP-DNJ with the commercial inhibitor (PDMP) implicated glucosylceramide synthase as the target responsible for root growth inhibition. L-ido-AEP-DNJ was twenty-fold more potent than PDMP. Liquid chromatography-mass spectrometry (LC-MS) analysis of ceramide:glucosylceramide ratios in inhibitor-treated Arabidopsis seedlings showed a decrease in the relative quantity of the latter, confirming that glucosylceramide synthesis is perturbed in inhibitor-treated plants. Bioinformatic analysis of glucosylceramide synthase indicates gene conservation across higher plants. Previous T-DNA insertional inactivation of glucosylceramide synthase in Arabidopsis caused seedling lethality, indicating a role in growth and development. The compounds identified herein represent chemical alternatives that can overcome issues caused by genetic intervention. These inhibitors offer the potential to dissect the roles of glucosylceramides in polyploid crop species. [ABSTRACT FROM AUTHOR]

Extensins are plant cell wall glycoproteins that act as scaffolds for the deposition of the main wall carbohydrate polymers, which are interlocked into the supramolecular wall structure through intra- and inter-molecular iso-di-tyrosine crosslinks within the extensin backbone. In the conserved canonical extensin repeat, Ser-Hyp4, serine and the consecutive C4-hydroxyprolines (Hyps) are substituted with an α-galactose and 1-5 β- or α-linked arabinofuranoses (Arafs), respectively. These modifications are required for correct extended structure and function of the extensin network. Here, we identified a single Arabidopsis thaliana gene, At3g57630, in clade E of the inverting Glycosyltransferase family GT47 as a candidate for the transfer of Araf to Hyp-arabinofuranotriose (Hyp-β1,4Araf-β1,2Araf-β1,2Araf) side chains in an α-linkage, to yield Hyp-Araf4 which is exclusively found in extensins. T-DNA knock-out mutants of At3g57630 showed a truncated root hair phenotype, as seen for mutants of all hitherto characterized extensin glycosylation enzymes; both root hair and glycan phenotypes were restored upon reintroduction of At3g57630. At3g57630 was named Extensin Arabinose Deficient transferase, ExAD, accordingly. The occurrence of ExAD orthologs within the Viridiplantae along with its' product, Hyp-Araf4, point to ExAD being an evolutionary hallmark of terrestrial plants and charophyte green algae. [ABSTRACT FROM AUTHOR]