The banana genome hub: a community database for genomics in the Musaceae

The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.

GPVI inhibition by glenzocimab synergistically inhibits atherosclerotic plaque-induced platelet activation when combined with conventional dual antiplatelet therapy

Introduction

Aspirin and a potent platelet P2Y12 inhibitor, such as prasugrel or ticagrelor, are not always sufficient to prevent thrombus formation in patients with ST-elevation MI (STEMI), leading to “slow flow” or “no reflow” effects after stenting. GPIIb/IIIa inhibitors, such as eptifibatide, may help in this setting, but are not used routinely due to their bleeding risk. GPVI has critical roles in thrombosis and a minimal role in haemostasis. Here we tested whether depletion of GPVI has effects on thrombus formation after MI in an animal model and investigated the effects of a novel platelet GPVI inhibitor, glenzocimab (a Fab fragment of a monoclonal antibody), on platelet activation and thrombus formation when combined with aspirin and ticagrelor.

Methods

We used intravital microscopy in a murine model of ST-elevation myocardial infarction and ischaemia-reperfusion injury to investigate microvascular thrombosis. We investigated the antithrombotic effects of adding glenzocimab (previously known as ACT017) to blood from healthy donors and 20 patients with ACS treated with aspirin and ticagrelor. We compared the effect of glenzocimab with the GPIIb/IIIa inhibitor eptifibatide ex-vivo. We stimulated platelets with collagen and atherosclerotic plaque material that was sourced from patients undergoing carotid endarterectomy. We investigated effects on platelet aggregation, spreading, signalling, adhesion, thrombin generation, thrombus formation and clot stability ex vivo.

Results

Genetic depletion of GPVI in an animal model of myocardial infarction reduced microvascular thrombosis. Ex vivo, aspirin and ticagrelor partially inhibited atherosclerotic plaque-induced platelet aggregation (assessed by multiple electrode aggregometry) by 48% compared to control (34±3 vs. 65±4 U; P<0.001; Figure 1). Atherosclerotic plaque-induced platelet aggregation, adhesion, secretion and activation were critically dependent on platelet GPVI activation and were potently inhibited by glenzocimab. Glenzocimab alone reduced atherosclerotic plaque-induced platelet aggregation by 75% compared to control (16±4 vs. 65±4 U; P<0.001; Figure 1) and by over 95% when combined with aspirin and ticagrelor (3±1 vs 65±4 U; P<0.001; Figure 1). Furthermore, glenzocimab provided multiple synergistic antithrombotic effects when added to the blood of aspirin and ticagrelor-treated patients with ACS ex vivo. Glenzocimab and the GPIIb/IIIa inhibitor, eptifibatide, had many similar antithrombotic effects but glenzocimab had less effect on mechanisms of general haemostasis compared to eptifibatide, as assessed by ROTEM (Figure 2).

Conclusions

The addition of glenzocimab to aspirin and ticagrelor provides synergistic inhibition of multiple critical mechanisms of atherothrombosis. Glenzocimab and the GPIIb/IIIa inhibitor, eptifibatide, share many similar antithrombotic effects, although glenzocimab has less impact on mechanisms involved in haemostasis compared to eptifibatide.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Academy of Medical Sciences UK Clinical Lecturer Starter GrantRoyal Embassy of Saudi Arabia

Vasorelaxant effects of pramanicin, an anti-fungal agent: selective action on endothelial cells

A newly discovered antifungal agent, pramanicin, within the therapeutically effective concentration range (4-100 microM), inhibits the tone of phenylephrine (PE)-precontracted dog carotid arterial rings in a concentration-dependent manner and leads to gradual development of relaxation. However, pramanicin had no effect on rings precontracted with 100 mM KCl or on endothelium-denuded rings. Thus, inhibition by pramanicin of PE-induced contraction was endothelium-dependent. Preincubation of 100 microM pramanicin with carotid arterial rings for 30 min did not significantly affect the concentration-contraction response to PE, but almost completely inhibited the endothelium-dependent relaxation response to subsequent addition of 3 microM carbachol or 100 microM pramanicin. This irreversible inhibition of endothelium-dependent relaxation, which is independent of extracellular Ca2+, suggests possible endothelial cell damage by pramanicin. Pretreatment of the endothelium-intact vascular rings with L-N(G)-nitro-arginine (100 microM) inhibited the relaxation of PE-precontracted rings induced by 3 microM carbachol or 100 microM pramanicin, suggesting that the generation of nitric oxide (NO) in endothelial cells mediates the slow vascular relaxation induced by pramanicin. We conclude that pramanicin has little direct effect on the contractility of smooth muscle cells, but causes an initial slow endothelium-dependent, NO-mediated vascular relaxation. This is followed by a cytotoxic effect on vascular endothelial cells, eventually resulting in the loss of vasorelaxant function.

Twisted amides: synthesis and structure of 1,6-dipivaloyl-3,4,7,8- tetramethyl-2,5-dithioglycoluril

[structure: see text] The 1,6-dipivaloyl derivative of 3,4,7,8-tetramethyl-2,5-dithioglycoluril (6) was prepared and the crystal structure determined by X-ray diffraction; 6 is a twisted amide in which severe ring strain and nonbonded interactions compel both pivaloyl groups to twist dramatically out of the ring plane. The amide oxygen atoms point in opposite directions with respect to the mean plane through the glycoluril core, and the bridgehead methyl groups are forced out of the symmetric syn geometry (eta = 30.5 degrees ). The structure of 7, a rearrangement product generated during synthesis of 6, was also determined by single-crystal X-ray diffraction.

Simulations of chemical exchange lineshapes in CP/MAS spectra using floquet theory and sparse matrix methods

This paper presents a general method for simulating the effect of chemical exchange on MAS NMR spectra of solid samples. The complication in MAS spectra is that the Hamiltonian itself is time-dependent, due to the spinning of the sample. The approach taken in this work is to use Floquet theory to convert the problem into a time-independent form, and then use established methods (used in liquid NMR simulations) to calculate the lineshape. Floquet theory has been admired for its elegance, but criticized for its computational inefficiencies. This is because it removes the time dependence of the system by expanding the problem in a Fourier-like series. This makes a relatively small, time-dependent calculation into a much larger time-independent one. Typically, we use twice as many Floquet blocks as there are spinning sidebands, so the increase in size is substantial. The problem that this creates stems from the fact that the usual Householder methods for diagonalizing a matrix scale as the cube of the size of the matrix. This would make a Floquet calculation prohibitively long. However, the Floquet matrix is inherently sparse, so sparse matrix methods can produce substantial computational savings. Also, fully diagonalizing a matrix is expensive, but converting the matrix to a tridiagonal form (using iterative Lanczos methods) is much cheaper. The use of the Lanczos methods makes the Floquet calculations feasible as a general method for systems of more than one spin. We show how to set up the full matrix describing chemical exchange in a spinning sample, but the details of how the Lanczos methods work are not included-they are described elsewhere. We then validate the theory by simulating the MAS spectra of dimethyl sulfone both with natural abundance (13)C and with methyl groups labeled with (13)C. The latter system has both dipolar and chemical shielding anisotropy terms contributing to the spectrum. Copyright 2000 Academic Press.

Synthesis and inhibitory action on HMG-CoA synthase of racemic and optically active oxetan-2-ones (beta-lactones)

A homologous series of both C3-unsubstituted and C3-methyl substituted oxetan-2-ones (beta-lactones) was investigated as potential inhibitors of yeast 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) synthase. Several reported methods for racemic beta-lactone synthesis were studied for preparation of the target series. In addition, a novel aluminum-based Lewis acid obtained by combination of Et2AlCl with (1R,2R)-2-[(diphenyl)hydroxymethyl] cyclohexan-1-ol was studied for the asymmetric [2 + 2] cycloaddition of aldehydes and trimethylsilylketene. This Lewis acid exhibited good reactivity but variable enantioselectivity (22-85% ee). In in vitro assays using both native and recombinant HMG-CoA synthase from Saccharomyces cerevisiae, oxetan-2-ones mono-substituted at C4 with linear alkyl chains gave IC50s that decreased monotonically with chain length up to 10 carbons and then rose rapidly for longer chains. The trans isomers of 3-methyl-4-alkyl-oxetan-2-ones showed a similar trend but had 1.3- to 5.6-fold lower IC50s. The results imply a substantial hydrophobic pocket in this enzyme that interacts with both C-3 and C-4 substituents of oxetan-2-one inhibitors.

Development of the brachial spinal cord in the marsupial Macropus eugenii (tammar wallaby)

The development of the brachial spinal cord was studied in the marsupial Macropus eugenii (tammar wallaby) on postnatal days 1-34. On day 1 the spinal cord was histologically immature, with a deep central canal, proliferating neuroepithelium and roof and floor plates. The lateral motor column had formed, and forelimb muscles contained primary myotubes. The spinal cord gradually attained a mature appearance between days 1-34. The results confirm the suitability of the wallaby spinal cord for studies of early mammalian development.

Development of hindlimb muscle spindles in the marsupial Macropus eugenii (tammar wallaby)

The development of muscle spindles was studied in the hindlimb of pouch young of the marsupial Macropus eugenii (tammar wallaby) from birth to 100 days. Primary myogenesis was evident in hindlimb muscles at birth. Presumptive muscle spindles were identified as early as day 30 postnatally. The intrafusal muscle fibres developed sequentially, to form the full juvenile complement by day 50, followed by development of the periaxial space. The formation of muscle spindles in the marsupial's hindlimb after birth was in contrast to the mainly prenatal development of spindles noted in placental mammals.

Terpenoid biosynthesis and the stereochemistry of enzyme-catalysed allylic addition-elimination reactions

Allylic addition-elimination reactions are widely used in the enzyme-catalysed formation of terpenoid metabolites. It has earlier been shown that the isoprenoid chain elongation reaction catalysed by farnesyl pyrophosphate synthase involving successive condensations of dimethylallyl pyrophosphate (DMAPP) and geranyl pyrophosphate (GPP) with isopentenyl pyrophosphate (IPP) corresponds to such an SE' reaction with net syn stereochemistry for the sequential electrophilic addition and proton elimination steps. Studies of the enzymic cyclization of farnesyl pyrophosphate (FPP) to pentalenene have now established the stereochemical course of two additional biological SE' reactions. Incubation of both (9R)- and (9S)-[9-3H,4,8-14]FPP with pentalenene synthase and analysis of the resulting labelled pentalenene has revealed that H-9re of FPP becomes H-8 of pentalenene, while H-9si undergoes net intramolecular transfer to the adjacent carbon, becoming H-1re (H-1 alpha) of pentalenene, as confirmed by subsequent experiments with [10-2H, 11-13C]FPP. These results correspond to net anti-stereochemistry in the intramolecular allylic addition-elimination reaction. The stereochemical course of a second SE' reaction has now been examined by analogous incubations of (4S,8S)-[4,8-3H,4,8-14C]FPP and (4R,8R)-[4,8-3H, 4.8-14C]FPP with pentalenene synthase. Determination of the distribution of label in the derived pentalenenes showed stereospecific loss of the original H-8si proton. Analysis of the plausible conformation of the presumed reaction intermediates revealed that the stereochemical course of the latter reaction cannot properly be described as either syn or anti, since cyclization and subsequent double bond formation require significant internal motions to allow proper overlap of the scissile C-H bond with the developing carbocation.

Induction of locomotion in spinal tadpoles by excitatory amino acids and their agonists

Bath application of the excitatory amino acids L-aspartate and/or L-glutamate or their agonists N-methyl-D,L-aspartate and/or kainate elicited swimming movements in spinal tadpoles. Swimming cycles induced by the amino acids were in the frequency range of natural movements, and could be evoked after sectioning all dorsal roots in the exposed spinal segments. Locomotion was only elicited by L-aspartate or L-glutamate at low concentrations when the bath medium was rapidly circulated over the exposed surface of the spinal cord, and was of much shorter duration than the agonist-induced movements. These results indicate some differences between the actions of L-aspartate and L-glutamate and their agonists on the tadpole spinal cord.

Effects of an ectopic hindlimb on the brachial motoneurons in Xenopus

A forelimb bud of Xenopus tadpoles was replaced with the much larger hindlimb but at developmental stage 50, prior to the onset of the normal period of motoneuron death. At the conclusion of the motoneuron death period, there were generally no significant differences between the total numbers and nuclear area distributions of the brachial motoneurons supplying the ectopic hindlimb, and the remaining forelimb. It was concluded that factors in addition to the amount of muscle, or premuscle in the limb may be important in determining the totals and sizes of surviving motoneurons.

Production of new polyene antibiotics by Streptomyces cellulosae after addition of ethyl (Z)-16-phenylhexadec-9-enoate

Ethyl (Z)-16-phenylhexadec-9-enoate (3), an analog of ethyl oleate (2), was synthesized and added to cultures of Streptomyces cellulosae ATCC 12625 which normally produce fungichromin (1) as the principal polyene antibiotic. These cultures showed drastic reduction of fungichromin biosynthesis but afforded four new polyene antibiotics with a truncated four carbon side chain which are designated as isochainin (11) (an isomer of chainin (10], 14-hydroxyisochainin (12), 1'-hydroxyisochainin (13), and 1',14-dihydroxyisochainin (14). The close correspondence of 13C NMR chemical shifts between these compounds and fungichromin suggests that the stereochemistry at every site is exactly analogous.

Innervation and behaviour of ectopic limbs in Xenopus

The hindlimb bud of Xenopus tadpoles was replaced with a forelimb bud, or vice versa, prior to axon invasion of the limb. Ectopic hindlimbs supported 94% as many brachial motoneurons as the remaining forelimb, and ectopic forelimbs supported 46% as many lumbar motoneurons as the remaining hindlimbs, on average, after the period of motoneuron death. The patterns of movement of ectopic limbs were characteristic of the innervating spinal cord segments, and not the limbs. The anatomical patterns of nerve trunks were characteristic of the ectopic limbs, and not the sources of innervation. HRP transport studies showed a resemblance between the locations of lumbar motoneurons supplying ectopic forelimb muscles and those supplying the homologous muscles of the hindlimb. It was concluded that motoneurons could survive the period of cell death following connection to muscles for which their patterns of activity were inappropriate, and the projections to ectopic limb muscles were specific although the nerve paths within the limbs were different.

Ionic responses and growth stimulation induced by nerve growth factor and epidermal growth factor in rat pheochromocytoma (PC12) cells

Rat pheochromocytoma cells (clone PC12) respond to nerve growth factor (NGF) by the acquirement of a phenotype resembling neuronal cells. In an earlier study we showed that NGF causes an increase in Na+,K+ pump activity, as monitored by ouabain-sensitive Rb+ influx. Here we show that addition of epidermal growth factor (EGF) to PC12 cells resulted in a stimulation of Na+,K+ pump activity as well. The increase of Na+,K+ pump activity by NGF or EGF was due to increased Na+ influx. This increased Na+ influx was sensitive to amiloride, an inhibitor of Na+,H+ exchange. Furthermore, no changes in membrane potential were observed upon addition of NGF or EGF. Amiloride-sensitive Na+,H+ exchange in PC12 cells was demonstrated by H+ efflux measurements and the effects of weak acids on Na+ influx. These observations suggest that both NGF and EGF activate an amiloride-sensitive, electroneutral Na+,H+ exchange mechanism in PC12 cells. These findings were surprising in view of the opposite ultimate biological effects of NGF and EGF, e.g., growth arrest vs. growth stimulation. However, within 24 h after addition, NGF was found to stimulate growth of PC12 cells, comparable to EGF. In the presence of amiloride, this stimulated growth by NGF and EGF was abolished. In contrast, amiloride did not affect NGF-induced neurite outgrowth of PC12 cells. From these observations it is concluded that in PC12 cells: (a) NGF has an initial growth stimulating effect; (b) neurite outgrowth is independent of increased amiloride-sensitive Na+ influx; and (c) growth stimulation by NGF and EGF is associated with increased amiloride-sensitive Na+ influx.

Salute to some nursing pioneers

This is indeed a very wide meaning for the word, ‘Pioneer’, and it was with some trepidation that I approached this subject. After all, it could end up by being a sort of Biographical Directory of Nurses in South Africa and this is certainly not what our readers would like in this particular journal. In any case, Searle’s History of the Development of Nursing in South Africa covers this field very fully and adequately. So just what sort of people do we regard as pioneers of nursing in our country? Where do we begin? Can one be totally objective about it or would my choice be different from that of readers because of a more subjective attitude.