Large-scale chromatin de-compaction induced by low light is not accompanied by nucleosomal displacement

Arabidopsis thaliana is widely used as a model to study chromatin compaction dynamics during development and in response to the environment. Signals such as prolonged heat treatment, low light and pathogen infestation are known to induce large-scale de-condensation of nuclear chromatin. Here we demonstrate that the response to different environments varies at the nucleosomal level. Our results show that in contrast to previous reports on heat and biotic infestation, low light intensity signaling does not alter nucleosomal occupancy, despite the marked effects of low light on global chromatin compaction.Key words: Arabidopsis, chromatin, nucleosomes, MNase IThanks to its relatively simple chromatin organization, Arabidopsis thaliana became the model of choice to study dynamics in nuclear chromatin compaction in plants.^1–3 At the microscopic level, highly condensed ‘heterochromatic’ domains (chromocenters), containing compact DNA (mainly repetitive sequences), and less condensed gene-rich ‘euchromatic’ domains can be distinguished upon staining with DAPI (4′,6-diamidino-2-phenylindole). This division however, is not static and compaction changes throughout development (reviewed in ref. ⁴). Chromatin for example de-condensates prior to flowering⁵ and increases with cell differentiation during leaf maturation³ and seedling establishment.⁶ Vice versa, artificially induced cell de-differentiation during protoplastization, results in loosening of compact chromatin.^7,8 Chromatin compaction is also influenced by various environmental signals. These include infestation by pathogenic microorganisms such as Pseudomonas syringae, light and heat signals.^9–11In our recent paper, published in Plant Physiology,¹² we demonstrate that a ∼90% decrease in light intensity (low light) induces a reversible reduction in global chromatin compaction. In addition, also specifically lowering the blue-light wavelengths in the spectrum, or lowering the red-to-far red (R/Fr) ratio induced a significant reduced compaction of the nuclear chromatin. This is interesting from a functional perspective because (1) these are the relevant signals perceived by plants in natural shade conditions occurring in dense-vegetations and (2) because these wavelengths are specifically detected by the light-sensitive photoreceptor proteins. Previously, we demonstrated that the R/Fr-photoreceptor Phytochrome-B (PhyB) is a positive regulator of chromatin compaction in standard light conditions.¹⁰ We now showed that PhyB also controls low light-induced chromatin organization, but that its effect depend on the genetic background of the phyb mutant under study. Likely, PhyB exerts its effects on light-mediated chromatin compaction via stabilization of CRYPTOCHROME 2 (CRY2) protein. This chromatin-associated blue light photoreceptor is a general positive regulator of low light-induced chromatin de-compaction and in addition controls chromatin compaction during floral transition.⁵In addition, we demonstrated that global chromatin de-compaction during floral transition and low light treatment also occurs in euchromatic domains.^5,12 To study possible chromatin changes at the nucleosomal level, we performed Micrococcal Nuclease I (MNase I) analysis. No differences were observed in the nucleosomal occupancy between standard and low light conditions in DNA gels or Southern blots hybridized with different probes for repeated sequences associated to heterochromatin, and dispersed upon low light treatment (Fig. 1). This suggests that the large-scale heterochromatin (de)compaction response observed at the microscopic level under low light conditions is not necessarily accompanied by nucleosomal displacement. These results are in line with the de-condensation conditions induced by protoplastization, where no changes in H3K9Me2 or in DNA methylation (5-mC) levels were found.⁷ However, these results are in contrast to the results of Pecinka and colleagues,¹¹ who demonstrated that prolonged heat stress results in heterochromatin de-condensation and loss of nucleosomes. Moreover, it is in contrast with Pavet and co-workers,⁹ who found reduced 5-mC levels upon infection with P. syringae. Although the results of Pecinka and colleaugues¹¹ were obtained by real-time PCR which may be more sensitive than our Southern blots, we conclude that the response of plants to their environment at the chromatin compaction level may be tailored to the specific signal it is confronted with and that this probably can be dissected at the nucleosomal level.Open in a separate windowFigure 1MNase I analysis of low light treated plants. Southern blots with 3 different probes hybridized to DNA from Col-0 plants cultured under standard (200 µmol m⁻² s⁻¹; control) and low light (15 µmol m⁻² s⁻¹) conditions. For each part, the first two lanes represent control DNA samples (no MNase I), followed by lanes with increasing MNase I concentrations (0.02, 0.1, 0.75 and 3 units MNase I). (A) 5S rDNA probe, (B) 45S rDNA probe, (C) pAl1 probe (180 bp centromeric repeat). M = molecular weight marker.     

In Vivo Kinetics of Formate Metabolism in Folate-deficient and Folate-replete Rats

It is now established that the mitochondrial production of formate is a major process in the endogenous generation of folate-linked one-carbon groups. We have developed an in vivo approach involving the constant infusion of [¹³C]formate until isotopic steady state is attained to measure the rate of endogenous formate production in rats fed on either a folate-replete or folate-deficient diet. Formate was produced at a rate of 76 μmol·h⁻¹·100 g of body weight⁻¹ in the folate-replete rats, and this was decreased by 44% in folate-deficient rats. This decreased formate production was confirmed in isolated rat liver mitochondria where formate production from serine, the principal precursor of one-carbon groups, was decreased by 85%, although formate production from sarcosine and dimethylglycine (choline metabolites) was significantly increased. We attribute this unexpected result to the demonstrated production of formaldehyde by sarcosine dehydrogenase and dimethylglycine dehydrogenase from their respective substrates in the absence of tetrahydrofolate and subsequent formation of formate by formaldehyde dehydrogenase. Comparison of formate production with the ingestion of dietary formate precursors (serine, glycine, tryptophan, histidine, methionine, and choline) showed that ∼75% of these precursors were converted to formate, indicating that formate is a significant, although underappreciated end product of choline and amino acid oxidation. Ingestion of a high protein diet did not result in increased production of formate, suggesting a regulation of the conversion of these precursors at the mitochondrial level to formate.     

Sweat gland density and response during high-intensity exercise in athletes with spinal cord injuries

Sweat production is crucial for thermoregulation. However, sweating can be problematic for individuals with spinal cord injuries (SCI), as they display a blunting of sudomotor and vasomotor responses below the level of the injury. Sweat gland density and eccrine gland metabolism in SCI are not well understood. Consequently, this study examined sweat lactate (S-LA) (reflective of sweat gland metabolism), active sweat gland density (SGD), and sweat output per gland (S/G) in 7 SCI athletes and 8 able-bodied (AB) controls matched for arm ergometry VO₂peak. A sweat collection device was positioned on the upper scapular and medial calf of each subject just prior to the beginning of the trial, with iodine sweat gland density patches positioned on the upper scapular and medial calf. Participants were tested on a ramp protocol (7 min per stage, 20 W increase per stage) in a common exercise environment (21±1°C, 45-65% relative humidity). An independent t-test revealed lower (p<0.05) SGD (upper scapular) for SCI (22.3 ±14.8 glands · cm⁻²) vs. AB. (41.0 ± 8.1 glands · cm⁻²). However, there was no significant difference for S/G between groups. S-LA was significantly greater (p<0.05) during the second exercise stage for SCI (11.5±10.9 mmol · l⁻¹) vs. AB (26.8±11.07 mmol · l⁻¹). These findings suggest that SCI athletes had less active sweat glands compared to the AB group, but the sweat response was similar (SLA, S/G) between AB and SCI athletes. The results suggest similar interglandular metabolic activity irrespective of overall sweat rate.     

A Dutch guideline for the treatment of scoliosis in neuromuscular disorders

Background

Children with neuromuscular disorders with a progressive muscle weakness such as Duchenne Muscular Dystrophy and Spinal Muscular Atrophy frequently develop a progressive scoliosis. A severe scoliosis compromises respiratory function and makes sitting more difficult. Spinal surgery is considered the primary treatment option for correcting severe scoliosis in neuromuscular disorders. Surgery in this population requires a multidisciplinary approach, careful planning, dedicated surgical procedures, and specialized after care.

Methods

The guideline is based on scientific evidence and expert opinions. A multidisciplinary working group representing experts from all relevant specialties performed the research. A literature search was conducted to collect scientific evidence in answer to specific questions posed by the working group. Literature was classified according to the level of evidence.

Results

For most aspects of the treatment scientific evidence is scarce and only low level cohort studies were found. Nevertheless, a high degree of consensus was reached about the management of patients with scoliosis in neuromuscular disorders. This was translated into a set of recommendations, which are now officially accepted as a general guideline in the Netherlands.

Conclusion

In order to optimize the treatment for scoliosis in neuromuscular disorders a Dutch guideline has been composed. This evidence-based, multidisciplinary guideline addresses conservative treatment, the preoperative, perioperative, and postoperative care of scoliosis in neuromuscular disorders.     

Observational Learning and Predator Inspection in Guppies (Poecilia reticulata)

Prior work has demonstrated that, following a predator inspection visit of their own, guppies prefer to associate with individuals who inspected a predator most closely. Based on this work, as well as studies of social learning in the context of mate choice, we predicted that male guppies that observed but did not participate in an inspection trial would subsequently choose to associate with the closer of two inspectors. Our experimental protocol consisted of three treatments: a control test in which an observer watched two fish consecutively, only one of which was exposed to a predator, a sequential test in which an observer watched two fish consecutively, both of which were exposed to the predator, and a social test in which an observer watched two fish inspect simultaneously. We found no preferences by the observer for either of the fish in any of the trials. Our results suggest that direct interaction is a critical component to the development of preferences in male guppies. We discuss our findings in light of game theoretical treatments of cooperation.     

Monoclonal antibodies against chicken type V collagen: production, specificity, and use for immunocytochemical localization in embryonic cornea and other organs

Two monoclonal antibodies have been produced against chick type V collagen and shown to be highly specific for separate, conformational dependent determinants within this molecule. When used for immunocytochemical tissue localization, these antibodies show that a major site for the in situ deposition of type V is within the extracellular matrices of many dense connective tissues. In these, however, it is largely in a form unavailable to the antibodies, thus requiring a specific “unmasking” treatment to obtain successful immunocytochemical staining. The specificity of these two IgG antibodies was determined by inhibition ELISA, in which only type V and no other known collagen shows inhibition. In ELISA, mixtures of the two antibodies give an additive binding reaction to the collagen, suggesting that each is against a different antigenic determinant. That both antigenic determinants are conformational dependent, being either in, or closely associated with, the collagen helix is demonstrated by the loss of antibody binding to molecules that have been thermally denatured. The temperature at which this occurs, as assayed by inhibition ELISA, is very similar to that at which the collagen helix melts, as determined by optical rotation. This gives strong additional evidence that the antibodies are directed against the collagen. The antibodies were used for indirect immunofluorescence analyses of cryostat sections of corneas and other organs from 17 to 18-day-old chick embryos. Of all tissues examined only Bowman’s membrane gave a strong staining reaction with cryostat sections of unfixed material. Staining in other areas of the cornea and in other tissues was very light or nonexistent. When, however, sections were pretreated with pepsin dissolved in dilute HAc or, surprisingly, with the dilute HAc itself dramatic new staining by the antibodies was observed in most tissues examined. The staining, which was specific for the anti-type V collagen antibodies, was largely confined to extracellular matrices of dense connective tissues. Experiments using protease inhibitors suggested that the “unmasking” did not involve proteolysis. We do not yet know the mechanism of this unmasking; however, one possibility is that the dilute acid causes swelling or conformational changes in a type-V collagen-containing supramolecular structure. Further studies should allow us to determine whether this is the case.