Evaluating plant lineage losses and gains in temperate forest understories: a phylogenetic perspective on climate change and nitrogen deposition

Global change has accelerated local species extinctions and colonizations, often resulting in losses and gains of evolutionary lineages with unique features. Do these losses and gains occur randomly across the phylogeny? We quantified: temporal changes in plant phylogenetic diversity (PD); and the phylogenetic relatedness (PR) of lost and gained species in 2672 semi-permanent vegetation plots in European temperate forest understories resurveyed over an average period of 40 yr. Controlling for differences in species richness, PD increased slightly over time and across plots. Moreover, lost species within plots exhibited a higher degree of PR than gained species. This implies that gained species originated from a more diverse set of evolutionary lineages than lost species. Certain lineages also lost and gained more species than expected by chance, with Ericaceae, Fabaceae, and Orchidaceae experiencing losses and Amaranthaceae, Cyperaceae, and Rosaceae showing gains. Species losses and gains displayed no significant phylogenetic signal in response to changes in macroclimatic conditions and nitrogen deposition. As anthropogenic global change intensifies, temperate forest understories experience losses and gains in specific phylogenetic branches and ecological strategies, while the overall mean PD remains relatively stable.

Transcriptome analysis of iron over-accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling

On account of its competence to accept and donate electrons, iron (Fe) is an essential element across all forms of life, including plants. Maintaining Fe homeostasis requires precise orchestration of its uptake, trafficking, and translocation in order to meet the demand for Fe sinks such as plastids. Plants harboring defects in the systemic Fe transporter OPT3 (OLIGOPEPTIDE TRANSPORTER 3) display constitutive Fe deficiency responses and accumulate toxic levels of Fe in their leaves. Similarly, ectopic expression of IRONMAN (IMA) genes, encoding a family of phloem-localized signaling peptides, triggers the uptake and accumulation of Fe by inhibiting the putative Fe sensor BRUTUS. This study aims at elucidating the mechanisms operating between OPT3-mediated systemic Fe transport, activation of IMA genes in the phloem, and activation of Fe uptake in the root epidermis. Transcriptional profiling of opt3-2 mutant and IMA1/IMA3 overexpressing (IMA Ox) lines uncovered a small subset of genes that were consistently differentially expressed across all three genotypes and Fe-deficient control plants, constituting potential novel regulators of cellular Fe homeostasis. In particular, expression of the the F-box protein At1g73120 was robustly induced in all genotypes, suggesting a putative function in the posttranslational regulation of cellular Fe homeostasis. As further constituents of this module, two plastid-encoded loci that putatively produce transfer ribonucleic acid (tRNA)-derived small ribonucleic acids are possibly involved in retrograde control of root Fe uptake.

Insertion of YFP at P5CS1 and AFL1 shows the potential, and potential complications, of gene tagging for functional analyses of stress-related proteins

Crispr/CAS9-enabled homologous recombination to insert a tag in frame with an endogenous gene can circumvent difficulties such as context-dependent promoter activity that complicate analysis of gene expression and protein accumulation patterns. However, there have been few reports examining whether such gene targeting/gene tagging (GT) can alter expression of the target gene. The enzyme encoded by Δ1 -pyrroline-5-carboxylate synthetase 1 (P5CS1) is key for stress-induced proline synthesis and drought resistance, yet its expression pattern and protein localisation have been difficult to assay. We used GT to insert YFP in frame with the 5' or 3' ends of the endogenous P5CS1 and At14a-Like 1 (AFL1) coding regions. Insertion at the 3' end of either gene generated homozygous lines with expression of the gene-YFP fusion indistinguishable from the wild type allele. However, for P5CS1 this occurred only after selfing and advancement to the T5 generation allowed initial homozygous lethality of the insertion to be overcome. Once this was done, the GT-generated P5CS1-YFP plants revealed new information about P5CS1 localisation and tissue-specific expression. In contrast, insertion of YFP at the 5' end of either gene blocked expression. The results demonstrate that GT can be useful for functional analyses of genes that are problematic to properly express by other means but also show that, in some cases, GT can disrupt expression of the target gene.

Protein Phosphorylation Orchestrates Acclimations of Arabidopsis Plants to Environmental pH

Environment pH (pHe) is a key parameter dictating a surfeit of conditions critical to plant survival and fitness. To elucidate the mechanisms that recalibrate cytoplasmic and apoplastic pH homeostasis, we conducted a comprehensive proteomic/phosphoproteomic inventory of plants subjected to transient exposure to acidic or alkaline pH, an approach that covered the majority of protein-coding genes of the reference plant Arabidopsis thaliana. Our survey revealed a large set-of so far undocumented pHe-dependent phospho-sites, indicative of extensive post-translational regulation of proteins involved in the acclimation to pHe. Changes in pHe altered both electrogenic H+ pumping via P-type ATPases and H+/anion co-transport processes, putatively leading to altered net trans-plasma membrane translocation of H+ ions. In pH 7.5 plants, the transport (but not the assimilation) of nitrogen via NRT2-type nitrate and AMT1-type ammonium transporters was induced, conceivably to increase the cytosolic H+ concentration. Exposure to both acidic and alkaline pH resulted in a marked repression of primary root elongation. No such cessation was observed in nrt2.1 mutants. Alkaline pH decreased the number of root hairs in the wild type but not in nrt2.1 plants, supporting a role of NRT2.1 in developmental signaling. Sequestration of iron into the vacuole via alterations in protein abundance of the vacuolar iron transporter VTL5 was inversely regulated in response to high and low pHe, presumptively in anticipation of associated changes in iron availability. A pH-dependent phospho-switch was also observed for the ABC transporter PDR7, suggesting changes in activity and, possibly, substrate specificity. Unexpectedly, the effect of pHe was not restricted to roots and provoked pronounced changes in the shoot proteome. In both roots and shoots, the plant-specific TPLATE complex components AtEH1 and AtEH2-essential for clathrin-mediated endocytosis-were differentially phosphorylated at multiple sites in response to pHe, indicating that the endocytic cargo protein trafficking is orchestrated by pHe.

Combining multiple investigative approaches to unravel functional responses to global change in the understorey of temperate forests

Plant communities are being exposed to changing environmental conditions all around the globe, leading to alterations in plant diversity, community composition, and ecosystem functioning. For herbaceous understorey communities in temperate forests, responses to global change are postulated to be complex, due to the presence of a tree layer that modulates understorey responses to external pressures such as climate change and changes in atmospheric nitrogen deposition rates. Multiple investigative approaches have been put forward as tools to detect, quantify and predict understorey responses to these global-change drivers, including, among others, distributed resurvey studies and manipulative experiments. These investigative approaches are generally designed and reported upon in isolation, while integration across investigative approaches is rarely considered. In this study, we integrate three investigative approaches (two complementary resurvey approaches and one experimental approach) to investigate how climate warming and changes in nitrogen deposition affect the functional composition of the understorey and how functional responses in the understorey are modulated by canopy disturbance, that is, changes in overstorey canopy openness over time. Our resurvey data reveal that most changes in understorey functional characteristics represent responses to changes in canopy openness with shifts in macroclimate temperature and aerial nitrogen deposition playing secondary roles. Contrary to expectations, we found little evidence that these drivers interact. In addition, experimental findings deviated from the observational findings, suggesting that the forces driving understorey change at the regional scale differ from those driving change at the forest floor (i.e., the experimental treatments). Our study demonstrates that different approaches need to be integrated to acquire a full picture of how understorey communities respond to global change.

Giant magnetocaloric effect in spin supersolid candidate Na2BaCo(PO4)2

Supersolid, an exotic quantum state of matter that consists of particles forming an incompressible solid structure while simultaneously showing superfluidity of zero viscosity1, is one of the long-standing pursuits in fundamental research2,3. Although the initial report of 4He supersolid turned out to be an artefact4, this intriguing quantum matter has inspired enthusiastic investigations into ultracold quantum gases5-8. Nevertheless, the realization of supersolidity in condensed matter remains elusive. Here we find evidence for a quantum magnetic analogue of supersolid-the spin supersolid-in the recently synthesized triangular-lattice antiferromagnet Na2BaCo(PO4)2 (ref. 9). Notably, a giant magnetocaloric effect related to the spin supersolidity is observed in the demagnetization cooling process, manifesting itself as two prominent valley-like regimes, with the lowest temperature attaining below 100 mK. Not only is there an experimentally determined series of critical fields but the demagnetization cooling profile also shows excellent agreement with the theoretical simulations with an easy-axis Heisenberg model. Neutron diffractions also successfully locate the proposed spin supersolid phases by revealing the coexistence of three-sublattice spin solid order and interlayer incommensurability indicative of the spin superfluidity. Thus, our results reveal a strong entropic effect of the spin supersolid phase in a frustrated quantum magnet and open up a viable and promising avenue for applications in sub-kelvin refrigeration, especially in the context of persistent concerns about helium shortages10,11.

Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq

Ribosome profiling (Ribo-seq) measures ribosome density along messenger RNA (mRNA) transcripts and is used to estimate the "translational fitness" of a given mRNA in response to environmental or developmental cues with high resolution. Here, we describe a protocol for Ribo-seq in plants adapted for the model plant Arabidopsis thaliana. We describe steps for lysis and nucleolytic digestion and ribosome footprinting. We then detail library construction, sequencing, and data analysis.

Prognostic Performance of Inflammatory Biomarkers Based on Complete Blood Counts in COVID-19 Patients

With the end of the pandemic, COVID-19 has entered an endemic phase with expected seasonal spikes. Consequently, the implementation of easily accessible prognostic biomarkers for patients with COVID-19 remains an important area of research. In this monocentric study at a German tertiary care hospital, we determined the prognostic performance of different clinical and blood-based parameters in 412 COVID-19 patients. We evaluated the neutrophil-to-lymphocyte ratio (NLR), systemic immune-inflammation index (SII), pan-immune-inflammation value (PIV), and absolute eosinopenia (AEP, 0/µL) of COVID-19 patients (n = 412). The Siddiqui and Mehra staging proposal, the WHO clinical progression scale, and COVID-19-associated death were used as COVID-19 outcome measures. With respect to Siddiqi and Mehra staging, patient age of older than 75 years, high C-reactive protein (CRP), absolute eosinopenia (AEP), cardiovascular comorbidities, and high ferritin were significant independent predictors for severe COVID-19. When outcome was determined according to the WHO clinical progression scale, patient age of older than 75 years, high CRP, high LDH, AEP, high neutrophil-to-lymphocyte ratio (NLR), and the presence of pulmonal comorbidities were significant independent predictors for severe COVID-19. Finally, COVID-19-associated death was predicted independently by patient age of older than 75 years, high LDH, high NLR, and AEP. Eosinopenia (< 40/µL) was observed in 74.5% of patients, and AEP in almost 45%. In conclusion, the present real-world data indicate that the NLR is superior to more complex systemic immune-inflammation biomarkers (e.g., SII and PIV) in COVID-19 prognostication. A decreased eosinophil count emerged as a potential hallmark of COVID-19 infection, whereas AEP turned out to be an accessible independent biomarker for COVID-19 severity and mortality.

The Rising Problem of Hip Fractures in Geriatric Patients-Analysis of Surgical Influences on the Outcome

BACKGROUND

Hip fractures in geriatric patients often have a poor outcome in terms of mortality, mobility as well as independence. Different surgical influence factors are known that improve the outcome.

METHODS

In this observational cohort study, 281 patients of a geriatric trauma unit were analyzed prospectively. Demographic factors, as well as data regarding the trauma mechanism and perioperative treatment, were recorded. The nutritional status was also analyzed. The follow-up was set to 120 days.

RESULTS

The key conclusion of this study is that a high ASA classification, the use of anticoagulatory medicine and malnutrition are significantly associated with higher mortality together with worse independence (p < 0.05). There is no significant difference in outcome concerning the time to surgery within the first 24 h.

CONCLUSIONS

Malnutrition seems to be an important risk factor for an adverse outcome of geriatric patients and therefore warrants a focus in multidisciplinary treatment. The risk factor ASA cannot be improved during the pre-surgery phase, but requires intensified care by a multidisciplinary team specialized in orthogeriatrics.

Alkalinity modulates a unique suite of genes to recalibrate growth and pH homeostasis

Alkaline soils pose a conglomerate of constraints to plants, restricting the growth and fitness of non-adapted species in habitats with low active proton concentrations. To thrive under such conditions, plants have to compensate for a potential increase in cytosolic pH and restricted softening of the cell wall to invigorate cell elongation in a proton-depleted environment. To discern mechanisms that aid in the adaptation to external pH, we grew plants on media with pH values ranging from 5.5 to 8.5. Growth was severely restricted above pH 6.5 and associated with decreasing chlorophyll levels at alkaline pH. Bicarbonate treatment worsened plant performance, suggesting effects that differ from those exerted by pH as such. Transcriptional profiling of roots subjected to short-term transfer from optimal (pH 5.5) to alkaline (pH 7.5) media unveiled a large set of differentially expressed genes that were partially congruent with genes affected by low pH, bicarbonate, and nitrate, but showed only a very small overlap with genes responsive to the availability of iron. Further analysis of selected genes disclosed pronounced responsiveness of their expression over a wide range of external pH values. Alkalinity altered the expression of various proton/anion co-transporters, possibly to recalibrate cellular proton homeostasis. Co-expression analysis of pH-responsive genes identified a module of genes encoding proteins with putative functions in the regulation of root growth, which appears to be conserved in plants subjected to low pH or bicarbonate. Our analysis provides an inventory of pH-sensitive genes and allows comprehensive insights into processes that are orchestrated by external pH.

Functional trait trade-offs define plant population stability across different biomes

Ecological theory posits that temporal stability patterns in plant populations are associated with differences in species' ecological strategies. However, empirical evidence is lacking about which traits, or trade-offs, underlie species stability, especially across different biomes. We compiled a worldwide collection of long-term permanent vegetation records (greater than 7000 plots from 78 datasets) from a large range of habitats which we combined with existing trait databases. We tested whether the observed inter-annual variability in species abundance (coefficient of variation) was related to multiple individual traits. We found that populations with greater leaf dry matter content and seed mass were more stable over time. Despite the variability explained by these traits being low, their effect was consistent across different datasets. Other traits played a significant, albeit weaker, role in species stability, and the inclusion of multi-variate axes or phylogeny did not substantially modify nor improve predictions. These results provide empirical evidence and highlight the relevance of specific ecological trade-offs, i.e. in different resource-use and dispersal strategies, for plant populations stability across multiple biomes. Further research is, however, necessary to integrate and evaluate the role of other specific traits, often not available in databases, and intraspecific trait variability in modulating species stability.

The Arabidopsis Deubiquitylase OTU5 Suppresses Flowering by Histone Modification-Mediated Activation of the Major Flowering Repressors FLC, MAF4, and MAF5

Distinct phylogeny and substrate specificities suggest that 12 Arabidopsis Ovarian Tumor domain-containing (OTU) deubiquitinases participate in conserved or plant-specific functions. The otu5-1 null mutant displayed a pleiotropic phenotype, including early flowering, mimicking that of mutants harboring defects in subunits (e.g., ARP6) of the SWR1 complex (SWR1c) involved in histone H2A.Z deposition. Transcriptome and RT-qPCR analyses suggest that downregulated FLC and MAF4-5 are responsible for the early flowering of otu5-1. qChIP analyses revealed a reduction and increase in activating and repressive histone marks, respectively, on FLC and MAF4-5 in otu5-1. Subcellular fractionation, GFP-fusion expression, and MNase treatment of chromatin showed that OTU5 is nucleus-enriched and chromatin-associated. Moreover, OTU5 was found to be associated with FLC and MAF4-5. The OTU5-associated protein complex(es) appears to be distinct from SWR1c, as the molecular weights of OTU5 complex(es) were unaltered in arp6-1 plants. Furthermore, the otu5-1 arp6-1 double mutant exhibited synergistic phenotypes, and H2A.Z levels on FLC/MAF4-5 were reduced in arp6-1 but not otu5-1. Our results support the proposition that Arabidopsis OTU5, acting independently of SWR1c, suppresses flowering by activating FLC and MAF4-5 through histone modification. Double-mutant analyses also indicate that OTU5 acts independently of the HUB1-mediated pathway, but it is partially required for FLC-mediated flowering suppression in autonomous pathway mutants and FRIGIDA-Col.

Iron sensing in plants

The ease of accepting or donating electrons is the raison d'être for the pivotal role iron (Fe) plays in a multitude of vital processes. In the presence of oxygen, however, this very property promotes the formation of immobile Fe(III) oxyhydroxides in the soil, which limits the concentration of Fe that is available for uptake by plant roots to levels well below the plant's demand. To adequately respond to a shortage (or, in the absence of oxygen, a possible surplus) in Fe supply, plants have to perceive and decode information on both external Fe levels and the internal Fe status. As a further challenge, such cues have to be translated into appropriate responses to satisfy (but not overload) the demand of sink (i.e., non-root) tissues. While this seems to be a straightforward task for evolution, the multitude of possible inputs into the Fe signaling circuitry suggests diversified sensing mechanisms that concertedly contribute to govern whole plant and cellular Fe homeostasis. Here, we review recent progress in elucidating early events in Fe sensing and signaling that steer downstream adaptive responses. The emerging picture suggests that Fe sensing is not a central event but occurs in distinct locations linked to distinct biotic and abiotic signaling networks that together tune Fe levels, Fe uptake, root growth, and immunity in an interwoven manner to orchestrate and prioritize multiple physiological readouts.

Protein kinase MtCIPK12 modulates iron reduction in Medicago truncatula by regulating riboflavin biosynthesis

Iron (Fe) is an essential micronutrient, and deficiency in available Fe is one of the most important limiting factors for plant growth. In some species including Medicago truncatula, Fe deficiency results in accumulation of riboflavin, a response associated with Fe acquisition. However, how the plant's Fe status is integrated to tune riboflavin biosynthesis and how riboflavin levels affect Fe acquisition and utilization remains largely unexplored. We report that protein kinase CIPK12 regulates ferric reduction by accumulation of riboflavin and its derivatives in roots of M. truncatula via physiological and molecular characterization of its mutants and over-expressing materials. Mutations in CIPK12 enhance Fe accumulation and improve photosynthetic efficiency, whereas overexpression of CIPK12 shows the opposite phenotypes. The Calcineurin B-like proteins CBL3 and CBL8 interact with CIPK12, which negatively regulates the expression of genes encoding key enzymes in the riboflavin biosynthesis pathway. CIPK12 negatively regulates Fe acquisition by suppressing accumulation of riboflavin and its derivatives in roots, which in turn influences ferric reduction activity by riboflavin-dependent electron transport under Fe deficiency. Our findings uncover a new regulatory mechanism by which CIPK12 regulates riboflavin biosynthesis and Fe-deficiency responses in plants.

Remission and low disease activity in Polish patients with systemic lupus erythematosus - real-life, five-year follow-up outcomes

OBJECTIVE

Remission in systemic lupus erythematosus (SLE) or Lupus Low Disease Activity State (LLDAS) are associated with less organ damage and thus create new perspectives for effective damage-limiting treatment. The aim of this study was to assess the occurrence of remission defined by The Definition of Remission In SLE (DORIS) and of LLDAS as well as their predictors in the Polish SLE cohort.

PATIENTS AND METHODS

In this retrospective study data were collected on patients with SLE that achieved at least one year of DORIS remission or LLDAS and were followed up for 5 years. Clinical and demographic data were gathered; DORIS and LLDAS predictors were determined by univariate regression analysis.

RESULTS

The full analysis set included 80 patients at baseline and 70 at follow-up. Over half of patients with SLE (39; 55.7%) fulfilled the DORIS remission criteria. In this group, 53.8% (21) of patients were in remission on-treatment and 46.1% (18) in remission off-treatment. LLDAS was fulfilled by a cohort of 43 (61.4%) patients with SLE. Among patients that achieved DORIS or LLDAS at follow-up, 77% were not treated with glucocorticoids (GCs). The most important predictors for DORIS and LLDAS off-treatment were mean SLEDAI-2K score with cut-off of ≤8.0, treatment with mycophenolate mofetil or antimalarials, and the age at disease onset above 43 years.

CONCLUSIONS

Remission and LLDAS are achievable goals in treating SLE as over half of study patients fulfilled the DORIS remission and LLDAS criteria. The identified predictors for DORIS and LLDAS indicate the importance of effective therapy leading to reduction of GC use.

Characterization data of reference materials used for phase II of the priority program DFG SPP 2005 "Opus Fluidum Futurum - Rheology of reactive, multiscale, multiphase construction materials"

A thorough characterization of base materials is the prerequisite for further research. In this paper, the characterization data of the reference materials (CEM I 42.5 R, limestone powder, calcined clay and a mixture of these three components) used in the second funding phase of the priority program 2005 of the German Research Foundation (DFG SPP 2005) are presented under the aspects of chemical and mineralogical composition as well as physical and chemical properties. The data were collected based on tests performed by up to eleven research groups involved in this cooperative program.

Influence of Malnutrition on Outcome after Hip Fractures in Older Patients

Background: Malnutrition might lead to a worse outcome in hip fractures of older patients. The purpose of this study is to analyze different indicators of malnutrition that lead to worse outcomes. Methods: 252 patients of a geriatric trauma unit were analyzed prospectively. Different demographic, as well as data on the trauma and whether osteoporosis prophylaxis or anticoagulation was present, were recorded. The nutritional status with respect to laboratory parameters as well as nutritional risk score was also analyzed. Results: The main finding of this study is that a poor nutritional status is statistically significantly associated with higher mortality as well as worse independence (p < 0.05). A postoperatively prescribed osteoporosis prophylaxis is protective of mortality and independence (p < 0.05). Conclusions: Malnutrition of geriatric patients increases the risk for death, worse mobility, and independence after hip fractures. Osteoporosis prophylaxis prescribed during an inpatient stay enables patients to retain their independence. The nutritional status of geriatric patients with hip fractures should be obtained and provisions made.

Development and validation of COVID-19 Radiological Risk Score (COVID-RRS): a multivariable radiological score to estimate the in-hospital mortality risk in COVID-19 patients

OBJECTIVE

To develop and validate in-hospital mortality risk score comprising radiological aberrances in chest computed tomography (CT) performed on admission.

PATIENTS AND METHODS

Single-center, longitudinal cohort study in adult patients admitted with Coronavirus Disease 2019 (COVID-19) to our ward. Patients were followed-up during hospitalization until discharge or death. Eligibility criteria for the study comprised positive real-time reverse transcription-polymerase chain reaction test (RT-PCR) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and ground-glass opacities in chest CT. In-hospital death was the outcome of interest. Radiological, laboratory, and clinical data were analyzed. Radiological determinants of mortality were used as variables in multivariate logistic regression analysis, and results were used to build a radiological risk score.

RESULTS

371 patients were enrolled in development and validation cohorts (181 and 190 respectively), with a total of 47 non-survivors. Univariate analysis data determined 12 predictive factors (nine risk and three protective). In multivariate analysis, we developed COVID-RRS (COVID-19 Radiological Risk Score) - a radiological score predicting in-hospital COVID-19 mortality risk comprising estimated lung involvement percentage, pleural effusion, and domination of consolidation-type changes in chest CT. Our score was superior in the prediction of COVID-19 mortality to the percentage of lung involvement alone, Chest Computed Tomography Severity Score (CTSS), and Total Severity Score (TSS) in both groups with AUC of 0.910 and 0.902, respectively (p <0.001).

CONCLUSIONS

Additional imaging features independently contribute to COVID-19 mortality risk. Our model comprising lung involvement estimation, pleural effusion, and domination of consolidations performed significantly better than scores based on the extent of the changes alone. COVID-RRS is a simple, reliable, and ready-to-use tool for clinical practice.

Chromatin Enrichment for Proteomics in Plants (ChEP-P)

Chromatin enrichment for proteomics (ChEP) is a technique that allows for unbiased proteomic profiling of the chromatin landscape using mass spectrometry. While the method has been successfully employed to survey chromatin-associated proteins in various organisms and cell types, ChEP has not yet been applied to plant materials. Here, we describe a detailed ChEP protocol which has been modified for plants and designated ChEP-P (ChEP in plants). The protocol outlined here includes all necessary steps to perform a label-free quantitative ChEP-P experiment, supporting the identification of more than 3500 proteins in Arabidopsis thaliana.

Tandem Mass Tag-Based Phosphoproteomics in Plants

Mass spectrometry-based proteomics provide a powerful tool for plant research, allowing global detection of steady-state levels of proteins under a given experimental setup. Here, we provide an optimized protocol for proteomic profiling using tandem mass tag (TMT) labeling followed by liquid chromatography-mass spectrometry (LC-MS/MS) to quantitate phosphopeptides and non-phosphopeptides from the same samples. The outlined protocol comprises a series of successive steps, namely, SDS (sodium dodecyl sulfate) protein extraction, protein precipitation, digestion, TMT labeling, phosphopeptide enrichment, high pH reversed-phase fractionation, LC-MS/MS analysis, protein identification, and data analysis. Our proteome-scale protocol requires 0.1 mg protein per sample and allows for the reliable and accurate quantification of more than 8000 proteins in Arabidopsis plant samples across multiple conditions, including low abundant peptides.

2022 American College of Rheumatology/EULAR Classification Criteria for Takayasu Arteritis

OBJECTIVE

To develop and validate new classification criteria for Takayasu arteritis (TAK).

METHODS

Patients with vasculitis or comparator diseases were recruited into an international cohort. The study proceeded in 6 phases: 1) identification of candidate criteria items, 2) collection of candidate items present at diagnosis, 3) expert panel review of cases, 4) data-driven reduction of candidate items, 5) derivation of a points-based classification score in a development data set, and 6) validation in an independent data set.

RESULTS

The development data set consisted of 316 cases of TAK and 323 comparators. The validation data set consisted of an additional 146 cases of TAK and 127 comparators. Age ≤60 years at diagnosis and imaging evidence of large-vessel vasculitis were absolute requirements to classify a patient as having TAK. The final criteria items and weights were as follows: female sex (+1), angina (+2), limb claudication (+2), arterial bruit (+2), reduced upper extremity pulse (+2), reduced pulse or tenderness of a carotid artery (+2), blood pressure difference between arms of ≥20 mm Hg (+1), number of affected arterial territories (+1 to +3), paired artery involvement (+1), and abdominal aorta plus renal or mesenteric involvement (+3). A patient could be classified as having TAK with a cumulative score of ≥5 points. When these criteria were tested in the validation data set, the model area under the curve was 0.97 (95% confidence interval [95% CI] 0.94-0.99) with a sensitivity of 93.8% (95% CI 88.6-97.1%) and specificity of 99.2% (95% CI 96.7-100.0%).

CONCLUSION

The 2022 American College of Rheumatology/EULAR classification criteria for TAK are now validated for use in research.

More losses than gains during one century of plant biodiversity change in Germany

Long-term analyses of biodiversity data highlight a 'biodiversity conservation paradox': biological communities show substantial species turnover over the past century^1,2, but changes in species richness are marginal^1,3-5. Most studies, however, have focused only on the incidence of species, and have not considered changes in local abundance. Here we asked whether analysing changes in the cover of plant species could reveal previously unrecognized patterns of biodiversity change and provide insights into the underlying mechanisms. We compiled and analysed a dataset of 7,738 permanent and semi-permanent vegetation plots from Germany that were surveyed between 2 and 54 times from 1927 to 2020, in total comprising 1,794 species of vascular plants. We found that decrements in cover, averaged across all species and plots, occurred more often than increments; that the number of species that decreased in cover was higher than the number of species that increased; and that decrements were more equally distributed among losers than were gains among winners. Null model simulations confirmed that these trends do not emerge by chance, but are the consequence of species-specific negative effects of environmental changes. In the long run, these trends might result in substantial losses of species at both local and regional scales. Summarizing the changes by decade shows that the inequality in the mean change in species cover of losers and winners diverged as early as the 1960s. We conclude that changes in species cover in communities represent an important but understudied dimension of biodiversity change that should more routinely be considered in time-series analyses.

ReSurveyGermany: Vegetation-plot time-series over the past hundred years in Germany

Vegetation-plot resurvey data are a main source of information on terrestrial biodiversity change, with records reaching back more than one century. Although more and more data from re-sampled plots have been published, there is not yet a comprehensive open-access dataset available for analysis. Here, we compiled and harmonised vegetation-plot resurvey data from Germany covering almost 100 years. We show the distribution of the plot data in space, time and across habitat types of the European Nature Information System (EUNIS). In addition, we include metadata on geographic location, plot size and vegetation structure. The data allow temporal biodiversity change to be assessed at the community scale, reaching back further into the past than most comparable data yet available. They also enable tracking changes in the incidence and distribution of individual species across Germany. In summary, the data come at a level of detail that holds promise for broadening our understanding of the mechanisms and drivers behind plant diversity change over the last century.

Measurement(s)	vegetation-plot resurvey data of vascular plant species
Technology Type(s)	vegetation-plot records
Factor Type(s)	Cover of species in plots
Sample Characteristic - Organism	Vascular plant species
Sample Characteristic - Environment	Terrestrial habitats
Sample Characteristic - Location	Germany

SUFU haploinsufficiency causes a recognisable neurodevelopmental phenotype at the mild end of the Joubert syndrome spectrum

BACKGROUND

Joubert syndrome (JS) is a recessively inherited ciliopathy characterised by congenital ocular motor apraxia (COMA), developmental delay (DD), intellectual disability, ataxia, multiorgan involvement, and a unique cerebellar and brainstem malformation. Over 40 JS-associated genes are known with a diagnostic yield of 60%-75%.In 2018, we reported homozygous hypomorphic missense variants of the SUFU gene in two families with mild JS. Recently, heterozygous truncating SUFU variants were identified in families with dominantly inherited COMA, occasionally associated with mild DD and subtle cerebellar anomalies.

METHODS

We reanalysed next generation sequencing (NGS) data in two cohorts comprising 1097 probands referred for genetic testing of JS genes.

RESULTS

Heterozygous truncating and splice-site SUFU variants were detected in 22 patients from 17 families (1.5%) with strong male prevalence (86%), and in 8 asymptomatic parents. Patients presented with COMA, hypotonia, ataxia and mild DD, and only a third manifested intellectual disability of variable severity. Brain MRI showed consistent findings characterised by vermis hypoplasia, superior cerebellar dysplasia and subtle-to-mild abnormalities of the superior cerebellar peduncles. The same pattern was observed in two out of three tested asymptomatic parents.

CONCLUSION

Heterozygous truncating or splice-site SUFU variants cause a novel neurodevelopmental syndrome encompassing COMA and mild JS, which likely represent overlapping entities. Variants can arise de novo or be inherited from a healthy parent, representing the first cause of JS with dominant inheritance and reduced penetrance. Awareness of this condition will increase the diagnostic yield of JS genetic testing, and allow appropriate counselling about prognosis, medical monitoring and recurrence risk.

Discovery of Clinical Candidate CHF-6366: A Novel Super-soft Dual Pharmacology Muscarinic Antagonist and β2 Agonist (MABA) for the Inhaled Treatment of Respiratory Diseases

The development of molecules embedding two distinct pharmacophores acting as muscarinic antagonists and β₂ agonists (MABAs) promises to be an excellent opportunity to reduce formulation issues and boost efficacy through cross-talk and allosteric interactions. Herein, we report the results of our drug discovery campaign aimed at improving the therapeutic index of a previous MABA series by exploiting the super soft-drug concept. The incorporation of a metabolic liability, stable at the site of administration but undergoing rapid systemic metabolism, to generate poorly active and quickly eliminated fragments was pursued. Our SAR studies yielded MABA 29, which demonstrated a balanced in vivo profile up to 24 h, high instability in plasma and the liver, as well as sustained exposure in the lung. In vitro safety and non-GLP toxicity studies supported the nomination of 29 (CHF-6366) as a clinical candidate, attesting to the successful development of a novel super-soft MABA compound.

Chemical Affinity of Ag-Exchanged Zeolites for Efficient Hydrogen Isotope Separation

We report an ion-exchanged zeolite as an excellent candidate for large-scale application in hydrogen isotope separation. Ag(I)-exchanged zeolite Y has been synthesized through a standard ion-exchange procedure. The D₂/H₂ separation performance has been systematically investigated via thermal desorption spectroscopy (TDS). Undercoordinated Ag⁺ in zeolite AgY acts as a strong adsorption site and adorbs preferentially the heavier isotopologue even above liquid nitrogen temperature. The highest D₂/H₂ selectivity of 10 is found at an exposure temperature of 90 K. Furthermore, the high Al content of the zeolite structure leads to a high density of Ag sites, resulting in a high gas uptake. In the framework, approximately one-third of the total physisorbed hydrogen isotopes are adsorbed on the Ag sites, corresponding to 3 mmol/g. A density functional theory (DFT) calculation reveals that the isotopologue-selective adsorption of hydrogen at Ag sites contributes to the outstanding hydrogen isotope separation, which has been directly observed through cryogenic thermal desorption spectroscopy. The overall performance of zeolite AgY, showing good selectivity combined with high gas uptake, is very promising for future technical applications.

Silver-exchanged zeolite Y was synthesized for efficient and effective separation of hydrogen isotopes above liquid nitrogen temperature via chemical affinity sieving. The highest D₂/H₂ selectivity of 10 is achieved at 90 K combined with a high gas uptake, making zeolite AgY a promising candidate for large-scale deuterium enrichment.

POS1261 CLINICAL RESPONSE PREDICTORS OF TOCILIZUMAB THERAPY IN PATIENTS WITH SEVERE COVID-19

Background

Aberrant immune response is hallmark of severe COVID-19, irrespectively from viral replication. Immunomodulatory therapies such as interleukin-6 (IL-6) receptor inhibitors were proven to be beneficial in reducing in-hospital mortality1. Yet, it remains unclear which patients can benefit most from such therapy.

Objectives

To identify predictors of clinical response to tocilizumab (TCZ) added to dexamethasone in patients hospitalized with severe COVID-19.

Methods

We prospectively assessed clinical and laboratory details of 120 patients hospitalized due to severe COVID-19 treated with TCZ (two doses of 8 mg/kg 24h apart) in our ward between 1st Feb 2021 and 31st Dec 2021. Severe COVID-19 was defined as SpO2 <94% on room air with ground glass opacities in chest computed tomography (CT). Clinical response was defined as respiratory improvement on day 5 after TCZ infusion compared to day of treatment initiation, no further deterioration and survival. Decision of adding TCZ to dexamethasone as emergency therapy was made collectively by rheumatologists experienced in COVID-19 treatment. Laboratory and clinical parameters from hospital admission day and from TCZ institution day were analyzed. Statistical analysis was conducted with PQStat v.1.8.2 and predictors were identified in univariate logistic regression.

Results

We identified 86 (71.7%) clinical responders and 34 (28.3%) non-responders. 20 (58.8%) of the second group needed ICU admission, 18 (52.9%) died on ICU and 2 patients (5.9%) died on the ward. Responders were significantly younger (mean age 56.1 vs. 63.5 years, p=0.006), had lesser comorbidity burden (median Charleson Comorbidity Index 2 vs. 3, p=0.005), lower median lung involvement (50 vs. 70%, p<0.001), higher median baseline PaO2/FiO2 index (203 vs. 106, p<0.001) and less of them needed high-flow oxygen therapy on TCZ initiation day (12.7% vs 32.4%, p=0.025).

Identified predictors of clinical response are shown in Table 1.

Table 1.

Predictors of good response to TCZ therapy in severe COVID-19. Apart from PaO2/FiO2 all parameters identified as predictors were measured on TCZ initiation day.

PredictorOR95%CIp valueLDH <447 U/l12.674.42-36.31<0.001<70% of lungs involved in CT6.762.63-17.36<0.0019-12 days from symptoms onset6.431.82-22.730.004RR <20/min5.402.29-12.75<0.001hs-TnI <26 ng/l4.801.55-14.810.006BUN <22.2 mg/dl4.712.02-10.99<0.001SpO2/FiO2 >1224.471.92-10.40<0.001fibrinogen ≥490 mg/dl4.461.86-10.72<0.001no history of asthma/COPD4.391.55-16.710.030no history of atrial fibrillation4.201.23-14.330.022baseline PaO2/FiO2 >200 mmHg4.041.59-10.270.00325(OH)D3 ≥30 ng/ml3.981.40-11.280.009age <65 years3.691.60-8.460.002no history of ischaemic heart disease3.561.29-9.790.014procalcitonin 0.06-0.12 ng/ml3.201.20-8.540.020D-Dimer ≤1.28 µg/ml3.121.37-7.090.006IL-6 47.4-137.0 pg/ml3.071.90-4.98<0.001

OR – odds ratio, 95%CI – 95% confidence interval, LDH – lactate dehydrogenase, RR – respiratory rate, hs-TnI – high sensitivity troponin I, BUN – blood urea nitrogen, COPD – chronic obstructive pulmonary disease, 25(OH)D3 – 25-hydroxycholecalciferol, IL-6 – interleukin 6

Conclusion

Administration of TCZ early in severe disease, with moderate IL-6 concentration and low organ damage indices is most beneficial in patients with severe COVID-19, especially in younger patients without respiratory and cardiac comorbidities.

References

[1]RECOVERY Collaborative Group. Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet Lond Engl. 2021;397:1637-1645.

Disclosure of Interests

None declared

Protein and antibody purification followed by immunoprecipitation of MYB and GATA zinc finger-type maize proteins with magnetic beads

Co-immunoprecipitation (Co-IP) is a widely used and powerful approach for studying protein-protein interactions in vivo. Here, we describe a protocol for antibody purification and immobilization followed by immunoprecipitation from plant tissue extracts using magnetic beads. The protocol has been used to detect regulators in the Zea mays phenylpropanoid pathway. The protocol is amenable to a variety of downstream assays, including western blotting and mass spectrometry.

For complete details on the use and execution of this protocol, please refer to Vélez-Bermúdez et al. (2015).

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Protein expression and purification of MBP fusions

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Affinity purification of antibodies

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Immunoprecipitation from maize cell extracts with magnetic beads

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Amenable to downstream assays like mass spec and western blot

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Infection by phloem-limited phytoplasma affects mineral nutrient homeostasis in tomato leaf tissues

Phytoplasmas are sieve-elements restricted wall-less, pleomorphic pathogenic microorganisms causing devastating damage to over 700 plant species worldwide. The invasion of sieve elements by phytoplasmas has several consequences on nutrient transport and metabolism, anyway studies about changes of the mineral-nutrient profile following phytoplasma infections are scarce and offer contrasting results. Here, we examined changes in macro- and micronutrient concentration in tomato plant upon 'Candidatus Phytoplasma solani' infection. To investigate possible effects of 'Ca. P. solani' infection on mineral element allocation, the mineral elements were separately analysed in leaf midrib, leaf lamina and root. Moreover, we focused our analysis on the transcriptional regulation of genes encoding trans-membrane transporters of mineral nutrients. To this aim, a manually curated inventory of differentially expressed genes encoding transporters in tomato leaf midribs was mined from the transcriptional profile of healthy and infected tomato leaf midribs. Results highlighted changes in ion homeostasis in the host plant, and significant modulations at transcriptional level of genes encoding ion transporters and channels.

A Quick Method to Quantify Iron in Arabidopsis Seedlings

Iron (Fe) is an indispensable micronutrient for plant growth and development. Since both deficiency, as well as a surplus of Fe, can be detrimental to plant health, plants need to constantly tune uptake rates to maintain an optimum level of Fe. Quantification of Fe serves as an important parameter for analyzing the fitness of plants from different accessions, or mutants and transgenic lines with altered expression of specific genes. To quantify metals in plant samples, methods based on inductively coupled plasma-optical emission spectrometry (ICP-OES) or inductively coupled plasma-mass spectrometry (ICP-MS) have been widely employed. Although these methods are highly accurate, these methodologies rely on sophisticated equipment which is not always available. Moreover, ICP-OES and ICP-MS allow for surveying several metals in the same sample, which may not be necessary if only the Fe status is to be determined. Here, we outline a simple and cost-efficient protocol to quantify Fe concentrations in roots and shoots of Arabidopsis seedlings, by using a spectroscopy-based assay to quantify Fe²⁺-BPDS₃ complexes against a set of standards. This protocol provides a fast and reproducible method to determine Fe levels in plant samples with high precision and low costs, which does not depend on expensive equipment and expertise to operate such equipment.

Ethylene Response Factor109 Attunes Immunity, Photosynthesis, and Iron Homeostasis in Arabidopsis Leaves

Iron (Fe) is an essential micronutrient element for all organisms including plants. Chlorosis of young leaves is a common symptom of Fe deficiency, reducing the efficiency of photosynthesis, and, ultimately, crop yield. Previous research revealed strong responsiveness of the putative key transcription factor ERF109 to the Fe regime. To elucidate the possible role of ERF109 in leaf Fe homeostasis and photosynthesis, we subjected Arabidopsis thaliana erf109 knockout lines and Col-0 wild-type plants to transcriptome profiling via RNA-seq. The transcriptome profile of Fe-sufficient erf109 leaves showed a 71% overlap with Fe-deficient Col-0 plants. On the other hand, genes that were differentially expressed between Fe-deficient and Fe-sufficient Col-0 plants remained unchanged in erf109 plants under conditions of Fe deficiency. Mutations in ERF109 increased the expression of the clade Ib bHLH proteins bHLH38, bHLH39, bHLH101, the nicotianamine synthase NAS4, and the Fe storage gene FER1. Moreover, mutations in ERF109 led to significant down-regulation of defense genes, including CML37, WRKY40, ERF13, and EXO70B2. Leaves of erf109 exhibited increased Fe levels under both Fe-sufficient and Fe-deficient conditions. Reduced Fv/Fm and Soil Plant Analysis Development (SPAD) values in erf109 lines under Fe deficiency indicate curtailed ability of photosynthesis relative to the wild-type. Our findings suggest that ERF109 is a negative regulator of the leaf response to Fe deficiency. It further appears that the function of ERF109 in the Fe response is critical for regulating pathogen defense and photosynthetic efficiency. Taken together, our study reveals a novel function of ERF109 and provides a systematic perspective on the intertwining of the immunity regulatory network and cellular Fe homeostasis.

A cluster-randomised trial to evaluate an intervention to promote handwashing in rural Nigeria

Handwashing with soap at critical times helps prevent diarrhoeal diseases. Changing handwashing practices through behaviour change communication remains a challenge. This study designed and tested a scalable intervention to promote handwashing with soap. A cluster-randomised, controlled trial compared our intervention against standard practice. Subjects were men, women and children in 14 villages in Cross-River state, Nigeria. The primary outcome was the proportion of observed key events on which hands were washed with soap. Binomial regression analysis calculated prevalence differences between study arms. The intervention had minimal effect on the primary outcome (+2.4%, p = 0.096). The intervention was associated with increased frequency of handwashes without soap before food contact (+13%, p = 0.017). The intervention failed to produce significant changes in handwashing with soap at key times. The low dose delivered (two contact points) may have increased scalability at the cost of effectiveness, particularly in the challenging context of inconvenient water access.

How Plants Recalibrate Cellular Iron Homeostasis

Insufficient iron supply poses severe constraints on plants, restricting species with inefficient iron uptake mechanisms from habitats with low iron availability and causing yield losses in agricultural ecosystems. Iron deficiency also poses a severe threat on human health. Anemia resulting from insufficient iron intake is affecting one of four people in the world. It is, therefore, imperative to understand the mechanisms by which plants acquire iron against a huge soil-cell gradient and how iron is distributed within the plant to develop strategies that increase its concentration in edible plant parts. Research into the processes that are employed by plants to adjust cellular iron homeostasis revealed an astonishingly complex puzzle of signaling nodes and circuits, which are intertwined with the perception and communication of other environmental cues such as pathogens, light, nutrient availability and edaphic factors such as pH. In a recent Spotlight issue in this journal, a collection of review articles summarized the state-of-the-art in plant iron research, covering the most active and, debatably, most important topics in this field. Here, we highlight breakthroughs that were reported after the publication date of this review collection, focusing on exciting and potentially influential studies that have changed our understanding of plant iron nutrition.

A highly virulent variant of HIV-1 circulating in the Netherlands

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log₁₀ increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.

Genomically Hardwired Regulation of Gene Activity Orchestrates Cellular Iron Homeostasis in Arabidopsis

Iron (Fe) is an essential micronutrient which plays pivotal roles as electron donor and catalyst across organisms. In plants, variable, often insufficient Fe supply necessitates mechanisms that constantly attune Fe uptake rates and recalibrate cellular Fe homoeostasis. Here, we show that short-term (0.5, 6, and 12 h) exposure of Arabidopsis thaliana plants to Fe deficiency triggered massive changes in gene activity governed by transcription and alternative splicing (AS), regulatory layers that were to a large extent mutually exclusive. Such preclusion was not observed for genes that are directly involved in the acquisition of Fe, which appears to be concordantly regulated by both expression and AS. Generally, genes with lower splice site strengths and higher intron numbers were more likely to be regulated by AS, no dependence on gene architecture was observed for transcriptionally controlled genes. Conspicuously, specific processes were associated with particular genomic features and biased towards either regulatory mode, suggesting that genomic hardwiring is functionally biased. Early changes in splicing patterns were, in many cases, congruent with later changes in transcript or protein abundance, thus contributing to the pronounced transcriptome-proteome discordance observed in plants.

From 1D to 3D Graphitic Carbon Nitride (Melon): A Bottom-Up Route via Crystalline Microporous Templates

Herein, we present a novel bottom-up preparation route for heptazine-based polymers (melon), also known as graphitic carbon nitride. The growth characteristics of isolated 1D melon strings in microporous templates are presented and studied in detail. Removal of the microporous silicate template via etching is accompanied by the self-assembly of a 1D melon to stacked 3D structures. The advantages and limitations of the bottom-up approach are shown by using microporous templates with different pore sizes (ETS-10, ZSM-5, and zeolite Y). In accordance with the molecular size of the heptazine units (0.67 nm), a 1D melon can be deposited in ETS-10 with a pore width of about 0.78 nm, whereas its formation in the smaller 0.47 nm pores of ZSM-5 is sterically impeded. The self-assembly of isolated 1D melon to stacked 3D structures offers a novel experimental perspective to the controversial debate on the polymerization degree in 2D sheets of graphitic carbon nitride as micropore sizes below 1 nm confine the condensation degree of heptazine to isolated 1D strands at a molecular level. The growth characteristics and structural features were investigated by X-ray diffraction, N2 physisorption, scanning transmission electron microscopy/energy-dispersive X-ray analysis, 13C CP-NMR spectroscopy, and attenuated total reflection-infrared spectroscopy.

Directional turnover towards larger-ranged plants over time and across habitats

Species turnover is ubiquitous. However, it remains unknown whether certain types of species are consistently gained or lost across different habitats. Here, we analysed the trajectories of 1827 plant species over time intervals of up to 78 years at 141 sites across mountain summits, forests, and lowland grasslands in Europe. We found, albeit with relatively small effect sizes, displacements of smaller- by larger-ranged species across habitats. Communities shifted in parallel towards more nutrient-demanding species, with species from nutrient-rich habitats having larger ranges. Because these species are typically strong competitors, declines of smaller-ranged species could reflect not only abiotic drivers of global change, but also biotic pressure from increased competition. The ubiquitous component of turnover based on species range size we found here may partially reconcile findings of no net loss in local diversity with global species loss, and link community-scale turnover to macroecological processes such as biotic homogenisation.

Crystal Structures of Two Titanium Phosphate-Based Proton Conductors: Ab Initio Structure Solution and Materials Properties

Transition-metal phosphates show a wide range of chemical compositions, variations of the valence states, and crystal structures. They are commercially used as solid-state catalysts, cathode materials in rechargeable batteries, or potential candidates for proton-exchange membranes in fuel cells. Here, we report on the successful ab initio structure determination of two novel titanium pyrophosphates, Ti(III)p and Ti(IV)p, from powder X-ray diffraction (PXRD) data. The low-symmetry space groups P2₁/c for Ti(III)p and P1̅ for Ti(IV)p required the combination of spectroscopic and diffraction techniques for structure determination. In Ti(III)p, trivalent titanium ions occupy the center of TiO₆ polyhedra, coordinated by five pyrophosphate groups, one of them as a bidentate ligand. This secondary coordination causes the formation of one-dimensional six-membered ring channels with a diameter d_max of 3.93(2) Å, which is stabilized by NH₄⁺ ions. Annealing Ti(III)p in inert atmospheres results in the formation of a new compound, denoted as Ti(IV)p. The structure of this compound shows a similar three-dimensional framework consisting of [PO₄]^3– tetrahedra and Ti^IV+O₆ octahedra and an empty one-dimensional channel with a diameter d_max of 5.07(1) Å. The in situ PXRD of the transformation of Ti(III)p to Ti(IV)p reveals a two-step mechanism, i.e., the decomposition of NH₄⁺ ions in a first step and subsequent structure relaxation. The specific proton conductivity and activation energy of the proton migration of Ti(III)p, governed by the Grotthus mechanism, belong to the highest and lowest, respectively, ever reported for this class of materials, which reveals its potential application in electrochemical devices like fuel cells and water electrolyzers in the intermediate temperature range.

The crystal structures of two novel transition-metal phosphates were solved via the combination of spectroscopic and diffraction methods. The reaction mechanism of the transformation of the structures was studied in situ. Additionally, the proton conductivity of the compounds was analyzed.

Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling

Background

Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE 6 (AL6), a bona fide histone reader that preferentially binds trimethylated lysin 4 on histone 3 (H3K4me3), is critical for recalibration of cellular phosphate (Pi) homeostasis and root hair elongation under Pi-deficient conditions.

Results

Here, we demonstrate that AL6 is also involved in the response of Arabidopsis seedlings to jasmonic acid (JA) during skotomorphogenesis, possibly by modulating chromatin dynamics that affect the transcriptional regulation of JA-responsive genes. Dark-grown al6 seedlings showed a compromised reduction in hypocotyl elongation upon exogenously supplied JA, a response that was calibrated by the availability of Pi in the growth medium. A comparison of protein profiles between wild-type and al6 mutant seedlings using a quantitative Chromatin Enrichment for Proteomics (ChEP) approach, that we modified for plant tissue and designated ChEP-P (ChEP in Plants), yielded a comprehensive suite of chromatin-associated proteins and candidates that may be causative for the mutant phenotype.

Conclusions

Altered abundance of proteins involved in chromatin organization in al6 seedlings suggests a role of AL6 in coordinating the deposition of histone variants upon perception of internal or environmental stimuli. Our study shows that ChEP-P is well suited to gain holistic insights into chromatin-related processes in plants. Data are available via ProteomeXchange with identifier PXD026541.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08160-6.