Adequate Patient Characterization in COPD: Reasons to Go Beyond GOLD Classification

The Global Initiative for Chronic Obstructive Lung Disease (GOLD) serves as a guide to treat and manage different severity classes of patients with COPD. It was suggested that the five categories of FEV1 % predicted (GOLD 0–4), can be applied for selecting different therapeutic approaches. However, validation of these selective properties is very poor. To determine the relevance of the GOLD staging system for estimating the severity of clinical problems, GOLD 2 (n=70) and GOLD 3 (n=65) patients were drawn from a prospective cohort of patients with COPD and evaluated crosssectionally by a newly developed Nijmegen Integral Assessment Framework (NIAF). The NIAF is a detailed assessment of a wide range of aspects of health status (HS). Significant, though small, differences were found in Static Lung Volumes, Exercise Capacity, Subjective Pulmonary Complaints, Subjective Impairment, and Health-Related QoL, besides Airflow of course. Moreover, overlap between scores of these five HS sub-domains was substantial, indicating small clinical relevance for discernment. No significant differences were found in nine other aspects of HS. It is concluded that GOLD stages do not discriminate in any aspect of HS other than airflow obstruction, and therefore do not help the clinician in deciding which treatment modalities are appropriate

Stable isotope record of Triceratops from a mass accumulation (Lance Formation, Wyoming, USA) provides insights into Triceratops behaviour and ecology

Our understanding of Late Cretaceous dinosaur ecosystems from North America has considerably improved through stable isotope analyses on fossil bones and teeth. Oxygen and carbon stable isotopic compositions of structurally-bound carbonate in these fossil apatites are commonly used to infer variations of ingested water and food sources, which are in turn related to environmental and climatic conditions. Incremental isotopic records potentially provide insights into seasonality and migratory behaviour. So far, these reconstructions are based on vertebrate remains from spatiotemporally diverse datasets. Here, we present oxygen (δ18O) and carbon (δ13C) isotopic records from a large, spatially and temporally well-constrained, Triceratops bonebed from the Upper Maastrichtian Lance Formation (eastern Wyoming. USA). These isotopic compositions allow to elucidate the palaeoecology of these large herbivores and their ecosystem in detail, as well as their habitat use, diet and possible migration. The δ18O signature from incrementally sampled Triceratops teeth reveal relatively low intra-tooth variation (average 1.3 ‰), comparable to contemporaneous dinosaur species as well as modern herbivorous mammals. Average δ13C values (−5.4 ‰) are somewhat higher than for modern C3 plant grazers, and hint towards complex interactions during carbon uptake by non-avian herbivorous dinosaurs. Calculated δ18O of drinking water (−14.8 ‰) combined with the local sedimentology of fine-grained siliciclastic deposits with high total organic and low carbonate contents strongly suggest a freshwater environment. Additionally, the combined average δ18O and δ13C Triceratops isotope signatures indicate a living environment intermediate between inland forests and coastal floodplains, expanding on earlier theories of ornithischian niche partitioning. Our robust dataset provides meaningful tests of habitat and palaeoecological hypotheses for Triceratops, and highlights the application of spatiotemporally well-constrained fossil remains

Development of a battery of instruments for detailed measurement of health status in patients with COPD in routine care: the Nijmegen Clinical Screening Instrument

Contains fulltext : 80284.pdf (publisher's version ) (Closed access)PURPOSE: To compose a battery of instruments that provides a detailed assessment of health status (HS) in COPD but that is applicable and clinically meaningful in routine care. METHODS: In a previous study, we developed the Nijmegen Integral Assessment Framework (NIAF) that organizes existing tests and instruments by the sub-domains of HS they measure. Based on clinical and statistical criteria (correlation coefficients and Cronbach alpha's) we selected for each sub-domain instruments from the NIAF. A COPD-study group was used to determine c-scores, and two control groups were used to determine the score ranges indicating normal functioning versus clinically relevant problems for each sub-domain. Existing questionnaire completion software (TestOrganiser) was adapted to enhance clinical applicability. RESULTS: The NCSI measures eleven sub-domains of physiological functioning, symptoms, functional impairment, and quality of life. The TestOrganiser automatically processes the data and produces the graphical PatientProfileChart, which helps to easily interpret results. This envisages the problem areas and discrepancies between the different sub-domains. CONCLUSION: The NCSI provides a valid and detailed picture of a patient's HS within 15-25 min. In combination with the PatientProfileChart, the NCSI can be used perfectly in routine care as screening instrument and as a guide in patient-tailored treatment

Ambient temperature‐directed flowering time regulation : the role of alternative splicing

As a consequence of a sessile lifestyle, plants are constantly facing a fluctuating environment. In order to both profit maximally and protect themselves from these environmental cues, plants evolved ways to sense and respond to signals. Ambient temperature is one of the cues for which plants have acquired a strategy to enhance their chance of survival and reproduction. Small changes in ambient temperature can have major effects on plant architecture and development, such as the transition from the vegetative to the reproductive flowering phase. The moment of flowering is an important event in the life cycle of a plant, since reproductive success depends on it. In Chapter 1, I introduced the concept of alternative splicing, a molecular mechanism with a pivotal role in ambient temperature regulation of flowering time. In the model plant Arabidopsis thaliana, approximately 60% of the intron-containing genes show alternative splicing. Gene splicing varies depending on developmental stage and tissue type, but also environmental changes trigger differential splicing. Splicing is conducted by a large cellular machinery called the spliceosome, which recognizes intron-defining sequences and other cis-regulatory elements acting as splicing enhancers or silencers. Moreover, factors like chromatin structure, histone marks, RNA polymerase II (polII) elongation speed and the secondary structure of the pre-mRNA all play a role in the splicing outcome. Due to alternative splicing, a single gene can yield various transcripts. However, this does not cause an equal expansion of the proteome. Part of the transcripts are targeted for nonsense-mediated decay, or will be translated into unstable proteins. This is a way of regulating gene expression at the post-transcriptional or –translational level. Other transcripts will be translated into functional proteins that may be structurally and functionally different. Hence, alternative splicing creates additional complexity in the transcriptome, providing plants with molecular tools to respond to their environment, including the translation of ambient temperature alterations into a flowering time response. In Chapter 2, we reviewed the current knowledge on molecular mechanisms that control the ambient-temperature directed flowering time pathway in the plant model species Arabidopsis thaliana. Several different mechanisms have been proposed, like alternative splicing of FLOWERING LOCUS M (FLM) (described in Chapter 4) and protein degradation of SHORT VEGETATIVE PHASE (SVP), two mechanisms that probably work in a cooperative manner to release floral repression at higher ambient temperatures. Another mechanism that is involved at high ambient temperature is the replacement of the canonical histone H2A by the variant H2A.Z. As a consequence of this replacement, chromatin becomes less tightly wrapped around the nucleosomes, which allows transcription of flowering time activators, such as PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Lastly, we discuss microRNAs (miRNA) that can either repress or activate flowering (miR156 and miR172, respectively). These miRNAs have been proposed to be regulated by low and high ambient temperature. However, due to the lack of mutant analyses, more research is necessary to show the true involvement of these factors. Altogether, there are several mechanisms acting partly in cooperation to regulate thermosensitive floral timing. In Chapter 3, we analysed ambient temperature-directed alternative splicing events that occur after a temperature shift by RNAseq. We performed the experiment in two different accessions of A. thaliana, and in one variant of B. oleracea (cauliflower). We showed that flowering time genes are overrepresented amongst the ambient temperature induced alternatively spliced genes, but also genes encoding components of the splicing machinery itself, indicating that alternative splicing is one of the potential mechanisms by which plants are able to sense temperature and adapt floral timing. Analysis of a mutant for one of these alternatively-spliced splicing related factors, ATU2AF65A, showed a temperature-dependent flowering time phenotype, confirming its proposed role in the flowering time response upon temperature fluctuations. Based on these findings, we proposed a two-step model in which splicing related genes are targeted for differential splicing upon ambient temperature fluctuations, which results in changes in the composition of the spliceosome, causing differential splicing of downstream genes that affect the development and architecture of the plant, including flowering time. In Chapter 4, we investigated the molecular mode-of-action of FLM, one of the differentially spliced flowering time regulating genes that we identified in Chapter 3. We showed that in A. thaliana Col-0, the main splice forms of FLM are FLMβ and FLMδ. FLMβ forms an obligate heterodimer with SVP, and this complex represses floral integrators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) by binding to the regulatory regions of these genes. FLMδ also dimerizes with SVP, but this complex is not able to bind to DNA. When temperature rises, more FLMδ is produced at the cost of FLMβ. Hence, less repressive complexes can be formed. However, the fact that FLMδ is still able to binds SVP makes it function as a dominant negative form, titrating out SVP and preventing repressive SVP/FLMβ-complex formation. Chapter 5 is a short comment written to clarify the concept of thermoplasticity in flowering time control. Occasionally, this concept is confused with adaptation to different ambient temperature environments on the long term. Thermoplasticity is the ability to adapt flowering time to fluctuations in ambient temperature within one life cycle. Furthermore, some genes have been marked as players in the ambient temperature response, whereas these appear to be general flowering repressors or activators, affecting flowering time in a similar manner at low and high ambient temperature. In order to interpret novel findings on thermosensitive flowering time control, it is essential to distinguish between these various concepts. In chapter 6, we unveiled the first indications that differential splicing of FLM can be caused by differences in polymerase II elongation rate. We mimicked a situation in which FLM is transcribed at a higher rate, by expressing the genomic FLM gene under a strong artificial promoter. Preliminary results showed that plants harbouring this construct have altered flowering time and temperature-responsiveness, which can be explained by the altered FLMβ/FLMδ ratio that we observed. In chapter 7, we assessed the functional conservation between FLM and closely related genes at the intraspecific level in A. thaliana. FLM (also called MAF1) is a member of the FLC-clade, that consists of FLC, FLM and MAF2-5. FLC is widely known for its function in the vernalization pathway, whereas MAF2 has been shown to regulate flowering time through alternative splicing in a way very similar to FLM. For the other MAF genes, not much is known. We showed that all of these genes produce splicing isoforms that function in a more or less similar way to FLM and MAF2. Despite the high functional conservation at the intraspecific level, FLM and MAF orthologues are not widely present. Through synteny analysis, we showed that FLM and MAF2 are very recent genes, which are only present in a small group of Brassicaceae species. MAF3-5 originated less recently, but are not present outside the Brassicaceae. For FLC, it was previously shown that it originated from an ancestor of the seed plants, and in many plant species belonging to other families, presence of more than one FLC-like gene has been reported. This raises the question what the function of these genes is. In tomato, we showed that the FLC-like gene MBP8 becomes differentially spliced upon temperature changes, suggesting a function in the ambient temperature pathway. A binding assay showed high similarities of the different MBP8 isoforms to FLM and MAF isoforms, but suggests a slightly different functionality, since all three isoforms showed binding to the DNA. Further research is necessary to confirm the role of MBP8 in thermosensitive flowering time control, and elucidate the functionality of the different splice forms. In Chapter 8, I discussed the finding of this thesis in a broader perspective, and make suggestions for future research. Over the last few years, several mechanisms that act in the temperature-directed floral pathway have been revealed. In this thesis, we showed that alternative splicing plays an important role, and we demonstrated how temperature may affect the splicing outcome directly through the effect of temperature on transcription elongation rate. It is becoming clear that most likely a single thermosensor does not exist in plants, and a model in which temperature is sensed through thermodynamic properties of DNA, RNA and proteins, is gaining support. Future research is assigned to the exiting task to elucidate the exact mechanisms by which temperature-sensing is achieved in different plant species and to determine how conserved the currently identified molecular mechanisms are

Plasticity versus Adaptation of Ambient-Temperature Flowering Response

It is challenging to understand how plants adapt flowering time to novel environmental conditions, such as global warming, while maintaining plasticity in response to daily fluctuating temperatures. A recent study shows a role for transposons and highlights the need to investigate how these different responses evolved

Pioneer Factors in Animals and Plants—Colonizing Chromatin for Gene Regulation

Unlike most transcription factors (TF), pioneer TFs have a specialized role in binding closed regions of chromatin and initiating the subsequent opening of these regions. Thus, pioneer TFs are key factors in gene regulation with critical roles in developmental transitions, including organ biogenesis, tissue development, and cellular differentiation. These developmental events involve some major reprogramming of gene expression patterns, specifically the opening and closing of distinct chromatin regions. Here, we discuss how pioneer TFs are identified using biochemical and genome-wide techniques. What is known about pioneer TFs from animals and plants is reviewed, with a focus on the strategies used by pioneer factors in different organisms. Finally, the different molecular mechanisms pioneer factors used are discussed, highlighting the roles that tertiary and quaternary structures play in nucleosome-compatible DNA-binding

Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants

Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica species exposed to temperature alterations, we showed that alternative splicing is an important mechanism in ambient temperature sensing and adaptation. We found that amongst the differentially alternatively spliced genes, splicing related genes are enriched, suggesting that the splicing machinery itself is targeted for alternative splicing when temperature changes. Moreover, we showed that many different components of the splicing machinery are targeted for ambient temperature regulated alternative splicing. Mutant analysis of a splicing related gene that was differentially spliced in two of the genotypes showed an altered flowering time response to different temperatures. We propose a two-step mechanism where temperature directly influences alternative splicing of the splicing machinery genes, followed by a second step where the altered splicing machinery affects splicing of downstream genes involved in the adaptation to altered temperatures

Stable isotope record of Triceratops from a mass accumulation (Lance Formation, Wyoming, USA) provides insights into Triceratops behaviour and ecology

Our understanding of Late Cretaceous dinosaur ecosystems from North America has considerably improved through stable isotope analyses on fossil bones and teeth. Oxygen and carbon stable isotopic compositions of structurally-bound carbonate in these fossil apatites are commonly used to infer variations of ingested water and food sources, which are in turn related to environmental and climatic conditions. Incremental isotopic records potentially provide insights into seasonality and migratory behaviour. So far, these reconstructions are based on vertebrate remains from spatiotemporally diverse datasets. Here, we present oxygen (δ18O) and carbon (δ13C) isotopic records from a large, spatially and temporally well-constrained, Triceratops bonebed from the Upper Maastrichtian Lance Formation (eastern Wyoming. USA). These isotopic compositions allow to elucidate the palaeoecology of these large herbivores and their ecosystem in detail, as well as their habitat use, diet and possible migration. The δ18O signature from incrementally sampled Triceratops teeth reveal relatively low intra-tooth variation (average 1.3 ‰), comparable to contemporaneous dinosaur species as well as modern herbivorous mammals. Average δ13C values (−5.4 ‰) are somewhat higher than for modern C3 plant grazers, and hint towards complex interactions during carbon uptake by non-avian herbivorous dinosaurs. Calculated δ18O of drinking water (−14.8 ‰) combined with the local sedimentology of fine-grained siliciclastic deposits with high total organic and low carbonate contents strongly suggest a freshwater environment. Additionally, the combined average δ18O and δ13C Triceratops isotope signatures indicate a living environment intermediate between inland forests and coastal floodplains, expanding on earlier theories of ornithischian niche partitioning. Our robust dataset provides meaningful tests of habitat and palaeoecological hypotheses for Triceratops, and highlights the application of spatiotemporally well-constrained fossil remains

Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants

<div><p>Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica species exposed to temperature alterations, we showed that alternative splicing is an important mechanism in ambient temperature sensing and adaptation. We found that amongst the differentially alternatively spliced genes, splicing related genes are enriched, suggesting that the splicing machinery itself is targeted for alternative splicing when temperature changes. Moreover, we showed that many different components of the splicing machinery are targeted for ambient temperature regulated alternative splicing. Mutant analysis of a splicing related gene that was differentially spliced in two of the genotypes showed an altered flowering time response to different temperatures. We propose a two-step mechanism where temperature directly influences alternative splicing of the splicing machinery genes, followed by a second step where the altered splicing machinery affects splicing of downstream genes involved in the adaptation to altered temperatures.</p></div