Development of psoriasis in IBD patients under TNF-antagonist therapy is associated neither with anti-TNF-antagonist antibodies nor trough levels

Background: The cause of anti-TNF-induced psoriasis is still unknown.

Objective: We aimed to evaluate if the appearance of psoriasis under anti-TNF therapy is associated with anti-TNF antibody levels and TNF-antagonist trough levels.

Methods: In this case-control study we identified 23 patients (21 with Crohn’s disease [CD], two with ulcerative colitis [UC]) who developed psoriasis under infliximab (IFX, n?=?20), adalimumab (ADA, n?=?2), and certolizumab pegol (CZP, n=?1) and compared them regarding the anti-TNF-antagonist antibody levels with 85 IBD patients (72 with CD, 13 with UC) on anti-TNF therapy without psoriasis.

Results: Median disease duration was not different between the two groups (7 years in the group with psoriasis under TNF-antagonists vs. 10 years in the control group, p?=?0.072). No patient from the psoriasis group had antibodies against TNF-antagonists compared to 10.6% in the control group (p?=?0.103). No difference was found in IFX trough levels in the group of patients with psoriasis compared to the control group (2.6?μg/mL [IQR 0.9–5.5] vs. 3.4?μg/mL [IQR 1.4–8.1], p?=?0.573). TNF-antagonist therapy could be continued in 91.3% of patients with TNF-antagonist related psoriasis and most patients responded to topical therapies.

Conclusion: Anti-TNF-induced psoriasis seems to be independent of anti-TNF antibodies and trough levels. Interruption of Anti-TNF therapy is rarely necessary.     

Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms

Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana. Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.Landsberg erecta (Ler) is presumably the second-most-used strain of Arabidopsis thaliana after the reference accession Columbia (Col-0). It is broadly known as Ler-0, which is an abbreviation for its accession code La-1 and a mutation in the ERECTA gene. In 1957, George Rédei, at the University of Missouri–Columbia, irradiated La-1 samples, which were provided by Friedrich Laibach and were collected in Landsberg an der Warthe (now called Gorzów Wielkopolski), Poland, where Ler-0–related genotypes are still present (1). Some seeds of the original batch were irradiated with X-rays, resulting, among others, in the isolation of the erecta (er) mutant (2, 3). Will Feenstra received this mutant from George Rédei in 1959 because he was interested in its erect growth habit and introduced it as the standard strain in the Department of Genetics at Wageningen University. There, he started a mutant induction program that was later continued by Jaap van der Veen and Maarten Koornneef. Mutants from this program as well as parental lines of recombinant inbred lines were mainly distributed as Ler-0 lines to other laboratories, reflecting the increasing interest in A. thaliana. Some descendants of Ler-0 were later renamed to Ler-1 and -2 to identify genotypes used in different laboratories, but most likely all derived from the original mutant isolated by Rédei, and we will collectively refer to them as “Ler.”First comparative analyses of the Ler genome included cytogenetic studies using pachytene cells and in situ hybridization (4, 5), suggesting a large inversion on the short arm of chromosome 4, as well as differences between 5S rDNA clusters compared with the genome of Col-0 (4). The first large-scale analysis of the Ler genome sequence was published together with the Col-0 reference sequence in 2000 (6). Within 92 Mb of random shotgun dideoxy sequencing reads, 25,274 SNPs and 14,570 indels were identified. Although this was a severe underestimation (7–11), the authors already observed that many of the large indels contained entire active genes, half of which were found at different loci in the genome of Ler, whereas others were entirely absent (6).The advent of next-generation sequencing greatly expanded the knowledge of natural genetic diversity in A. thaliana (reviewed in refs. 12 and 13). However, genome-wide studies on gene absence/presence polymorphisms were not repeated, because short-read analyses focused on small-scale changes only. To resolve large variation, reference-guided assemblies (8, 9, 14) and structural variation-identifying tools (15) were introduced. However, such methods mostly reveal local differences, which do not include the complement of large-scale rearrangements including inversions or transpositions.So far, two de novo assemblies of Ler have been published. The first was based on Illumina short-read data and resulted in an assembly with an N50 of 198 kb, showing similar performance as a reference-guided assembly (8). The second was based on a set of previously released Pacific Bioscience’s single-molecule, real-time sequencing (PacBio) data (16) and assembled the genome into 38 contigs with an N50 of 11.2 Mb (17). This drastic improvement outlines the potential of long-read sequencing technologies such as PacBio sequencing (18) to overcome the limitations of short-read methods because long reads can span many of the repetitive regions, which are presumably the most common reason for assembly breaks in short-read assemblies. Alternatively, low-fold long-read sequencing could be combined with cheaper short-read sequencing, either by using the short reads for error-correcting the long reads (19) or for integrating long-read information into short-read assemblies or vice versa (20).Despite the unprecedented contiguity of this long-read assembly, both earlier studies focused on methodological aspects and did not perform any whole-genome comparisons of the Ler genome or gene annotations, and, as a consequence, comprehensive reports on large-scale rearrangements and nonreference genes are still sparse. We have generated an advanced de novo assembly of Ler consisting of 117 Mb arranged into five sequences representing the five chromosomes, which is based on a combination of short-read assembly, long-read-based gap closure, and scaffolding based on genetic maps. This chromosome-scale assembly and its comparison with the reference assembly revealed features that are typically not analyzed within next-generation sequencing assemblies, including the location of a polymorphic rDNA cluster and centromeric repeats, as well as the exact makeup of all large rearrangements including a 1.2-Mb inversion on the short arm of chromosome 4. This inversion suppresses meiotic recombination in Ler and Col-0 hybrids, and we show that this suppression introduced genetically isolated inversion haplotypes into the worldwide population of A. thaliana. De novo gene annotation revealed hundreds of copy-number polymorphisms as well as novel genes that are entirely absent in one or the other genome. Finally, we report on variation in different Ler genomes, suggesting that some Ler lines feature unexpected footprints of an additional mutagenesis event.     

Identifying the origin of local flexibility in a carbohydrate polymer

Correlating the structures and properties of a polymer to its monomer sequence is key to understanding how its higher hierarchy structures are formed and how its macroscopic material properties emerge. Carbohydrate polymers, such as cellulose and chitin, are the most abundant materials found in nature whose structures and properties have been characterized only at the submicrometer level. Here, by imaging single-cellulose chains at the nanoscale, we determine the structure and local flexibility of cellulose as a function of its sequence (primary structure) and conformation (secondary structure). Changing the primary structure by chemical substitutions and geometrical variations in the secondary structure allow the chain flexibility to be engineered at the single-linkage level. Tuning local flexibility opens opportunities for the bottom-up design of carbohydrate materials.

Natural polymers adopt a multitude of three-dimensional structures that enable a wide range of functions (1). Polynucleotides store and transfer genetic information; polypeptides function as catalysts and structural materials; and polysaccharides play important roles in cellular structure (2–6), recognition (5), and energy storage (7). The properties of these polymers depend on their structures at various hierarchies: sequence (primary structure), local conformation (secondary structure), and global conformation (tertiary structure).Automated solid-phase techniques provide access to these polymers with full sequence control (8–12). The correlation between the sequence, the higher hierarchy structures, and the resulting properties is relatively well established for polynucleotides (13, 14) and polypeptides (15, 16), while comparatively little is known for polysaccharides (17). Unlike polypeptides and polynucleotides, polysaccharides are based on monosaccharide building blocks that can form multiple linkages with different configurations (e.g., α- or β-linkages) leading to extremely diverse linear or branched polymers. This complexity is exacerbated by the flexibility of polysaccharides that renders structural characterization by ensemble-averaged techniques challenging (17). Imaging single-polysaccharide molecules using atomic force microscopy has revealed the morphology and properties of polysaccharides at mesoscopic, submicrometer scale (18–22). However, imaging at such length scales precludes the observation of individual monosaccharide subunits required to correlate the polysaccharide sequence to its molecular structure and flexibility, the key determinants of its macroscopic functions and properties (23).Imaging polysaccharides at subnanometer resolution by combining scanning tunnelling microscopy (STM) and electrospray ion-beam deposition (ES-IBD) (24, 25) allows for the observation of their monosaccharide subunits to reveal their connectivity (26–28) and conformation space (29). Here, we use this technique to correlate the local flexibility of an oligosaccharide chain to its sequence and conformation, the lowest two structural hierarchies. By examining the local freedom of the chain as a function of its primary and secondary structures, we address how low-hierarchy structural motifs affect local oligosaccharide flexibility—an insight critical to the bottom-up design of carbohydrate materials (30).We elucidate the origin of local flexibility in cellulose, the most abundant polymer in nature, composed of glucose (Glc) units linked by β-1,4–linkages (31–33). Unveiling what affects the flexibility of cellulose chains is important because it gives rise to amorphous domains in cellulose materials (34–37) that change the mechanical performance and the enzyme digestibility of cellulose (38). Cellohexaose, a Glc hexasaccharide (Fig. 1A), was used as a model for a single-cellulose chain as it has been shown to resemble the cellulose polymer behavior (12). Modified analogs prepared by Automated Glycan Assembly (AGA) (11, 12) were designed to manipulate particular intramolecular interactions responsible for cellulose flexibility. Cellohexaose, ionized as a singly deprotonated ion in the gas phase ([M-H]⁻¹) was deposited on a Cu(100) surface held at 120 K by ES-IBD (24) (Materials and Methods). The ions were landed with 5-eV energy, well suited to access diverse conformation states of the molecule without inducing any chemical change in the molecule (29). The resulting cellohexaose observed in various conformation states allowed its mechanical flexibility (defined by the variance in the geometrical bending between two residues) to be quantified for every intermonomer linkage. The observed dependence of local flexibility on the oligosaccharide sequence and conformation thus exemplifies how primary and secondary structures tune the local mechanical flexibility of a carbohydrate polymer.Open in a separate windowFig. 1.STM images of cellohexaose (AAAAAA) and its analogs (AXAAXA). Structures and STM images of cellohexaose (A) and its substituted analogs (B–E). Cellohexaose contains six Glcs (labeled as A; colored black) linked via β-1,4–glycosidic bonds. The cellohexaose analogs contain two substituted Glcs, as the second and the fifth residues from the nonreducing end, that have a single methoxy (–OCH₃) at C(3) (labeled as B; colored red), two methoxy groups at C(3) and C(6) (labeled as C; colored green), a single carboxymethoxy (–OCH₂COOH) at C(3) (labeled as D; colored blue), and a single fluorine (–F) at C(3) (labeled as F; colored purple).The effect of the primary structure on the chain flexibility was explored using sequence-defined cellohexaose analogs (Fig. 1). Cellohexaose, AAAAAA (Fig. 1A), was compared with its substituted analogs, ABAABA, ACAACA, ADAADA, and AFAAFA (written from the nonreducing end) (Fig. 1 B–E), where A is Glc, B is Glc methylated at OH(3), C is Glc methylated at OH(3) and OH(6), D is Glc carboxymethylated at OH(3), and F is Glc deoxyfluorinated at C(3). These substitutions are designed to alter the intramolecular hydrogen bonding between the first and the second as well as between the fourth and fifth Glc units (Fig. 1). These functional groups also affect the local steric environment (i.e., the bulky carboxymethyl group) (Fig. 1D) and the local electronic properties (i.e., the electronegative fluorine group) (Fig. 1E). When compared with the unsubstituted parent cellohexaose, these modified cellohexaoses exhibit different aggregation behavior and are more water soluble (12).All cellohexaose derivatives adsorbed on the surface were imaged with STM at 11 K (Fig. 1). The oligosaccharides were deposited as singly deprotonated species and were computed to adsorb on the surface via a single covalent RO–Cu bond, except for ADAADA which was deposited as doubly deprotonated species and was computed to adsorb on the surface via two covalent RCOO–Cu bonds (R = sugar chain). All cellohexaoses appear as chains containing six protrusions corresponding to the six constituent Glcs. The unmodified cellohexaose chains (Fig. 1A) mainly adopt a straight geometry, while the substituted cellohexaoses (Fig. 1 B–E) adopt both straight- and bent-chain geometries. Chemical substitution thus increases the geometrical freedom of the cellulose chain, consistent with the reported macroscopic properties (12).Large-chain bending between neighboring Glc units is observed exclusively for the substituted cellohexaose (Fig. 1). The large, localized bending reveals the substitution site and allows for the nonreducing and the reducing ends of the chain to be identified. These chains are understood to bend along the surface plane via the glycosidic linkage without significant tilting of the pyranose ring that remains parallel to the surface (illustrated in SI Appendix, Fig. S1), as indicated by the ∼2.0-Å height of every Glc (29).The bending angle measured for AA and AX linkages (Fig. 2; Materials and Methods has analysis details) shows that, while both AA and AX prefer the straight, unbent geometry, AX displays a greater variation of bending angles than AA. AX angular distribution is consistently ∼10° wider than that for AA, indicating that AX has a greater conformational freedom than AA. This increased bending flexibility results from the absence of the intramolecular hydrogen bonding between OH(3) and O(5) of the neighboring residue. Methylation of OH(6), in addition to methylation of OH(3), results in similar flexibility (Fig. 2 B and C), suggesting the greater importance of OH(3) in determining the bending flexibility. Steric effects were found to be negligible since AD displayed similar flexibility to other less bulky AX linkages.Open in a separate windowFig. 2.Bending flexibility of AA linkage and substituted AX linkages. Chain bending (Fig. 1) is quantified as an angle formed between two neighboring Glcs (Materials and Methods). The results are given in A for AA, in B for AB, in C for AC, in D for AD, and in E for AF, showing that AX (where X = B, C, D, F) has a higher conformational freedom than AA. The angle distributions (bin size: 10°) are fitted with a Gaussian (solid line) shown with its half-width half-maximum. The computed potential energy curves are shown with the half-width at 0.4 eV and fitted with a parabola to estimate its stiffness (k; in millielectronvolts per degree²).Density functional theory (DFT) calculations support the observations, showing that substitution of OH(3) decreases the linkage stiffness by up to ∼40% (Fig. 2). Replacing OH(3) with other functional groups weakens the interglucose interactions by replacing the OH(3)··O(5) hydrogen bond with weak Van der Waals interactions. The similar flexibility between AB and AC linkages is attributed to the similar strength of the interglucose OH(2)··OH(6) hydrogen bond in AB (Fig. 2B) and the OH(2)··OMe(6) hydrogen bond in AC (Fig. 2C). The negligible steric effect in AD is attributed to the positional and rotational freedom of the bulky moiety that prevents any “steric clashes” and diminishes the contribution of steric repulsion in the potential energy curve. Comparing the potential landscape in the gas phase and on the surface shows that the stiffness of the adsorbed cellohexaoses is primarily dictated by their intramolecular interactions instead of molecule–surface interactions (SI Appendix, Fig. S2). Primary structure alteration by chemical substitution modifies the interglucose hydrogen bonds and enables chain flexibility to be locally engineered at the single-linkage level.We subsequently investigate how molecular conformation (secondary structure) affects the local bending flexibility. We define the local secondary structure as the geometry formed between two Glcs, here exemplified by the local twisting of the chain (Fig. 3). The global secondary structure is defined as the overall geometry formed by all Glcs in the chain, here exemplified by the linear and cyclic topologies of the chain (Fig. 4).Open in a separate windowFig. 3.Bending flexibility of untwisted and twisted AA linkages. (A) STM image of a cellohexaose containing two types of AA linkages: untwisted (HH and VV) and twisted (HV and VH; from the nonreducing end). The measured bending angles and the computed potential curve are given in B for HH, in C for HV, and in D for VV, showing that the twisted linkage (HV) is more flexible than the untwisted ones (HH and VV). In the molecular structures, interunit hydrogen bonds are given as dotted blue lines, and the pyranose rings are colored red for the horizontal ring (H) and green for vertical (V). The angle distributions (bin size: 10°) are fitted with a Gaussian distribution (solid line) labeled with its peak and half-width half-maximum. The computed potential curves are labeled with its half-width at 0.4 eV and fitted with a parabola to estimate its stiffness (k; in millielectronvolts per degree²).Open in a separate windowFig. 4.Bending flexibility of AA linkage in linear (LIN) and cyclic (CYC) chains. STM image, measured bending angle distribution, and computed potential of AA linkage are given in A for a linear cellohexaose conformer and in B for a cyclic cellohexaose conformer, showing that chain flexibility is reduced in conformations with cyclic topology. The same data are given in C for α-cyclodextrin that is locked in a conformation with cyclic topology. The measured angles (bin size: 10°) are each fitted with a Gaussian distribution (solid line) labeled with its peak and half-width half-maximum. The computed potentials are each labeled with its half-width at 0.4 eV and fitted with a parabola to estimate its stiffness (k; in millielectronvolts per degree²).The effect of local secondary structure on chain flexibility is exemplified by the bending flexibility of twisted and untwisted linkages in a cellohexaose chain (Fig. 3A). The untwisted and twisted linkages are present due to the Glc units observed in two geometries, H or V (Fig. 3), distinguished by their heights (h). H (h ∼ 2.0 Å) is a Glc with its pyranose ring parallel to the surface, while V (h ∼ 2.5 Å) has its ring perpendicular to the surface (29). These lead to HH and VV as untwisted linkages and HV and VH (written from nonreducing end) as twisted linkages.The twisted linkage is more flexible than the untwisted one, as shown by the unimodal bending angles for the untwisted linkage (HH and VV in Fig. 3 B and D, respectively) and the multimodal distribution for the twisted linkage (HV in Fig. 3C). DFT calculations attribute the increased bending flexibility to the reduction of accessible interunit hydrogen bonds from two to one. Linkage twisting increases the distance between the hydrogen-bonded pair, which weakens the interaction between Glc units and increases the flexibility at the twisting point. The increase in local chain flexibility conferred by chain twisting shows how local secondary structures affect chain flexibility.The effect of the global secondary structure on the local chain flexibility was examined by comparing the local bending flexibility of cellohexaose chains possessing different topologies. Cellohexaose can adopt either linear (Figs. 3A and ​and4A)4A) or cyclic topology (Fig. 4B), the latter characterized by the presence of a circular, head-to-tail hydrogen bond network (29). The cyclic conformation of cellohexaose is enabled by the head-to-tail chain folding from the 60° chain bending of the VV linkage. The VV segment in the cyclic chain is stiffer than in the linear chain since the bending angle distribution for the cyclic chain is 6° narrower than that for the linear chain. The observation is corroborated by DFT calculations that show that the VV linkage in the cyclic chain is about three times stiffer than that in the linear chain.To characterize the degree of chain stiffening due to the linear-to-cyclic chain folding, we compare the flexibility of the cyclic cellohexaose and α-cyclodextrin (an α-1,4–linked hexaglucose covalently locked in cyclic conformation). The α-cyclodextrin provides the referential local flexibility for a cyclic oligosaccharide chain. Strikingly, the local flexibility in α-cyclodextrin was found to be identical to that in the cyclic cellohexaose, as evidenced by the similar width of the bending angle distribution and the computed potentials (Fig. 4 B and C). The similar stiffness indicates that the folding-induced stiffening in cellohexaose is a general topological effect unaffected by the type of the interactions that give the cyclic conformation (noncovalent hydrogen bond in cellohexaose vs. covalent bond in α-cyclodextrin). The folding-induced stiffening is the result of the creation of a circular spring network that restricts the motion of Glc units and reduces their conformational freedom. The folding-induced stiffening reported here provides a mechanism by which carbohydrate structures can be made rigid. The dependence of the local chain flexibility on the chain topology shows how global secondary structures modify local flexibility.Using cellulose as an example, we have quantified the local flexibility of a carbohydrate polymer and identified structural factors that determine its flexibility. Modification of the carbohydrate primary structure by chemical substitution alters the mechanical flexibility at the single-linkage level. Changing secondary structure by chain twisting and folding provides additional means to modify the flexibility of each linkage. Control of these structural variables enables tuning of polysaccharide flexibility at every linkage as a basis for designing and engineering carbohydrate materials (30). Our general approach to identify structural factors affecting the flexibility of a specific molecular degrees of freedom in a supramolecular system should aid the design of materials and molecular machines (39) and the understanding of biomolecular dynamics.     

Validation of the peak to mean pressure decrease ratio as a new method of assessing aortic stenosis using the Gorlin formula and the cardiovascular magnetic resonance-based hybrid method

BACKGROUND: We sought to validate the recently introduced peak to mean pressure decrease ratio (PMPDR), using the Gorlin formula and a hybrid method which combines cardiovascular magnetic resonance (CMR)-derived stroke volume with transaortic Doppler measurements to calculate aortic valve area (AVA). METHODS: Data analysis in 32 patients with severe (AVA 相似文献   

Sirolimus versus paclitaxel coronary stents in clinical practice

Objectives: We aimed at comparing the long term clinical outcome of SES and PES in routine clinical practice. Background: Although sirolimus‐eluting stents (SES) more effectively reduce neointimal hyperplasia than paclitaxel‐eluting stents (PES), uncertainty prevails whether this difference translates into differences in clinical outcomes outside randomized controlled trials with selected patient populations and protocol‐mandated angiographic follow‐up. Methods: Nine hundred and four consecutive patients who underwent implantation of a drug‐eluting stent between May 2004 and February 2005: 467 patients with 646 lesions received SES, 437 patients with 600 lesions received PES. Clinical follow‐up was obtained at 2 years without intervening routine angiographic follow‐up. The primary endpoint was a composite of death, myocardial infarction (MI), or target vessel revascularization (TVR). Results: At 2 years, the primary endpoint was less frequent with SES (12.9%) than PES (17.6%, HR = 0.70, 95% CI 0.50–0.98, P = 0.04). The difference in favor of SES was largely driven by a lower rate of target lesion revascularisation (TLR; 4.1% vs. 6.9%, P = 0.05), whereas rates of death (6.4% vs. 7.6%, P = 0.49), MI (1.9% vs. 3.2%, P = 0.21), or definite stent thrombosis (0.6% vs. 1.4%, P = 0.27) were similar for both stent types. The benefit regarding reduced rates of TLR was significant in nondiabetic (3.6% vs. 7.1%, P = 0.04) but not in diabetic patients (5.6% vs. 6.1%, P = 0.80). Conclusions: SES more effectively reduced the need for repeat revascularization procedures than PES when used in routine clinical practice. The beneficial effect is maintained up to 2 years and may be less pronounced in diabetic patients. © 2010 Wiley‐Liss, Inc.     

Anticoagulation therapy and primary care internal medicine

The anticoagulation clinics at the University of Virginia Health Sciences Center and the University of California at Davis Medical Center are nurse-practitioner-operated, are affiliated with the general medicine clinic, and rely on portable prothrombin time (PT) monitors that use whole blood and provide timely as well as accurate results reported in PT seconds or as the international normalized ratio (INR). On-site PT/INR testing at these clinics simplifies anticoagulation, mandates direct patient contact, and facilitates primary as well as comprehensive care for patients requiring multispecialty services in large tertiary care centers. Encounters are relatively brief, averaging 19 minutes; 72% of the encounter time involves anticoagulation care and 28% involves primary care. Anticoagulation results using portable PT/INR monitors are safe and accurate based on comparisons with results from clinics relying on standard instruments. Supported in part by VA grants IIR 87-063 and IIR 90-036.