Unraveling the glyco-puzzle : glycan structure identification by capillary electrophoresis

State-of-the-art high-resolution separation techniques play an important role in the full structural elucidation of glycans. Capillary electrophoresis (CE) offers a rapid yet simple method for exhaustive carbohydrate profiling. CE is a versatile analytical platform, which can be operated in several separation modes, simply by altering separation conditions during operation. For in-depth glycan structural analysis, CE has also gained significantly from the additional resolution introduced by complementary and orthogonal separation techniques such as ion exchange or hydrophilic interaction chromatography. Commercially available mass spectrometry (MS) interfaces have not only brought this information-rich detection technique within reach, but CE also represents an expedient highly efficient separation inlet for MS, capable of separating isobaric oligosaccharide isomers prior to MS detection and MS/MS fragmentation based identification. This Perspective gives a sophisticated impression of the versatility of capillary electrophoresis for deep structural elucidation of carbohydrates derived from glycoproteins of biomedical interest. Different separation modes for the analysis of both charged and neutral glycans, such as influencing electroosmotic flow, using complexation/interaction based secondary equilibria, and the use of charged and neutral labels are compared. The merits of introducing orthogonal and complementary techniques, such as exoglycosidase digestion arrays, analytical/preparative chromatography and mass spectrometric detection, extending the dynamic range and resolution of CE are all thoroughly discussed

Security Theorems via Model Theory

A model-theoretic approach can establish security theorems for cryptographic protocols. Formulas expressing authentication and non-disclosure properties of protocols have a special form. They are quantified implications for all xs . (phi implies for some ys . psi). Models (interpretations) for these formulas are *skeletons*, partially ordered structures consisting of a number of local protocol behaviors. Realized skeletons contain enough local sessions to explain all the behavior, when combined with some possible adversary behaviors. We show two results. (1) If phi is the antecedent of a security goal, then there is a skeleton A_phi such that, for every skeleton B, phi is satisfied in B iff there is a homomorphism from A_phi to B. (2) A protocol enforces for all xs . (phi implies for some ys . psi) iff every realized homomorphic image of A_phi satisfies psi. Hence, to verify a security goal, one can use the Cryptographic Protocol Shapes Analyzer CPSA (TACAS, 2007) to identify minimal realized skeletons, or "shapes," that are homomorphic images of A_phi. If psi holds in each of these shapes, then the goal holds

Comorbidities of atopic dermatitis—what does the evidence say?

Atopic dermatitis (AD) is a common disease that is associated with atopic and nonatopic comorbidities. There has been a growing interest in this area of AD, because presence or risk of comorbidities can in many ways impact the management of patients with AD. Thus, some treatments for AD may improve its comorbidities as well, whereas others may increase their risk. In this review article, we discuss various comorbidities of AD mostly on the basis of the results of recent multiple systematic reviews and meta-analyses to update readers about this rapidly developing area of dermatology. We emphasize the important information provided by studies presenting both relative risk and absolute risk, and show that AD is associated with, among others, atopic comorbidities such as asthma, rhinitis, and food allergy, nonatopic comorbidities such as ocular, psychiatric, infectious, endocrine, autoimmune, and cardiovascular diseases, and certain cancers. Clinicians need to be aware of these and be cognizant about positive and negative effects of existing and new treatments for AD

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

Large noncoding RNAs are emerging as an important component in cellular regulation. Considerable evidence indicates that these transcripts act directly as functional RNAs rather than through an encoded protein product. However, a recent study of ribosome occupancy reported that many large intergenic ncRNAs (lincRNAs) are bound by ribosomes, raising the possibility that they are translated into proteins. Here, we show that classical noncoding RNAs and 5′ UTRs show the same ribosome occupancy as lincRNAs, demonstrating that ribosome occupancy alone is not sufficient to classify transcripts as coding or noncoding. Instead, we define a metric based on the known property of translation whereby translating ribosomes are released upon encountering a bona fide stop codon. We show that this metric accurately discriminates between protein-coding transcripts and all classes of known noncoding transcripts, including lincRNAs. Taken together, these results argue that the large majority of lincRNAs do not function through encoded proteins

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis.

Dupilumab is a fully human antibody to interleukin-4 receptor α that improves the signs and symptoms of moderate to severe atopic dermatitis (AD). To determine the effects of dupilumab on Staphylococcus aureus colonization and microbial diversity on the skin, bacterial DNA was analyzed from swabs collected from lesional and nonlesional skin in a double-blind, placebo-controlled study of 54 patients with moderate to severe AD randomized (1:1) and treated with either dupilumab (200 mg weekly) or placebo for 16 weeks. Microbial diversity and relative abundance of Staphylococcus were assessed by DNA sequencing of 16S ribosomal RNA, and absolute S. aureus abundance was measured by quantitative PCR. Before treatment, lesional skin had lower microbial diversity and higher overall abundance of S. aureus than nonlesional skin. During dupilumab treatment, microbial diversity increased and the abundance of S. aureus decreased. Pronounced changes were seen in nonlesional and lesional skin. Decreased S. aureus abundance during dupilumab treatment correlated with clinical improvement of AD and biomarkers of type 2 immunity. We conclude that clinical improvement of AD that is mediated by interleukin-4 receptor α inhibition and the subsequent suppression of type 2 inflammation is correlated with increased microbial diversity and reduced abundance of S. aureus

Integrated spatial genomics reveals global architecture of single nuclei

Identifying the relationships between chromosome structures, nuclear bodies, chromatin states and gene expression is an overarching goal of nuclear-organization studies. Because individual cells appear to be highly variable at all these levels, it is essential to map different modalities in the same cells. Here we report the imaging of 3,660 chromosomal loci in single mouse embryonic stem (ES) cells using DNA seqFISH+, along with 17 chromatin marks and subnuclear structures by sequential immunofluorescence and the expression profile of 70 RNAs. Many loci were invariably associated with immunofluorescence marks in single mouse ES cells. These loci form ‘fixed points’ in the nuclear organizations of single cells and often appear on the surfaces of nuclear bodies and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states. Using clonal analysis, we show that the global levels of some chromatin marks, such as H3 trimethylation at lysine 27 (H3K27me3) and macroH2A1 (mH2A1), are heritable over at least 3–4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+-based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems

Integrated spatial genomics reveals global architecture of single nuclei

Identifying the relationships between chromosome structures, nuclear bodies, chromatin states and gene expression is an overarching goal of nuclear-organization studies. Because individual cells appear to be highly variable at all these levels, it is essential to map different modalities in the same cells. Here we report the imaging of 3,660 chromosomal loci in single mouse embryonic stem (ES) cells using DNA seqFISH+, along with 17 chromatin marks and subnuclear structures by sequential immunofluorescence and the expression profile of 70 RNAs. Many loci were invariably associated with immunofluorescence marks in single mouse ES cells. These loci form ‘fixed points’ in the nuclear organizations of single cells and often appear on the surfaces of nuclear bodies and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states. Using clonal analysis, we show that the global levels of some chromatin marks, such as H3 trimethylation at lysine 27 (H3K27me3) and macroH2A1 (mH2A1), are heritable over at least 3–4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+-based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems

Efficacy and safety of lebrikizumab in moderate-to-severe atopic dermatitis: results from two phase III, randomized, double-blinded, placebo-controlled trials

Lebrikizumab, a high-affinity IgG-4 monoclonal antibody targeting interleukin (IL)-13, selectively prevents the formation of the IL-13Ra1/IL-4Ra heterodimer receptor signalling complex. Lebrikizumab demonstrated rapid, dose-dependent efficacy and an acceptable safety profile in patients with moderate-to-severe atopic dermatitis (AD) in a phase IIb trial (NCT03443024). Here, we report 16-week efficacy and safety outcomes of lebrikizumab monotherapy in patients with AD from two ongoing 52-week, randomized, double-blinded, placebo-controlled phase III trials – ADvocate1 (NCT04146363) and ADvocate2 (NCT04178967). Eligible patients with moderate-to-severe AD [adults and adolescents (12–17 years of age, weighing ≥40 kg)] were randomized 2: 1 to subcutaneous lebrikizumab 250 mg or placebo every 2 weeks. Efficacy analyses included proportions of patients achieving Investigator’s Global Assessment (IGA) 0/1, Eczema Area and Severity Index (EASI)-75 and Pruritus Numerical Rating Scale (NRS) ≥ 4-point improvement from baseline (P ≥ 4) at week 16. Nonefficacy-related missing data were imputed by multiple imputation. In ADvocate1, proportions of patients treated with lebrikizumab 250 mg (n = 283) and placebo (n = 141) achieving IGA 0/1 at week 16 were 43.0% and 12.8% (P \u3c 0.001); EASI-75 responses were 59.3% and 16.4% (P \u3c 0.001); P ≥ 4 proportions were 46.3% and 12.7% (P \u3c 0.001), respectively. In ADvocate2 (lebrikizumab, n = 281; placebo, n = 146), corresponding proportions for IGA 0/1 were 33.1% and 10.9% (P \u3c 0.001); EASI-75 responses were 50.8% and 18.2% (P \u3c 0.001); P ≥ 4 proportions were 38.3% and 11.3% (P \u3c 0.001), respectively. The percentage of patients reporting ≥1 TEAE was comparable in ADvocate1 (lebrikizumab, 45.4%; placebo, 51.1%) and ADvocate2 (lebrikizumab 53.0%; placebo 66.2%). Data from two ongoing pivotal phase III trials suggest that lebrikizumab 250 mg Q2W provides an efficacious treatment option with an acceptable safety profile for patients with moderate-to-severe AD

International observational atopic dermatitis cohort to follow natural history and treatment course: TARGET-DERM AD study design and rationale

INTRODUCTION: As new topical and systemic treatments become available for atopic dermatitis (AD), there is a need to understand how treatments are being used in routine clinical practice, their comparative effectiveness and their long-term safety in diverse clinical settings. METHODS AND ANALYSIS: The TARGET-DERM AD cohort is a longitudinal, observational study of patients with AD of all ages, designed to provide practical information on long-term effectiveness and safety unobtainable in traditional registration trials. Patients with physician-diagnosed AD receiving prescription treatment (topical or systemic) will be enrolled at academic and community clinical centres. Up to 3 years of retrospective medical records, 5 years of prospective medical records, and optional biological samples and patient-reported outcomes will be collected. The primary aims include characterisation of AD treatment regimens, evaluation of response to therapy, and description of adverse events. ETHICS AND DISSEMINATION: TARGET-DERM has been approved by a central IRB (Copernicus Group IRB, 5000 Centregreen Way Suite 200, Cary, North Carolina 27513) as well as local and institutional IRBs. No additional Ethics Committee reviews. Results will be reviewed by a publications committee and submitted to peer-reviewed journals. TRIAL REGISTRATION NUMBER: NCT03661866, pre-results