Evolutionary footprint of coevolving positions in genes

Motivation: The analysis of molecular coevolution provides information on the potential functional and structural implication of positions along DNA sequences, and several methods are available to identify coevolving positions using probabilistic or combinatorial approaches. The specific nucleotide or amino acid profile associated with the coevolution process is, however, not estimated, but only known profiles, such as the Watson-Crick constraint, are usually considered a priori in current measures of coevolution. Results: Here, we propose a new probabilistic model, Coev, to identify coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. The process of coevolution is modeled by a 16 × 16 instantaneous rate matrix that includes rates of transition as well as a profile of coevolution. We used simulated, empirical and illustrative data to evaluate our model and to compare it with a model of ‘independent' evolution using Akaike Information Criterion. We showed that the Coev model is able to discriminate between coevolving and non-coevolving positions and provides better specificity and specificity than other available approaches. We further demonstrate that the identification of the profile of coevolution can shed new light on the process of dependent substitution during lineage evolution. Availability: http://www2.unil.ch/phylo/bioinformatics/coev Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

A comprehensive theoretical and experimental study of coplanar waveguide shunt stubs

A comprehensive theoretical and experimental study of straight and bent coplanar waveguide (CPW) shunt stubs is presented. In the theoretical analysis, the CPW is assumed to be inside a cavity, while, the experiments are performed on open structures. A hybrid technique was developed to analyze the CPW discontinuities which proved to be accurate since the theoretical and experimental results agree very well. The effect of the cavity resonances on the behavior of the stubs with and without air-bridges is investigated. In addition, the encountered radiation loss due to the discontinuities is evaluated experimentally

A Novel Transition Between Rectangular Waveguide and Layered Ridge Dielectric Waveguide

A novel transition between rectangular waveguide and layered ridge dielectric waveguide (LRDW) is reported. The transition is also suitable for use with image guide, insulated image guide, dielectric ridge waveguide and other open dielectric waveguides. Both experimental and theoretical data are presented which compare the new transition to three transitions reported in the literature

Broadband Uniplanar Microstrip to Slot-Line Transitions

New in line uniplanar microstrip-to-slotline transitions for MIC/MMIC and phased array slotline antenna applications are described. Such transactions are compact and suitable to be used in an open environment or inside a package or a multichip module. The transitions share the concept of using a balun which consists of two microstrip lines connected to a slotline through a pair of coupled microstrips. The transitions are studied theoretically using the finite difference time domain (FDTD) technique and measured experimentally using an HP8510C Network Analyzer. For a back-to-back configuration, an insertion loss of less than 1.3 dB per transition is achieved over a 40% 3-dB bandwidth with a minimum of 0.6 dB at the design frequency

A theoretical and experimental study of coplanar waveguide shunt stubs

A comprehensive theoretical and experimental study of straight and bent coplanar waveguide (CPW) shunt stubs is presented. In the theoretical analysis, the CPW is assumed to be inside a cavity while, the experiments are performed on open structures. For the analysis of CPW discontinuities with air-bridges, a hybrid technique was developed which was validated through extensive theoretical and experimental comparisons. The effect of the cavity resonances on the behavior of the stubs with and without air-bridges is investigated. In addition, the encountered radiation loss due to the discontinuities is evaluated experimentally

Coplanar stripline components for high frequency application

In this paper, coplanar stripline discontinuities such as a slit, a right angle bend and a T-junction are characterized and their performance is parameterized with respect to frequency and geometry. Lumped equivalent circuits are presented for some of them. The element values are obtained from the measured discontinuity scattering (S) parameters. The experimental results are compared with theoretical data obtained using the Finite Difference Time Domain (FD-TD) technique for validation and show very good agreement

Selection on the Major Color Gene Melanocortin-1-Receptor Shaped the Evolution of the Melanocortin System Genes.

Modular genetic systems and networks have complex evolutionary histories shaped by selection acting on single genes as well as on their integrated function within the network. However, uncovering molecular coevolution requires the detection of coevolving sites in sequences. Detailed knowledge of the functions of each gene in the system is also necessary to identify the selective agents driving coevolution. Using recently developed computational tools, we investigated the effect of positive selection on the coevolution of ten major genes in the melanocortin system, responsible for multiple physiological functions and human diseases. Substitutions driven by positive selection at the melanocortin-1-receptor (MC1R) induced more coevolutionary changes on the system than positive selection on other genes in the system. Contrarily, selection on the highly pleiotropic POMC gene, which orchestrates the activation of the different melanocortin receptors, had the lowest coevolutionary influence. MC1R and possibly its main function, melanin pigmentation, seems to have influenced the evolution of the melanocortin system more than functions regulated by MC2-5Rs such as energy homeostasis, glucocorticoid-dependent stress and anti-inflammatory responses. Although replication in other regulatory systems is needed, this suggests that single functional aspects of a genetic network or system can be of higher importance than others in shaping coevolution among the genes that integrate it

Theoretical and Experimental Study of Microstrip-to-Slot Line Uniplanar Transition

Recent advances in MMCI technology make it possible to construct transitions from CPW-to-microstrip with via hole, microstrip-to-slot line and microshield line-to-CPW all of which have potential applications in the feed network of antennas. In this study we investigate the characteristics of the microstrip-to-slot line uniplanar transition using the finite element methods (FEM) and finite difference time domain (FDTD) techniques, and compared the theoretical results with the measurements. In both cases, the results agree with the measurements within a few percent

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification