Remodeling After Myocardial Infarction in Humans Is Not Associated With Interstitial Fibrosis of Noninfarcted Myocardium

AbstractObjectives. This study was specifically designed to evaluate whether noninfarcted hypertrophic myocardium in patients with end-stage heart failure after myocardial infarction (MI) is associated with an increase in interstitial fibrous tissue.Background. Postinfarction remodeling consists of complex alterations that involve both infarcted and noninfarcted myocardium. The question arises whether ventricular dysfunction is due to physical events, such as inadequate myocardial hypertrophy to compensate for increased tangential wall stress, or is caused by the development of progressive interstitial fibrosis in noninfarcted myocardium.Methods. Fifteen hearts were obtained as cardiac explants (n = 13) or at autopsy (n = 2) from patients with end-stage coronary artery disease. Sixteen normal hearts served as reference hearts. Samples were taken from the left ventricular (LV) wall that contained the infarcted area, the border area and noninfarcted myocardium remote from scar areas. Collagen was quantified biochemically and microdensitophotometrically. Collagen type I and III ratios were analyzed by using the cyanogen bromide method and immunohistochemical staining, followed by microdensitophotometric quantification.Results. In noninfarcted myocardium remote from the scar areas, total collagen levels and collagen type I/III ratios did not differ statistically from those in reference hearts. These observations contrasted with high total collagen content and high collagen type I/III ratios in scar and border areas.Conclusions. Remodeling of LV myocardium after MI in patients with end-stage heart failure is not necessarily associated with interstitial fibrosis in noninfarcted hypertrophic myocardium remote from scar areas. This finding raises questions regarding therapeutic interventions designed to prevent or retard the development of interstitial fibrosis.(J Am Coll Cardiol 1997;30:76–82

Multiple Labeling in Electron Microscopy: Its Application in Cardiovascular Research

The heart is a muscular pump kept together by a network of extracellular matrix components. An increase in collagens, as in chronic congestive heart failure (CHF), is thought to have a negative effect on cardiac compliance and, thus, on the clinical condition. Conventional electron microscopy allows for the study of cellular and extracellular components and scanning electron microscopy (SEM) can put these structures in three-dimensional perspective. However, in order to study extracellular matrix components in relation to cells, immunoelectron microscopy is superior. We have used this technique in our studies on heart failure. Heart specimens were fixed in 4% paraformaldehyde and 0.1% glutaraldehyde in sodium cacodylate buffer, dehydrated by the method of progressive lowering of temperature and embedded in LR Gold plastic. Immunolabeling could be achieved with different sized gold-conjugated secondary antibodies or protein-A gold conjugates. Depending on the objective, ultra small gold (USG) conjugates or a regular probe size can be used. Labeling efficiency could be increased by bridging antibodies. The double and triple staining procedures were based on single staining methods using one-and two-face labeling. The choice of antibodies and gold conjugates depended on the objectives. Immunoelectron microscopy, using multiple labeling, allowed a detailed study of the organization of the extracellular matrix and its relationship with cardiac myocytes. This may prove to be a useful tool for the study of chronic heart failure

Recurrent patterns of microdiversity in a temperate coastal marine environment

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 12 (2018): 237–252, doi:10.1038/ismej.2017.165.Temperate coastal marine environments are replete with complex biotic and abiotic interactions that are amplified during spring and summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond to successional releases of dissolved organic matter as algal cells are lysed. Annual seasonal shifts in the community composition of free-living bacterioplankton follow broadly predictable patterns, but whether similar communities respond each year to bloom disturbance events remains unknown owing to a lack of data sets, employing high-frequency sampling over multiple years. We capture the fine-scale microdiversity of these events with weekly sampling using a high-resolution method to discriminate 16S ribosomal RNA gene amplicons that are >99% identical. Furthermore, we used 2 complete years of data to facilitate identification of recurrent sub-networks of co-varying microbes. We demonstrate that despite inter-annual variation in phytoplankton blooms and despite the dynamism of a coastal–oceanic transition zone, patterns of microdiversity are recurrent during both bloom and non-bloom conditions. Sub-networks of co-occurring microbes identified reveal that correlation structures between community members appear quite stable in a seasonally driven response to oligotrophic and eutrophic conditions.PLB is supported by the European Research Council Advanced Investigator grant ABYSS 294757 to Antje Boetius. AF-G is supported by the European Union’s Horizon 2020 research and innovation program (Blue Growth: Unlocking the potential of Seas and Oceans) under grant agreement no. (634486) (project acronym INMARE). This study was funded by the Max Planck Society. Further support by the Department of Energy Joint Genome Institute (CSP COGITO) and DFG (FOR2406) is acknowledged by HT (TE 813/2-1) and RA (Am 73/9-1)

Solid solution decomposition and Guinier-Preston zone formation in Al-Cu alloys: A kinetic theory with anisotropic interactions

Using methods of statistical kinetic theory parametrized with first-principles interatomic interactions that include chemical and strain contributions, we investigated the kinetics of decomposition and microstructure formation in Al-Cu alloys as a function of temperature and alloy concentration. We show that the decomposition of the solid solution forming platelets of copper, known as Guinier-Preston (GP) zones, includes several stages and that the transition from GP1 to GP2 zones is determined mainly by kinetic factors. With increasing temperature, the model predicts a gradual transition from platelet-like precipitates to equiaxial ones and at intermediate temperatures both precipitate morphologies may coexist.Comment: 9 pages, 8 figure

A case study of a whole system approach to improvement in an acute hospital setting

From MDPI via Jisc Publications RouterChanges in healthcare tend to be project-based with whole system change, which acknowledges the interconnectedness of socio-technical factors, not the norm. This paper attempts to address the question of whole system change posed by the special issue and brings together other research presented in this special issue. A case study approach was adopted to understand the deployment of a whole system change in the acute hospital setting along four dimensions of a socio-technical systems framework: culture, system functioning, action, and sense-making. The case study demonstrates evidence of whole system improvement. The approach to change was co-designed by staff and management, projects involving staff from all specialities and levels of seniority were linked to each other and to the strategic objectives of the organisation, and learnings from first-generation projects have been passed to second and third-generation process improvements. The socio-technical systems framework was used retrospectively to assess the system change but could also be used prospectively to help healthcare organisations develop approaches to whole system improvement.19pubpub

Visual cross-platform analysis: digital methods to research social media images

Analysis of social media using digital methods is a flourishing approach. However, the relatively easy availability of data collected via platform application programming interfaces has arguably led to the predominance of single-platform research of social media. Such research has also privileged the role of text in social media analysis, as a form of data that is more readily gathered and searchable than images. In this paper, we challenge both of these prevailing forms of social media research by outlining a methodology for visual cross-platform analysis (VCPA), defined as the study of still and moving images across two or more social media platforms. Our argument contains three steps. First, we argue that cross-platform analysis addresses a gap in research methods in that it acknowledges the interplay between a social phenomenon under investigation and the medium within which it is being researched, thus illuminating the different affordances and cultures of web platforms. Second, we build on the literature on multimodal communication and platform vernacular to provide a rationale for incorporating the visual into cross-platform analysis. Third, we reflect on an experimental cross-platform analysis of images within social media posts (n = 471,033) used to communicate climate change to advance different modes of macro- and meso-levels of analysis that are natively visual: image-text networks, image plots and composite images. We conclude by assessing the research pathways opened up by VCPA, delineating potential contributions to empirical research and theory and the potential impact on practitioners of social media communication

How and why overcome the impediments to resolution: lessons from rhinolophid and hipposiderid bats

The phylogenetic and taxonomic relationships among the Old World leaf-nosed bats (Hipposideridae) and the closely related horseshoe bats (Rhinolophidae) remain unresolved. In this study, we generated a novel approximately 10-kb molecular data set of 19 nuclear exon and intron gene fragments for 40 bat species to elucidate the phylogenetic relationships within the families Rhinolophidae and Hipposideridae. We estimated divergence times and explored potential reasons for any incongruent phylogenetic signal. We demonstrated the effects of outlier taxa and genes on phylogenetic reconstructions and compared the relative performance of intron and exon data to resolve phylogenetic relationships. Phylogenetic analyses produced a well-resolved phylogeny, supporting the familial status of Hipposideridae and demonstrated the paraphyly of the largest genus, Hipposideros. A fossil-calibrated timetree and biogeographical analyses estimated that Rhinolophidae and Hipposideridae diverged in Africa during the Eocene approximately 42 Ma. The phylogram, the timetree, and a unique retrotransposon insertion supported the elevation of the subtribe Rhinonycterina to family level and which is diagnosed herein. Comparative analysis of diversification rates showed that the speciose genera Rhinolophus and Hipposideros underwent diversification during the Mid-Miocene Climatic Optimum. The intron versus exon analyses demonstrated the improved nodal support provided by introns for our optimal tree, an important finding for large-scale phylogenomic studies, which typically rely on exon data alone. With the recent outbreak of Middle East respiratory syndrome, caused by a novel coronavirus, the study of these species is urgent as they are considered the natural reservoir for emergent severe acute respiratory syndrome (SARS)-like coronaviruses. It has been shown that host phylogeny is the primary factor that determines a virus's persistence, replicative ability, and can act as a predictor of new emerging disease. Therefore, this newly resolved phylogeny can be used to direct future assessments of viral diversity and to elucidate the origin and development of SARS-like coronaviruses in mammals.Nicole M. Foley, Vu Dinh Thong, Pipat Soisook, Steven M. Goodman, Kyle N. Armstrong, David S. Jacobs, Sébastien J. Puechmaille and Emma C. Teelin

Analysis and comparison of very large metagenomes with fast clustering and functional annotation

<p>Abstract</p> <p>Background</p> <p>The remarkable advance of metagenomics presents significant new challenges in data analysis. Metagenomic datasets (metagenomes) are large collections of sequencing reads from anonymous species within particular environments. Computational analyses for very large metagenomes are extremely time-consuming, and there are often many novel sequences in these metagenomes that are not fully utilized. The number of available metagenomes is rapidly increasing, so fast and efficient metagenome comparison methods are in great demand.</p> <p>Results</p> <p>The new metagenomic data analysis method Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline (<b>RAMMCAP</b>) was developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort. It identifies raw read clusters and protein clusters that may include novel gene families, and compares metagenomes using clusters or functional annotations calculated by RAMMCAP. In this study, RAMMCAP was applied to the two largest available metagenomic collections, the "Global Ocean Sampling" and the "Metagenomic Profiling of Nine Biomes".</p> <p>Conclusion</p> <p>RAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from <url>http://tools.camera.calit2.net/camera/rammcap/</url>.</p

Species-specific Typing of DNA Based on Palindrome Frequency Patterns

DNA in its natural, double-stranded form may contain palindromes, sequences which read the same from either side because they are identical to their reverse complement on the sister strand. Short palindromes are underrepresented in all kinds of genomes. The frequency distribution of short palindromes exhibits more than twice the inter-species variance of non-palindromic sequences, which renders palindromes optimally suited for the typing of DNA. Here, we show that based on palindrome frequency, DNA sequences can be discriminated to the level of species of origin. By plotting the ratios of actual occurrence to expectancy, we generate palindrome frequency patterns that allow to cluster different sequences of the same genome and to assign plasmids, and in some cases even viruses to their respective host genomes. This finding will be of use in the growing field of metagenomics

A quantitative account of genomic island acquisitions in prokaryotes

<p>Abstract</p> <p>Background</p> <p>Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness.</p> <p>In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species.</p> <p>Results</p> <p>When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor.</p> <p>Conclusions</p> <p>This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters.</p