Juergen Schmitz

Juergen Schmitz
University of Münster | WWU · Institute of Experimental Pathology

PD Dr. rer. nat.

About

254
Publications
43,723
Reads
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5,984
Citations
Citations since 2017
40 Research Items
2133 Citations
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20172018201920202021202220230100200300
Introduction
My research is focused on the systematic and comparative use of genomic and high-throughput experimental data to extract genomic signals of diversity that correlate molecular changes with their evolutionary impacts in animals.
Additional affiliations
January 2003 - present
University of Münster
Position
  • Group Leader
January 1998 - December 2002
German Primate Center
Position
  • Group Leader
January 1992 - April 1997
Technische Universität Berlin
Position
  • Research Assistant

Publications

Publications (254)
Article
Full-text available
Tarsiers are phylogenetically located between the most basal strepsirrhines and the most derived anthropoid primates. While they share morphological features with both groups, they also possess uncommon primate characteristics, rendering their evolutionary history somewhat obscure. To investigate the molecular basis of such attributes, we present h...
Article
Full-text available
The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known t...
Article
The growing knowledge about the influence of transposable elements (TEs) on (1) long‐term genome and transcriptome evolution, (2) genomic, transcriptomic and epigenetic variation within populations, and (3) patterns of somatic genetic differences in individuals continues to spur the interest of evolutionary biologists in the role of TEs in adaptive...
Article
To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among var...
Article
Full-text available
Although first posited to be of a single origin, the two superfamilies of Phalangeriform marsupial possums (Phalangeroidea: cuscuses and brushtail possums and Petauroidea: possums and gliders) have long been considered, based on multiple sequencing studies, to have evolved from two separate origins. However, previous data from these sequence analys...
Article
Retrophylogenomics makes use of genome-wide retrotransposon presence/absence insertion patterns to resolve questions in phylogeny and population genetics. In the genomics era, evaluating high-throughput data requires the associated development of appropriately powerful statistical tools. The currently used KKSC 3-lineage statistical test for estima...
Article
Full-text available
Advances in RNA high-throughput sequencing and large-scale functional assays yield new insights into the multifaceted activities of transposed elements and many other previously undiscovered sequence elements. Currently, no tool for easy access, analysis, quantification, and visualization of alternatively spliced exons across multiple tissues or de...
Article
Full-text available
Evolution is change over time. Although neutral changes promoted by drift effects are most reliable for phylogenetic reconstructions, selection-relevant changes are of only limited use to reconstruct phylogenies. On the other hand, comparative analyses of neutral and selected changes of protein-coding DNA sequences (CDS) retrospectively tell us abo...
Article
Full-text available
Euarchontoglires, once described as Supraprimates, comprise primates, colugos, tree shrews, rodents, and lagomorphs in a clade that evolved about 90 million years ago (mya) from a shared ancestor with Laurasiatheria. The rapid speciation of groups within Euarchontoglires, and the subsequent inherent incomplete marker fixation in ancestral lineages,...
Article
Full-text available
Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the...
Article
Full-text available
The recent and exclusively in humans and a few other higher primates expressed APOL1 (Apolipoprotein L1) gene is linked to African human trypanosomiasis (also known as African sleeping sickness) as well as to different forms of kidney diseases. Whereas APOL1’s role as a trypanolytic factor is well established, pathobiological mechanisms explaining...
Article
Full-text available
The process of non-allelic gene conversion acts on homologous sequences during recombination, replacing parts of one with the other to make them uniform. Such concerted evolution is best described as paralogous ribosomal RNA gene unification that serves to preserve the essential house-keeping functions of the converted genes. Transposed elements (T...
Article
The terrestrial radiation of vertebrates required changes in skin that resolved the dual demands of maintaining a mechanical and physiological barrier while also facilitating ion and gas transport. Using the amphibious killifish Kryptolebias marmoratus, we found that transcriptional regulation of skin morphogenesis was quickly activated upon air ex...
Preprint
Retrophylogenomics makes use of genome-wide retrotransposon presence/absence insertion patterns to resolve questions in phylogeny and population genetics. In the genomics era, evaluating high-throughput data requires the associated development of appropriately powerful statistical tools. The currently used KKSC 3-lineage statistical test for evalua...
Preprint
Full-text available
The Devonian radiation of vertebrates from aquatic into terrestrial habitats required behavioral, physiological, and morphological adaptations. Changes to skin structure and function were likely crucial, but adaptations were needed to resolve contrasting demands of maintaining a mechanical and physiological barrier while also facilitating ion and g...
Article
Full-text available
The order Lagomorpha unifies pikas (Ochotonidae) and the hares plus rabbits (Leporidae). Phylogenetic reconstructions of the species within the family Leporidae based on traditional morphological or molecular sequence data provide support for conflicting hypotheses. The retroposon presence/absence patterns analyzed in this study revealed strong sup...
Article
How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, that were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multi-genome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious pr...
Article
Full-text available
Background Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered large...
Data
PTD1 and PTD2 are not CPPs. Fluorescence microscopy of HeLa cells incubated with 576 nM FITC-labeled PTD1, PTD2, Tat and NPP (green) for the indicated times. PFA-fixed cells were stained with Phalloidin TRITC (red) and Draq5 (blue). Fluorescence images were generated using a Zeiss LSM 510 microscope. Z-stacks of single cells were taken.
Data
Chloroquine releases endocytosed BSA into the cytosol. HeLa cells were incubated with 0, 150 or 300 μM Chloroquine together with 25 μg/ml BSA for 3 h. Cells were washed and quenched with 0.2 M glycine abrogate signals from the outside of the cell. Geo mean of FL3 fluorescence corrected by labeling efficiency is depicted. Bar graph represents the me...
Data
(A) Endocytic inhibitors do not inhibit catalytic activity of rNleC. HeLa cell lysates were incubated with the indicated endocytosis inhibitors (Dynasore 30 mM, Cytochalasin D 200 μM, Amiloride 19 mM, Filipin 3.8 mM, Nocodazole 16.5 mM and MβCD 50 mM) together with rNleC (50 μg/ml) for 30 min at 4°C. Cleavage of p65 was analyzed by Western blotting...
Data
PI uptake of endocytosis inhibitor treated cells. Adherent HeLa cells were pre-incubated with the indicated endocytosis inhibitors for 1 h and treated with FITC-labeled rNleC (50 μg/ml) for 4 h at 37°C. PI fluorescence was subsequently measured by flow cytometry. The bar graph shows the results of at least three independent experiments (mean ± SD).
Data
IL1β does not permeabilize cells. HeLa cells were incubated with 50 μg/ml rNleC for 30 min together with 1 μg/ml PI. Cells were stimulated with10 ng/ml IL1β (black bars) for 3.5 h or not (white bars), trypsinized and PI uptake was measured using flow cytometry. The bar graph shows the results of three independent experiments (mean ± SD).
Data
Recombinant proteins are not cytotoxic. The percentage of released LDH was measured to exclude a cytotoxic effect of rNleC or of the rNleC variants on HeLa cells. Experiments are presented as the mean ± SD of three individual experiments.
Data
IL1β does not influence the uptake of rNleC or rTat NleC. HeLa cells were incubated with 50 μg/ml protein for 30 min. Cells were stimulated with 10 ng/ml IL1β (black bars) for 3.5 h or not (white bars) and trypsinized. Trypsinized cells were quenched with Trypan Blue (final concentration 0.2%) and fluorescence was subsequently measured by flow cyto...
Data
Conformational changes at low pH. Complete spectra of TNS fluorescence of rNleC, rNleC variants and rGFP at pH 7.5, 7.0, 6.5, 6.0, 5.5, 5.0, 4.5, and 4.0. Data are presented after subtraction of background fluorescence and are the mean ± SD of three independent experiments.
Data
Alignment of informative AA sequence regions in fasta format.
Data
(A) Arginines are enriched in predicted PTDs. The number of arginine residues was counted. Arginine residues per sequence in % (left column) and arginine residues per sequence length in % (right column) were calculated. Arginines are enriched in predicted PTDs. (B) Catalytic activity of rNleCH187Y is not abrogated. HeLa cells or HeLa cell lysates w...
Data
Bafilomycin A1 blocks acidification of lysosomes. HeLa cells were incubated with 10 nM Bafilomycin A1 for the indicated times. 3 h prior to the end of the experiment 400 nM Lysotracker DND99 was added to the supernatant. Cells were trypsinized and the amount of acidified endosomes was measured using flow cytometry. The data are presented after subt...
Data
Sequential and structural homologies of NleC and AIP56. (A) Sequence alignment of the A subunit of AIP56 and NleC. (B) Overlay of structure predictions for NleC (blue) and the A subunit of AIP56 (yellow) with Swiss-PdbViewer 4.1.0. The catalytic domain (HEXXH) motif is marked in orange (NleC) or green (AIP56). (C) Hydrophobic amino acids in the seq...
Article
Full-text available
Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sci...
Article
Full-text available
Effector proteins secreted by the type 3 secretion system (T3SS) of pathogenic bacteria have been shown to precisely modulate important signaling cascades of the host for the benefit of the pathogens. Among others, the non-LEE encoded T3SS effector protein NleC of enteropathogenic Escherichia coli (EPEC) is a Zn-dependent metalloproteinase and supp...
Article
Full-text available
Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods - too short to fix polymorphic alleles - is described as incomplete lineage sorting....
Preprint
Full-text available
Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. Here, we resolve their deep phylogenetic relationships using presence/absence patterns of short interspersed elements (SINEs), a group of retroposons which is abundant in mammalian genomes but considered largely inactive in avian genomes. The resultant...
Data
Supplementary Figures 1-6, Supplementary Tables 1-10, Supplementary Methods and Supplementary References.
Article
Full-text available
Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo referen...
Article
Full-text available
Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fix...
Data
Table of critical values for one-directional and unbiased searches. Supplementary Table S2. Example. Supplementary Tables S3-S4. Example. (PDF)
Data
Confidence intervals for drift timeτ. Contains sections: Estimation of the confidence intervals for the drift time; evaluation of confidence interval for the drift time; simulation of confidence intervals for the drift time τ in a diploid population; examples of calculation of Ne confidence intervals for ancestral lineages. Supplementary Figure S1...
Data
Detailed description of the mathematical model. Contains sections: Model Assumptions; Binary tree; Ancestral hybridization; One-directional search; Supplementary References. (PDF)
Data
Comparative evaluation of branch points. Supplementary Table S9. (PDF)
Data
Values of Zα for different levels of significance α. Supplementary Table S1. (PDF)
Article
Full-text available
We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), of which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in...
Article
Full-text available
We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), of which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in...
Article
Full-text available
Freed from the competition of large raptors, Paleocene carnivores could expand their newly acquired habitats in search of prey. Such changing conditions might have led to their successful distribution and rapid radiation. Today, molecular evolutionary biologists are faced, however, with the consequences of such accelerated adaptive radiations, beca...
Article
Understanding how genetic novelties arise is a central goal of evolutionary biology. To this end, programmed DNA elimination and RNA splicing deserve special consideration. While programmed DNA elimination reshapes genomes by eliminating chromatin during organismal development, RNA splicing rearranges genetic messages by removing intronic regions d...
Article
Full-text available
Transposable elements, once described by Barbara McClintock as controlling genetic units, not only occupy the largest part of our genome but are also a prominent moving force of genomic plasticity and innovation. They usually replicate and reintegrate into genomes silently, sometimes causing malfunctions or misregulations, but occasionally millions...
Article
Full-text available
To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rat...