209 research outputs found
Tolerability safety and effectiveness of enhanced external counterpulsation versus individual shear rate therapy in patients with lower extremity atherosclerotic disease: A prospective pilot clinical trial
No full textBundesministerium für Bildung und Forschung https://doi.org/10.13039/50110000234
Pilk Richard Viidalepa perekonnaloole
No full textRichard Viidalepp (Widebaum before Estonianising his name, and later Viidebaum; Jan. 23, 1904 - June 3, 1986), the famous Estonian folklorist, was born in the Jalapuu farm in the village of Nurmsi in Central Estonia. The same farm was the home of Urve Buschmann, the author of the article and R. Viidalepp's niece. On the basis of the 1722 list of inhabitants in the Särgavere estate and the registers of the Järva Peetri congregation, the documented genealogy of Viidalepp's family starts with Jüri Jalapuu and his wife Els (?1730-?1761). In more recent registers their son Jüri (?1771-1843) already appears under the name Widebaum. The family was a typical Estonian family, including farmers, handicraftsmen, inventive technicians, later also intellectuals and artists. Some emigrated (the Finnish and American branches of the Viidebaums) and some were deported to Siberia. The fate of family members and descriptions of family history are illustrated by Richard Viidalepp's letters and family photographs. The last Viidalepps born in the Jalapuu farm moved to Tallinn in 1950
Einflussfaktoren auf den Verlauf und die Therapie beim Poplitealarterienaneurysma
No full textHintergrund: Das Poplitealarterienaneurysma (PAA) ist zwar das zweithäufigste Aneurysma des Menschen, jedoch insgesamt eine extrem seltene Erkrankung. Es mangelt an Studien, die klinische Einflussfaktoren untersuchen.
Patienten und Methodik: Von Januar 1994 bis einschließlich Dezember 2015 befanden sich N=88 Patienten und Patientinnen mit der Hauptdiagnose „Aneurysma der A. poplitea“ stationär im Universitätsklinikum Magdeburg. Die Daten zu Patienten, Krankheitsverlauf und Therapiemethoden wurden aus den Epikrisen, radiologischer und OP-Dokumentation sowie aus Ambulanzakten retrospektiv erhoben.
Ergebnisse: Die Symptomatik bei Erstvorstellung des Patienten ist signifikant mit der Thrombosierung des Aneurysmas assoziiert (p=0,049), während der Querdurchmesser des Aneurysmas keinen signifikanten Einfluss auf diese zeigt (p=0,591). Die Bypassoffenheit hängt signifikant vom OP-Material (autolog vs. alloplastisch, p=0,024 im Log-Rank-Test; p=0,004 in der Cox-Regression) ab. In der Cox-Regression sind außerdem das Alter (pro ein Jahr älter Risikoverringerung um 9%, p=0,014) und der Thrombosierungsgrad (Teilthrombosierung vs. vollständige Thrombosierung p=0,011) signifikante Einflussfaktoren auf die verschlussfreie Überlebenszeit eines Bypasses. Es konnten keine relevanten Einflussfaktoren auf das amputationsfreie Überleben gefunden werden.
Schlussfolgerungen: Die Thrombosierung eines Aneurysmas scheint mehr Einfluss auf den klinischen Verlauf und das Outcome zu haben als bisher angenommen. Weitere Studien sollten diese Erkenntnis validieren
A fluorescent host-guest complex of cucurbituril in solution: a molecular Jack O'Lantern
No full textFluorescence enhancement of a probe molecule in solution by the container molecule cucurbituril (CB) is reported for the first time. The fluorescence of the probe 2-anilinonaphthalene-6-sulfonate (2,6-ANS) in aqueous Na2SO4 solution is found to increase by a maximum factor of 5.0 upon addition of cucurbituril. This fluorescence enhancement is the result of the formation of a host-guest inclusion complex, in which the guest 2,6-ANS is incorporated inside the cavity of the host, cucurbituril. Measurement of the enhancement as a function of cucurbituril concentration yielded a value of the equilibrium constant (K) of 52 +/- 10 M-1. It is proposed that the mode of inclusion involves the phenyl group of the 2,6-ANS, because of the relatively small size of the cucurbituril cavity. It is further proposed that the observed enhancement is a result of loss of rotational mobility of the phenyl ring relative to the naphthyl fluorophore of 2,6-ANS upon inclusion of the phenyl ring, Since the name cucurbituril is derived from the Latin word for "pumpkin," this fluorescent host-guest complex is referred to as a "molecular Jack O'Lantern," with the 2,6-ANS serving as the candle.PT: J; CR: BEHREND R, 1905, LIEBIGS ANN CHEM, V339, P1 BORTOLUS P, 1996, ADV PHOTOCHEMISTRY P, P1 BUSCHMANN HJ, 1992, J INCLUS PHENOM MOL, V14, P91 BUSCHMANN HJ, 1997, J INCLUS PHENOM MOL, V29, P167 BUSCHMANN HJ, 1998, THERMOCHIM ACTA, V317, P95 BUSCHMANN HJ, 1999, J PHOTOCH PHOTOBIO A, V121, P99 CINTAS P, 1994, J INCLUS PHENOM MOL, V17, P205 CRAM DJ, 1997, CONTAINER MOL THEIR DANTZ DA, 1998, SUPRAMOL CHEM, V9, P79 DELAPENA AM, 1993, J INCLUS PHENOM MOL, V15, P131 DIAMOND D, 1996, CHEM SOC REV, V25, P15 FREEMAN WA, 1981, J AM CHEM SOC, V103, P7367 HOFFMANN R, 1994, J CHEM SOC FARADAY T, V90, P1507 JEON YM, 1996, J AM CHEM SOC, V118, P9790 KOSOWER EM, 1975, J AM CHEM SOC, V97, P2167 KOSOWER EM, 1978, J AM CHEM SOC, V100, P4179 LI S, 1992, CHEM REV, V92, P1457 MOCK WL, 1983, J ORG CHEM, V48, P3618 MOCK WL, 1995, TOP CURR CHEM, V175, P1 MOCK WL, 1996, COMPREHENSIVE SUPRAM, V2, P477 WAGNER BD, 1998, J PHOTOCH PHOTOBIO A, V114, P151 WAGNER BD, 1999, J PHYS CHEM B, V103, P10114 WAGNER BD, 2000, J INCL PHENOM MACRO, V38, P467 WHANG DM, 1998, J AM CHEM SOC, V120, P4899; NR: 24; TC: 16; J9: CAN J CHEM; PG: 4; GA: 473RESource type: Electronic(1
Eine neue Einsicht auf direkte Aktionen des Granulozyten-Kolonie- stimulierenden Faktors im Myokard
No full textGranulocyte colony-stimulating factor (G-CSF) is a known hematopoietic cytokine that promotes proliferation and differentiation of neutrophil progenitors. Since G-CSF is recognized to ameliorate myocardial ischemic injury, it was projected that this effect would translate into stimulating myocardial adaptations similar to the ones promoted by ischemic preconditioning. Accordingly, it was hypothesized that G-CSF stimulates coronary collateral growth (CCG) in a rat model of repetitive episodic ischemia (RI). Groups of animals were subjected to repetitive episodes of 40 sec left anterior descending coronary artery (LAD) occlusion every 20 min for 2h20min, 3 times/day for a total period of 5 days. CCG was deduced from collateral-dependent flow, i.e., flow to LAD dependent-region determined with neutron activated microspheres during occlusion, and expressed as the increase in the ratio between collateral-dependent and normal zone flows from the initial measurement to that of after 5 days of RI. Following RI, G-CSF treatments (100 microg/Kg/day, s.c.) increased CCG (0.47 +/- 0.15 versus vehicle 0.14 +/- 0.06, P<0.01). Surprisingly, G-CSF treatment without RI increased CCG (0.57 +/- 0.18, P<0.01 vs. vehicle) equal to G-CSF + RI. Because redox signalling is known to be critical for CCG and neutrophils are a rich source of NADPH oxidase and reactive oxygen species (ROS), it was further hypothesized that G-CSF stimulates production of ROS. ROS were evaluated by dihydroethidine (DHE) fluorescence, which was injected in the left ventricle (60 μg/kg) during two consecutive episodes of ischemia. DHE fluorescence was double in G-CSF + RI vs. vehicle + RI (P<0.01), and even higher values were found in G-CSF without RI stimulus (P<0.01). Interestingly, immunostaining with a specific neutrophil marker, myeloperoxidase, showed that the DHE signal did not localize in neutrophils but it appeared in cardiac myocytes. To unequivocally determine if G-CSF stimulated ROS production in cardiac myocytes, isolated cardiac myocytes were studied and it was found that the cytokine stimulates the production of ROS and angiogenic factors that are able to promote tube formation in human coronary artery endothelial cells (HCAECs). In addition to affecting neutrophils, G-CSF directly targets cardiac myocytes to produce ROS and angiogenic factors. This direct action of G-CSF in cardiomyocytes shows how this cytokine plays a pivotal role in triggering adaptations of the heart to ischemia including growth of the coronary collaterals.Granulozyten-Kolonie-stimulierender Faktor (engl. granulocyte colony- stimulating factor, G-CSF) ist ein bekanntes hämatopoetisches Zytokin, das die Proliferation und Differenzierung neutrophiler Voläuferzellen fördert. Da G-CSF den Verlauf ischämischer Myokardläsionen positiv beeinflussen kann, wurde angenommen, dass dieser Effekt auf der Stimulation myokardialer Anpassungsvorgänge ähnlich jener nach ischämischer Präkonditionierung beruht. Entsprechend wurde die Hypothese aufgestellt, dass G-CSF in einem Modell repetitiver episodischer Ischämie (RI) in der Ratte koronares Kollateralwachstum (engl. coronary collateral growth, CCG) stimulieren würde. Einzelne Versuchstiergruppen wurden dafür repetitiven Episoden einer 40 Sekunden andauernden Okklusion des Ramus interventricularis anterior der linken Koronorarterie (engl. left anterior descending coronary artery, LAD) ausgesetzt, die für eine Dauer von insgesamt 5 Tagen drei mal pro Tag für 2h 20min alle 20 Minuten wiederholt wurden. CCG wurde dann vom von Kollateralen abhängigen Blutfluss, d.h. vom mit Hilfe von Neutronen-aktivierten- Mikrosphären bestimmten Blutfluss im Strombahngebiet der LAD während der Okklusion, hergeleitet und als Steigerung des Verhältnisses der Durchblutung zwischen LAD- und nichtokkludierten Strombahngebieten von der ursprünglichen Messung zu der Messung 5 Tage nach RI ausgedrückt. Unter RI führte die Gabe von G-CSF (100 microg/kg/d, s.c.) zu gesteigertem CCG (0.47 +/- 0.15 versus Vehikel 0.14 +/- 0.06, P<0.01). Überaschenderweise steigerte G-CSF ohne RI das CCG (0.57 +/- 0.18, P<0.01 vs. Vehikel) wie G-CSF + RI. Da neutrophile Granulozyten reichlich NADPH Oxidase und reaktive Sauerstoffspezies (engl. reactive oxygen species, ROS) enthalten und letztere für das Kollateralwachstum essentiell sind, wurde weiter angenommen, dass G-CSF die Bildung von ROS stimuliert. Das Vorhandensein von ROS wurde dafür anhand der Fluoreszenz von Dihydroethidin (DHE) überprüft, welches während zwei konsekutiver ischämischer Episoden in den linken Ventrikel injiziert wurde. DHE-Fluoreszenz war doppelt so stark in G-CSF + RI gegenüber Vehikel + RI (P<0.01), und sogar noch höhere Werte wurden für G-CSF ohne RI gemessen (P<0.01). Interessanterweise zeigten Immunfärbungen mit Myeloperoxidase als spezifischem Neutrophilen-Marker, dass das DHE Signal nicht in Neutrophilen, dafür aber in Kardiomyozyten lokalisiert war. Um eindeutig festzustellen, ob G-CSF die ROS-Produktion in Kardiomyozyten stimuliert, studierten wir isolierte Kardiomyozyten und fanden heraus, dass G-CSF die Produktion von ROS und angiogenetischen Faktoren stimuliert, welche ihrerseits die Formation tubulärer Strukturen durch koronare Endothelzellen (engl. human coronary artery endothelial cells, HCAECs) fördern. Neben seinem Effekt auf neutrophile Granulozyten fördert G-CSF also auch direkt die Produktion von ROS und angiogenetischen Faktoren in Kardiomyozyten. Dieser direkte Einfluss von G-CSF auf Kardiomyozyten unterstreicht die entscheidende Rolle dieses Zytokins in der Auslösung adaptiver Mechanismen des Herzmuskels unter Ischämie, einschließlich des Wachstums koronarer Kollateralen
Induction of Arteriogenesis via Monocyte enhanced paracrine mechanisms: From preclinical arteriogenesis to clinical studies
No full textHabilitationBuschmannZusammenfassend konnten wir mit den vorliegenden Daten dieser
Habilitationsarbeit zahlreiche Aspekte der molekularen und physiologischen
Grundlagen der Arteriogenese beleuchten. Es ergab sich, dass die
zugrundeliegende Physiologie ausschlaggebend für ein potentiell zu erwartendes
klinisches Ergebnis ist und hier im besonderen, dass eine poststenotische
Steigerung der Kapillarisierung nicht den Blutfluss eines proximal
stenosierten Konduktanzgefässes kompensieren kann. Gerade bei der zerebralen
Arteriogenese findet sich hier eine gute Beweisführung für das Konzept der
Arteriogenese: Versorgung des von einer Minderperfusion bedrohten peripheren
Gewebes durch Kollateralarterien, die wiederum ausserhalb der region at risk
liegen. Somit dürfen sich klinische Ansätze nicht nur auf das ischämische
Gebiet (z.B. die Penumbra) konzentrieren, sondern sollten auch den Fokus auf
der kollateralen Zirkulation haben. Die wesentliche Rolle der Monozyten bei
frühen Phasen adaptiver Arteriogenese bestätigt sich auch in dieser Arbeit.
Neben zellbiologischen Aspekten, wie Hemmung der Monozyten-Apoptose, gehen wir
derzeit davon aus, dass zirkulierende mononukleäre Zellen ein umfassendes
parakrines Programm einleiten, das den kontrollierten Umbau einer
Kollateralarterie garantiert. Hierbei spielen, wie auch von Schaper et al.
gezeigt, Metalloproteasen sowie weitere Enzyme aus dem Kollagenstoffwechsel
eine wichtige Rolle (Arginase). Dennoch führt die Rolle der Monozyten auch zu
einem ying-yang Aspekt, dem gerade vor dem Hintergrund einer möglichen
klinischen Anwendung eine wesentliche Bedeutung zukommen kann: Es bleibt zu
untersuchen, ob die Applikation von zirkulierenden Monozyten (oder
Vorläuferzellen aus Monozytenfraktionen) zu einer Aggravation der
Atherosklerose führt. Für das CC-Chemokin MCP-1 (Monocyte Chemoattractant
Protein-1) konnten wir belegen, dass sich die Atheroskleroseentwicklung in der
Apo-E-Maus drastisch beschleunigte. Eine Applikation von GM-CSF hingegen ist
im Atherosklerosemodell des Kaninchens (Watanabe Kaninchen) nicht pro-
atherogen. Aufgrund der breiten klinischen Anwendung von GM-CSF liegt derzeit
kein Hinweis auf eine Erhöhung von mitogenen Prozessen vor (Tumorprogression,
Retinopathie). Dennoch müssen diese sicherheitsrelevanten Fragen experimentell
und klinisch beantwortet werden, bevor weitere zukünftige Phase 1 und 2
Studien begonnen werden.The present work focusses on the molecular and physiological mechanisms of
arteriogenesis, the rapid proliferation of collateral arteries. A key feature
of arteriogenesis is the role of circulating monocytes, which invade
collateral arterial tissue and participate in the adaptive remodelling of the
latter vessels. It is important to notice, that collateral arteries are the
only connection to peripheral tissue in case of arterial occlusion. Hence a
poststenotic enhancement of capillarization (angiogenesis) is not capable to
enhance tissue perfusion in these regions. In this work we point out, that
monocytes accelerate the speed of arteriogenesis and that monoyte activating
factors such as MCP-1, GM-CSF and TGF-beta are strongly pro-arteriogenic, once
given in an intra-arterial fashion into the collateral circulation. However it
has to be kept in mind, that any pro-monocyte cytokine may also aggravate
atherosclerosis in preclinical models, as investigated here in Apo-E mice. In
fact this does not seem to be the case for Colony-Stimulating Factors, which
are being broadly used in the clinic to enhance the number or circulating
granulocytes under conditions of cytopenia. In experimental models for
arteriogenesis we provide clear data about the perfusion-enhancing effect of
Colony-Stimulating Factors in the periphery. Moreover two of our studies are
being the first to show pro-arteriogenic efficacy of GM-CSF in the brain.
Clinical studies are currently on the way to prove these experimental
findings
Charakterisierung der frühen adaptiven zerebralen Arteriogenese
No full textArteriogenese bezeichnet das adaptive Wachstum von präexistenten kollateralen Arterien. Im Falle eines Arterienverschlusses ist Arteriogenese der endogen effizienteste Kompensationsmechanismus, um das Hypoperfusionsgebiet mit ausreichend Blut zu versorgen (Biologischer Bypasses). In dieser Arbeit wurde das frühe Wachstum von Kollateralgefäßen im Gehirn im ersten Modell für zerebrale Arteriogenese, dem 3-VO Modell (3-vessel occlusion), in der Ratte charakterisiert. (I) Die Untersuchung am nicht-ischämischen 3-VO Hypoperfusionsmodell zeigten, dass 7 Tage nach 3-VO die Arteria cerebri posterior (PCA) signifikant im Diameter anwächst. Histologische Untersuchungen konnten ein vermehrtes Zellwachstum in der PCA und das Einwandern von Makrophagen in den perivaskulären Bereich (24 Stunden und 3 Tage post 3-VO) darstellen und eine Aktivierung des Endothels 3 Tage nach 3-VO wurde mittels Rasterelektronenmikroskopie identifizieren. (II) Für eine genaue Anaylse des globalen Genexpressionsprofils der zerebralen Arteriogense wurde die wachsende PCA selektiv aus dem Gehirn entnommen und ein Genexpressionsprofil für die frühe zerebrale Arteriogenese erstellt (164 Gene dereguliert). Eine Unteruschung von biologischen und molekularen Prozessen zeigte, dass eine Vielzahl der deregulierten Gene in Zellproliferation und Inflammation involviert sind. Die Expression der Protease-Inhibitoren Kininogen und TIMP-1 wurde als “Marker” der frühen Arteriogenese in der PCA lokalisiert werden. Zusammenfassend zeigt diese Arbeit erstmals eine Übersicht der biologischen Prozesse in der zerebralen Arteriogenese und eröffnet neue Ideen für eine mögliche therapeutische Strategie.Arteriogenesis, the adaptive outward growth of pre-existing collateral arteries, is the most efficient endogenous rescue mechanisms in vertebrates against the occlusion of a major artery (biological bypass). Here, collateral growth was induced using the first model for cerebral arteriogenesis, the 3-vessel occlusion (3-VO) rat model. (I) 3-VO resulted in a significant diameter increase within 7 days in the posterior cerebral artery (PCA) and posterior communicating artery (Pcom), classifying the region of interest. Immunhistological staining demonstrated proliferative activation and macrophage invasion, already 24h post 3-VO within the PCA, confirming the arteriogenic phenotype. Furthermore, activation of the PCA endothelium was detected within 3 days post 3-VO by scanning electron microscopy. (II) For analysing the molecular mechanism of cerebral arteriogenesis, collateral tissue from the growing PCA was selectively isolated. Here, 24h post 3-VO 164 genes were detected to be significantly deregulated. Analysis of molecular annotations and networks associated with differentially expressed genes revealed that expression patterns contain gene transcripts predominantly involved in proliferation, inflammation, and migration. Early-phase cerebral arteriogenesis is characterized by protease inhibitor expression and showed that protease inhibitors TIMP-1 and kininogen are molecular markers of early-phase cerebral arteriogenesis. In summary, this work characterizes morphological features and genomic profiles of growing collaterals in the brain and develops novel ideas for a therapeutic stimulation of arteriogenesis
The systematic design and application of robust DNA barcodes
No full textHigh-throughput sequencing technologies are improving in quality, capacity, and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag, index, or barcode that is attached to the sequencing or amplification primer and hence accompanies every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence. Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and codes based on the Levenshtein distance. Levenshtein-based codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this thesis we demonstrate the decreased error correction capability of Levenshtein-based codes in a DNA context and suggest an adaptation of Levenshtein-based codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaptation, we take any DNA context into account and impose more strict rules for the selection of barcode sets. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors. We present an adaptation of Levenshtein-based codes to DNA contexts capable of guaranteed correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of correcting on average more random mutations than traditional Levenshtein-based or Hamming codes. As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance. However, not every platform is susceptible to a large number of both indel and substitution errors. The Illumina ""Sequencing by Synthesis"" platform shows a very large number of substitution errors as well as a very specific shift of the read that results in inserted and deleted bases at the 5'-end and the 3'-end (which we call phaseshifts). We argue in this scenario that the application of Sequence-Levenshtein-based codes is not efficient because it aims for a category of errors that barely occurs on this platform, which reduces the code size needlessly. As a solution, we propose the ""Phaseshift distance"" that exclusively supports the correction of substitutions and phaseshifts. Additionally, we enable the correction of arbitrary combinations of substitution and phaseshift errors. Thus, we address the lopsided number of substitutions compared to phaseshifts on the Illumina platform. To compare codes based on the Phaseshift distance to Hamming Codes as well as codes based on the Sequence-Levenshtein distance, we simulated an experimental scenario based on the error pattern we identified on the Illumina platform. Furthermore, we generated a large number of different sets of DNA barcodes using the Phaseshift distance and compared codes of different lengths and error correction capabilities. We found that codes based on the Phaseshift distance can correct a number of errors comparable to codes based on the Sequence-Levenshtein distance while offering the number of DNA barcodes comparable to Hamming codes. Thus, codes based on the Phaseshift distance show a higher efficiency in the targeted scenario. In some cases (e.g., with PacBio SMRT in Continuous Long Read mode), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives. For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements
The Systematic Design and Application of Robust DNA Barcodes
No full textHigh-throughput sequencing technologies are improving in quality, capacity, and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag, index, or barcode that is attached to the sequencing or amplification primer and hence accompanies every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.
Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and codes based on the Levenshtein distance.
Levenshtein-based codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this thesis we demonstrate the decreased error correction capability of Levenshtein-based codes in a DNA context and suggest an adaptation of Levenshtein-based codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaptation, we take any DNA context into account and impose more strict rules for the selection of barcode sets. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors.
We present an adaptation of Levenshtein-based codes to DNA contexts capable of guaranteed correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of correcting on average more random mutations than traditional Levenshtein-based or Hamming codes. As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.
However, not every platform is susceptible to a large number of both indel and substitution errors. The Illumina “Sequencing by Synthesis” platform shows a very large number of substitution errors as well as a very specific shift of the read that results in inserted and deleted bases at the 5’-end and the 3’-end (which we call phaseshifts). We argue in this scenario that the application of Sequence-Levenshtein-based codes is not efficient because it aims for a category of errors that barely occurs on this platform, which reduces the code size needlessly. As a solution, we propose the “Phaseshift distance” that exclusively supports the correction of substitutions and phaseshifts. Additionally, we enable the correction of arbitrary combinations of substitution and phaseshift errors. Thus, we address the lopsided number of substitutions compared to phaseshifts on the Illumina platform.
To compare codes based on the Phaseshift distance to Hamming Codes as well as codes based on the Sequence-Levenshtein distance, we simulated an experimental scenario based on the error pattern we identified on the Illumina platform. Furthermore, we generated a large number of different sets of DNA barcodes using the Phaseshift distance and compared codes of different lengths and error correction capabilities. We found that codes based on the Phaseshift distance can correct a number of errors comparable to codes based on the Sequence-Levenshtein distance while offering the number of DNA barcodes comparable to Hamming codes. Thus, codes based on the Phaseshift distance show a higher efficiency in the targeted scenario. In some cases (e.g., with PacBio SMRT in Continuous Long Read mode), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives.
For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements
Arteriogenesis as a new therapeutic intervention strategy in chronic artery disorders. Cellular mechanism and experimental models
No full text- …
