Publications by authors named "Michael Graf"

86 Publications

Yokoyama procedure for esotropia associated with high myopia: real-world data from a large-scale multicentre analysis.

Acta Ophthalmol 2021 Mar 2. Epub 2021 Mar 2.

Department of Ophthalmology, University of Bonn, Bonn, Germany.

Purpose: High myopic patients may develop strabismus due to globe dislocation out of the normal extraocular muscle cone. Surgical correction of this strabismus type is possible by joining the superior and lateral rectus muscles without the need for a scleral suture called the Yokoyama procedure. Data from large patient samples and the evaluation of a potential effect of an additional medial rectus recession (MRR) have been lacking so far.

Methods: We pooled retrospective patient data of 14 departments of ophthalmology in Germany and Switzerland and analysed determinants of postoperative results using multivariable regression models.

Results: We included 133 patients (mean age: 59.7 ± 13.4 years, surgery between 2008 and 2017) with a mean preoperative esotropia (both Yokoyama with and without MRR) of 23.8°±4.6°. The angle of preoperative esotropia increased with age. The postoperative esotropia was 8.7° ± 9.9°, and six patients were overcorrected. While preoperative esotropia was highly associated with postoperative results, we found no association of additional MRR with any of our postoperative outcome measures. The Yokoyama procedure had a higher absolute effect in patients with higher preoperative esotropia.

Conclusion: Our study confirms the positive effect of the Yokoyama procedure on strabismus due to high myopia in large-scale real-world data. In some cases, MRR may be needed because of muscle contracture, although additional MRR statistically did not affect the postoperative outcome. In patients with bilateral high myopic strabismus, correction of both eyes seems beneficial. The effect size of the Yokoyama procedure appears to be mainly driven by preoperative esotropia.
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http://dx.doi.org/10.1111/aos.14808DOI Listing
March 2021

[Bridle operation for incomplete oculomotor nerve paralysis (superior rectus and lateral rectus nasal inferior transposition)].

Authors:
Michael Gräf

Ophthalmologe 2021 Mar 1. Epub 2021 Mar 1.

Klinik und Poliklinik für Augenheilkunde, Universitätsklinikum Gießen und Marburg GmbH, Standort Gießen, Friedrichstr. 18, 35392, Gießen, Deutschland.

Purpose: To demonstrate the technique and effectiveness of the bridle operation for oculomotor nerve paralysis with maintained elevation.

Method: The bridle operation includes transposition of the lateral rectus muscle (passing behind inferior oblique and rectus muscles) and the superior rectus muscle (behind superior oblique tendon and medial rectus muscle) to the nasal inferior surface of the globe.

Results: In the reported case, this procedure corrected exo-hypertropia of 30-40°/20-30° without inducing cyclotropia.

Conclusion: The bridle operation expands the surgical arsenal for paralytic strabismus.
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http://dx.doi.org/10.1007/s00347-021-01339-yDOI Listing
March 2021

Absence of local moments in the kagome metal KVSbas determined by muon spin spectroscopy.

J Phys Condens Matter 2021 May 10;33(23). Epub 2021 May 10.

Department of Physics, Boston College, Chestnut Hill, MA 02467, United States of America.

We have carried out muon spin relaxation and rotation measurements on the newly discovered kagome metal KVSb, and find a local field dominated by weak magnetic disorder which we associate with the nuclear moments present, and a modest temperature dependence which tracks the bulk magnetic susceptibility. We find no evidence for the existence of Vlocal moments, suggesting that the physics underlying the recently reported giant unconventional anomalous Hall effect in this material warrants further studies.
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http://dx.doi.org/10.1088/1361-648X/abe8f9DOI Listing
May 2021

[Three-muscle surgery for large angle esotropia].

Ophthalmologe 2021 Jan 20. Epub 2021 Jan 20.

Klinik und Poliklinik für Augenheilkunde, Universitätsklinikum Gießen und Marburg, Standort Gießen, Friedrichstr. 18, 35392, Gießen, Deutschland.

Background: Bilateral medial rectus muscle recession with or without Cüppers' posterior fixation suture and recess and resect surgery are used to correct for large angle esotropia. There are only few reports on three muscle surgery (3MS). We analyzed the results of 3MS.

Patients And Methods: Between June 2016 and May 2020, 61 patients received 3MS for esotropia ≥ 27° (50 PD) together with oblique muscle surgery, if needed. Angles of strabismus were measured by simultaneous prism and cover testing (SPCT) and alternating prism and cover testing (APCT) at 5 m and 0.3 m. Grading was around 0.51 mm/degree (at 5 m). Medium-term results of 57 patients were available.

Results: Medians and ranges (min-max) were: age, 6 years (3-56 years). Preoperative APCT, far 34° (27-45°), near 36° (27-50°). Amount of surgery, 17 mm (15-21 mm), oblique muscle recession in 21 cases. The APCT after 5 months (3-24 months), far 2° (-10-18), near 2° (-8-18). Success rates (absolute deviation ≤ 6° [10 PD]), APCT far 68%, near 67%, SPCT far 79%, near 74%. Exotropia > 6° occurred in 4 cases (7%) at far and 3 (5%) at near, esotropia > 6° in 14 cases (25%) at far and 16 (28%) at near.

Conclusion: The use of 3MS is a suitable first step procedure to correct for large angle esotropia.
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http://dx.doi.org/10.1007/s00347-020-01318-9DOI Listing
January 2021

Microscopic Detection Analysis of Single Molecules in MoS Membrane Nanopores.

ACS Nano 2020 11 6;14(11):16131-16139. Epub 2020 Nov 6.

Department of Electrical and Computer Engineering, and N. Holonyak Jr. Micro & Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

A systematic microscopic analysis of the various resistive effects involved in the electronic detection of single biomolecules in a nanopore of a MoS nanoribbon is presented. The variations of the transverse electronic current along the two-dimensional (2D) membrane due to the translocation of DNA and protein molecules through the pore are obtained by model calculations based on molecular dynamics (MD) and Boltzmann transport formalism, which achieved good agreement with the experimental data. Our analysis points to a self-consistent interaction among ions, charge carriers around the pore rim, and biomolecules. It provides a comprehensive understanding of the effects of the electrolyte concentration, pore size, nanoribbon geometry, and also the doping polarity of the nanoribbon on the electrical sensitivity of the nanopore in detecting biomolecules. These results can be utilized for fine-tuning the design parameters in the fabrication of highly sensitive 2D nanopore biosensors.
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http://dx.doi.org/10.1021/acsnano.0c08382DOI Listing
November 2020

SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition.

Nat Immunol 2021 01 30;22(1):74-85. Epub 2020 Sep 30.

Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany.

T cell immunity is central for the control of viral infections. To characterize T cell immunity, but also for the development of vaccines, identification of exact viral T cell epitopes is fundamental. Here we identify and characterize multiple dominant and subdominant SARS-CoV-2 HLA class I and HLA-DR peptides as potential T cell epitopes in COVID-19 convalescent and unexposed individuals. SARS-CoV-2-specific peptides enabled detection of post-infectious T cell immunity, even in seronegative convalescent individuals. Cross-reactive SARS-CoV-2 peptides revealed pre-existing T cell responses in 81% of unexposed individuals and validated similarity with common cold coronaviruses, providing a functional basis for heterologous immunity in SARS-CoV-2 infection. Diversity of SARS-CoV-2 T cell responses was associated with mild symptoms of COVID-19, providing evidence that immunity requires recognition of multiple epitopes. Together, the proposed SARS-CoV-2 T cell epitopes enable identification of heterologous and post-infectious T cell immunity and facilitate development of diagnostic, preventive and therapeutic measures for COVID-19.
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http://dx.doi.org/10.1038/s41590-020-00808-xDOI Listing
January 2021

Bifunctional Nitrone-Conjugated Secondary Metabolite Targeting the Ribosome.

J Am Chem Soc 2020 10 19;142(43):18369-18377. Epub 2020 Oct 19.

Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.

Many microorganisms possess the capacity for producing multiple antibiotic secondary metabolites. In a few notable cases, combinations of secondary metabolites produced by the same organism are used in important combination therapies for treatment of drug-resistant bacterial infections. However, examples of conjoined roles of bioactive metabolites produced by the same organism remain uncommon. During our genetic functional analysis of oxidase-encoding genes in the everninomicin producer var. , we discovered previously uncharacterized antibiotics everninomicin N and O, comprised of an everninomicin fragment conjugated to the macrolide rosamicin via a rare nitrone moiety. These metabolites were determined to be hydrolysis products of everninomicin P, a nitrone-linked conjugate likely the result of nonenzymatic condensation of the rosamicin aldehyde and the octasaccharide everninomicin F, possessing a hydroxylamino sugar moiety. Rosamicin binds the erythromycin macrolide binding site approximately 60 Å from the orthosomycin binding site of everninomicins. However, while individual ribosomal binding sites for each functional half of everninomicin P are too distant for bidentate binding, ligand displacement studies demonstrated that everninomicin P competes with rosamicin for ribosomal binding. Chemical protection studies and structural analysis of everninomicin P revealed that everninomicin P occupies both the macrolide- and orthosomycin-binding sites on the 70S ribosome. Moreover, resistance mutations within each binding site were overcome by the inhibition of the opposite functional antibiotic moiety binding site. These data together demonstrate a strategy for coupling orthogonal antibiotic pharmacophores, a surprising tolerance for substantial covalent modification of each antibiotic, and a potential beneficial strategy to combat antibiotic resistance.
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http://dx.doi.org/10.1021/jacs.0c04675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8129991PMC
October 2020

[Highly dosed Anderson and Kestenbaum operations for anomalous head posture due to nystagmus].

Ophthalmologe 2020 Dec;117(12):1210-1217

Fachbereich Medizin, Justus-Liebig-Universität Gießen, Gießen, Deutschland.

Background: The correction of anomalous head posture associated with infantile nystagmus syndrome (INS) is carried out by the Kestenbaum procedure (KP) combining bilateral horizontal yoke muscle recession with resection of their antagonists or by the Anderson procedure (AP) which is confined to yoke muscle recession alone.

Aim Of The Study: To compare the results of highly dosed AP and KP for anomalous head turn (HT).

Patients And Methods: The AP (2013-2019) and KP (2003-2013) were used as the exclusive procedures during the respective time periods. A highly dosed AP was performed in a case series of 33 consecutive orthotropic patients with INS and KP in 19 orthotropic patients with INS. Medians and ranges (min-max) in groups AP/KP were: age at surgery 7 years (4-44 years)/6 years (4-27 years), HT 32.5° (20-45°)/30° (17-40°) and surgery on each eye AP 13 mm (10-16 mm) (standard dose), KP 10 mm (6-12 mm) + 10 mm (6-12 mm) (mean 0.6 mm/°HT).

Results: The HT was diminished to 10° (-3-20°)/10° (-7-20°) ca. 3 months after surgery. At the late visit (8-153 months), the residual HT was 10° (0-20°)/10° (-27-30°). The HT was reduced by 67% (20-100%)/64% (14-100%) at the last control. A residual HT ≤15° was present in 79%/81% of cases (91% after AP ≥13 mm; n = 23) and HT ≤10° in 55%/57%, (65% after AP ≥13 mm). The maximum adduction/abduction towards the recessed muscles was 30°/30° (10-37°/15-45°) after AP and 32°/30° (10-40°/12-45°) after KP. An associated head tilt was not improved by the intervention. Mean binocular visual acuity increased by <1 line in both procedures. After AP the mean increase was 1 line in children ≤6 years old and there was no increase in patients >6 years of age.

Conclusion: The effectiveness and success rates of AP and KP were similar with the dosing used. Less invasive surgery is an advantage in favor of AP as the primary procedure.
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http://dx.doi.org/10.1007/s00347-020-01086-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7717044PMC
December 2020

Transverse Detection of DNA Using a MoS Nanopore.

Nano Lett 2019 12 11;19(12):9075-9083. Epub 2019 Nov 11.

Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland.

Classical nanopore sensing relies on the measurement of the ion current passing through a nanopore. Whenever a molecule electrophoretically translocates through the narrow constriction, it modulates the ion current. Although this approach allows one to measure single molecules, the access resistance limits the spatial resolution. This physical limitation could potentially be overcome by an alternative sensing scheme taking advantage of the current across the membrane material itself. Such an electronic readout would also allow better temporal resolution than the ionic current. In this work, we present the fabrication of an electrically contacted molybdenum disulfide (MoS) nanoribbon integrated with a nanopore. DNA molecules are sensed by correlated signals from the ionic current through the nanopore and the transverse current through the nanoribbon. The resulting signal suggests a field-effect sensing scheme where the charge of the molecule is directly sensed by the nanoribbon. We discuss different sensing schemes such as local potential sensing and direct charge sensing. Furthermore, we show that the fabrication of freestanding MoS ribbons with metal contacts is reliable and discuss the challenges that arise in the fabrication and usage of these devices.
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http://dx.doi.org/10.1021/acs.nanolett.9b04180DOI Listing
December 2019

A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling.

Nucleic Acids Res 2019 09;47(16):8807-8820

Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.

Translation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related protein, New1, is encoded by a non-essential gene with cold sensitivity and ribosome assembly defect knock-out phenotypes. Since the exact molecular function of New1 is unknown, it is unclear if the ribosome assembly defect is direct, i.e. New1 is a bona fide assembly factor, or indirect, for instance due to a defect in protein synthesis. To investigate this, we employed yeast genetics, cryo-electron microscopy (cryo-EM) and ribosome profiling (Ribo-Seq) to interrogate the molecular function of New1. Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3. The structure of the ATPase-deficient (EQ2) New1 mutant locked on the 80S ribosome reveals that New1 binds analogously to the ribosome as eEF3. Finally, Ribo-Seq analysis revealed that loss of New1 leads to ribosome queuing upstream of 3'-terminal lysine and arginine codons, including those genes encoding proteins of the cytoplasmic translational machinery. Our results suggest that New1 is a translation factor that fine-tunes the efficiency of translation termination or ribosome recycling.
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http://dx.doi.org/10.1093/nar/gkz600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145556PMC
September 2019

Quality of Life After Total Mesorectal Excision and Rectal Replacement: Comparing Side-to-End, Colon J-Pouch and Straight Colorectal Reconstruction in a Randomized, Phase III Trial (SAKK 40/04).

Ann Surg Oncol 2019 Oct 21;26(11):3568-3576. Epub 2019 Jun 21.

Kreiskliniken Lörrach, Lörrach, Germany.

Background: Functional outcomes of different reconstruction techniques have an impact on patients' quality of life (QoL), but information on long-term QoL is lacking. We compared QoL among three reconstruction techniques after total mesorectal excision (TME).

Methods: Quality of life was assessed within a randomized, multicenter trial comparing rectal surgery using side-to-end anastomosis (SEA), colon J-pouch (CJP), and straight colorectal anastomosis (SCA) by the Functional Assessment of Cancer Therapy-Colorectal scale (FACT-C) before randomization and every 6 months up to 2 years post-TME. The primary QoL endpoint was the change in the Trial Outcome Index (TOI), including the FACT-C subscales of physical and functional well-being and colorectal cancer symptoms (CSS), from baseline to month 12. Pair-wise comparisons of changes from baseline (presurgery) to each timepoint between the three arms were analyzed by Mann-Whitney tests.

Results: For the QoL analysis, 257 of 336 randomized patients were in the per protocol evaluation (SEA = 95; CJP = 63; SCA = 99). Significant differences between the reconstruction techniques were found for selected QoL scales up to 12 months, all in favor of CJP. Patients with SEA or SCA reported a clinically relevant deterioration for TOI and CSS at 6 months, those with SCA for CSS also at 12 months after TME. Patients with CJP remained stable.

Conclusions: Although the three reconstruction techniques differ in their effects on QoL at months 6 and 12, these differences did not persist over the whole observation period of 24 months. Patients with a colon J-pouch may benefit with respect to QoL in the short-term.
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http://dx.doi.org/10.1245/s10434-019-07525-2DOI Listing
October 2019

High-dose Anderson operation for nystagmus-related anomalous head turn.

Graefes Arch Clin Exp Ophthalmol 2019 Sep 14;257(9):2033-2041. Epub 2019 Jun 14.

Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany.

Purpose: To evaluate the effectiveness of a high-dose Anderson procedure (AP) to correct infantile nystagmus-related anomalous head turn (HT).

Methods: Twenty-nine consecutive orthotropes with infantile nystagmus with and without associated sensory defect received high-dose AP. HT was measured while the patient tried to read letters at best-corrected visual acuity (BCVA) level at 5 m and 0.3 m. BCVA, binocular vision (BV), and alignment (prism and cover test) were measured. High-dose AP with recessions of 9-16 mm was performed. All measures were taken before and 3-6 and ≥ 8 months post surgery. Success was defined by postoperative HT ≤ 10°/HT ≤ 15°.

Results: Medians and ranges (minimum-maximum) were:. Age at surgery was 7 years (4-44). HT at 5 m and HT at 0.3 m were 35° (20-40) and 20° (0-35), respectively. After 4 months (3-6), HT was 10° (- 3-20) and 5° (- 5-20); success rates were 74%/96% and 83%/96%. After 15 months (8-45), HT was 12° (0-20) and 6° (0-15); success rates were 46%/75% and 92%/100%; residual HT > 15° occurred in 5/9 cases with recessions < 13 mm and 1/15 cases with recessions ≥ 13 mm. With recessions ≥ 13 mm, 60% (95% confidence intervals (C.I.), 33-83%) achieved HT ≤ 10° and 93% (95% C.I. 66-99%) achieved HT ≤ 15°. Overcorrection did not occur. Anomalous head posture components in vertical and frontal planes did not improve. Residual motility was 30° (10-45). The mean BCVA improved by only 0.037 logMAR (p = 0.06). BV and ocular alignment were constant, except in 2 patients whose exophoria decompensated.

Conclusions: Kestenbaum surgery is a common procedure to correct infantile nystagmus-related HT. Anderson surgery is confined to bilateral yoke muscle recession; hence, less invasive but nevertheless comparably effective, high dosage is provided.
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http://dx.doi.org/10.1007/s00417-019-04369-0DOI Listing
September 2019

Splitting of the lateral rectus muscle with medial transposition to treat oculomotor palsy: a retrospective analysis of 29 consecutive cases.

Graefes Arch Clin Exp Ophthalmol 2019 Sep 6;257(9):2005-2014. Epub 2019 Jun 6.

Department of Ophthalmology, Justus Liebig University Giessen, Universitaetsklinikum Giessen and Marburg GmbH, Giessen Campus, Friedrichstrasse 18, 35385, Giessen, Germany.

Purpose: The lateralis splitting technique has been an interesting option for treating large-angle exotropia due to complete 3rd nerve paralysis since its inception in the early 1990s. The purpose of this study is to report on our experience regarding the effectiveness and complications of this method.

Methods: Retrospective analysis of a consecutive series of 29 patients operated by one single experienced surgeon and examined according to a specific operative and perioperative protocol. Patients were examined preoperatively, on the 2nd day and 3rd month after surgery. Outcome measures include strabismus angle, horizontal motility, head turn, binocular function, and incidence and resolution of postoperative serous retinal detachment as seen with infrared imaging and spectral domain optical coherence tomography (SD-OCT).

Results: Surgery brought about a large and stable reduction of strabismus angle and head turn. It reduced horizontal motility, but moved the range of monocular excursion much closer to center. Eighty percent of patients with constant diplopia acquired some fields of single binocular vision. A significant number of cases (33.3%) developed transitory serous retinal detachment with varying onset and extent.

Conclusion: This is by far the largest published study regarding the outcome of lateralis splitting in NIII palsy. The procedure is difficult, yet a very useful option. Serous detachment is a serious complication, but usually transitory. Its cause and mechanisms are not fully understood and warrant further investigation.
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http://dx.doi.org/10.1007/s00417-019-04370-7DOI Listing
September 2019

Intracellular Antimicrobial Peptides Targeting the Protein Synthesis Machinery.

Adv Exp Med Biol 2019 ;1117:73-89

Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.

While antimicrobial peptides (AMPs) are well-known for their disruptive effects on bacterial membranes, the mechanism of many intracellular AMPs is still being elucidated. In the recent years, it has been demonstrated that the subclass of proline-rich AMPs (PrAMPs) can pass through the bacterial membrane and kill bacteria by inhibiting protein synthesis. PrAMPs are a product of the innate immune system and are secreted in response to bacterial infection. So far PrAMPs have been identified in many arthropods, such as beetles, wasps, and flies, as well as some mammals, such as sheep, cows, and goats. PrAMPs show high potency against Gram-negative bacteria, while exhibiting low toxicity in eukaryotes, suggesting that they may represent a promising avenue for the development of future antimicrobial agents to combat the increase of multidrug-resistant bacterial pathogens. Structural and biochemical data have revealed the PrAMP binding sites on the ribosome as well as insight into their mechanisms of action. While the binding site of all so far investigated PrAMPs is situated within nascent polypeptide exit tunnel, the mechanism of action is distinct between class I and II PrAMPs. Specifically, class I PrAMPs, such as Bac7, Onc112, pyrrhocoricin, and metalnikowin, block the delivery of aa-tRNA by EF-Tu to the ribosomal A-site, whereas the class II PrAMPs, such as apidaecin 1b and Api137, act during translation termination and inhibit protein synthesis by trapping of release factors on the 70S ribosome following hydrolysis of the nascent polypeptide chain.
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http://dx.doi.org/10.1007/978-981-13-3588-4_6DOI Listing
August 2019

[Temporary elevation deficit with exophthalmos in a 4-year-old child].

Ophthalmologe 2020 Jan;117(1):58-61

Klinik und Poliklinik für Augenheilkunde, Standort Gießen, Universitätsklinikum Gießen und Marburg GmbH, Friedrichstr. 18, 35385, Gießen, Deutschland.

A 4-year-old girl was referred as an emergency case because of diplopia and intermittent exophthalmos of the left eye. Symptoms had occurred together with recurrent episodes of a common cold. The examinations revealed no conspicuous findings. Photographic and video analysis revealed hypotropia of approximately 25 ° together with protrusion of the left eye. The patient history and findings were compatible with a superior oblique click syndrome with an atypical distal distinct thickening of the superior oblique tendon. Rheumatological and otorhinolaryngological findings were inconspicuous.
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http://dx.doi.org/10.1007/s00347-019-0880-8DOI Listing
January 2020

Fabrication and practical applications of molybdenum disulfide nanopores.

Nat Protoc 2019 04 22;14(4):1130-1168. Epub 2019 Mar 22.

Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland.

Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin membranes have the advantage of providing relatively high ionic currents at very small pore sizes. This increases the signal generated during translocation of biomolecules and improves the nanopores' efficiency when used for desalination or reverse electrodialysis applications. The atomic thickness of MoS nanopores approaches the inter-base distance of DNA, creating a potential candidate for DNA sequencing. In terms of geometry, MoS nanopores have a well-defined vertical profile due to their atomic thickness, which eliminates any unwanted effects associated with uneven pore profiles observed in other materials. This protocol details all the necessary procedures for the fabrication of solid-state devices. We discuss different methods for transfer of monolayer MoS, different approaches for the creation of nanopores, their applicability in detecting DNA translocations and the analysis of translocation data through open-source programming packages. We present anticipated results through the application of our nanopores in DNA translocations and osmotic power generation. The procedure comprises four parts: fabrication of devices (2-3 d), transfer of MoS and cleaning procedure (24 h), the creation of nanopores within MoS (30 min) and performing DNA translocations (2-3 h). We anticipate that our protocol will enable large-scale manufacturing of single-molecule-analysis devices as well as next-generation DNA sequencing.
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http://dx.doi.org/10.1038/s41596-019-0131-0DOI Listing
April 2019

Extracorporeal life support in hypothermic cardiac arrest: Reconsidering trauma as an absolute contraindication.

Resuscitation 2019 02 16;135:228-229. Epub 2018 Dec 16.

Dept. of Anesthesiology & Pain Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.

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http://dx.doi.org/10.1016/j.resuscitation.2018.11.011DOI Listing
February 2019

Reproducibility of CBCT image analysis: a clinical study on intrapersonal and interpersonal errors in bone structure determination.

Oral Radiol 2019 05 27;35(2):152-158. Epub 2018 Jul 27.

Department of Prosthetic Dentistry, Center of Dentistry, Ulm University, Albert-Einstein-Allee 1, 89081, Ulm, Germany.

Objective: For correct implant planning based on cone-beam computed tomography (CBCT), the bone contour must be accurately determined. Identification of the contour is difficult in bones with incomplete mineralization. In this clinical study, we investigated the intrapersonal and interpersonal reproducibilities of manual bone contour determination on CBCT images using a semi-automated computerized process.

Methods: The bone surface level in the area of the socket in 20 patients who had undergone tooth extraction from the upper jaw at 10 ± 1 weeks previously was determined on CBCT images. Two investigators with different levels of experience determined the bone structure initially (T) and repeated the procedure after 3 months (T). The bone structure marked on CBCT images was converted into a surface data set. The resulting data sets were superimposed on one another. In the analyses, the shortest distances between the datasets were identified and measured. The average deviations were statistically evaluated.

Results: The intrapersonal evaluation resulted in an average deviation of 0.18 mm across both investigators. The interpersonal analysis comparing the two investigators resulted in average deviations of 0.15 mm at T and 0.26 mm at T. Significant differences were not found.

Conclusions: The low intrapersonal deviation indicates that the procedure has satisfactory reproducibility. All deviations were within the range of the selected resolution of the CBCT device. Application of a semi-automated procedure to detect the bone border in areas with incomplete mineralization is a predictable process.

Trial Registration: The study was registered in the German Clinical Trials Register and the International Clinical Trials Registry Platform of the WHO: DRKS00004769, date of registration: 28 February 2013; and DRKS00005978, date of registration: 09 November 2015.
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http://dx.doi.org/10.1007/s11282-018-0340-1DOI Listing
May 2019

Clinical Outcome After Rectal Replacement With Side-to-End, Colon-J-Pouch, or Straight Colorectal Anastomosis Following Total Mesorectal Excision: A Swiss Prospective, Randomized, Multicenter Trial (SAKK 40/04).

Ann Surg 2019 05;269(5):827-835

Clinic for General and Visceral Surgery, Regional Hospital Lörrach, Lörrach, Germany.

Objective: To compare, in a phase 3, prospective, randomized, multi-center clinical trial functional outcome of reconstruction procedures following total mesorectal excision (TME).

Summary Background Data: Intestinal continuity reconstruction following TME is accompanied by postoperative defecation dysfunctions known as "anterior resection syndrome." Commonly used reconstruction techniques are straight colorectal anastomosis (SCA), colon J -pouch (CJP), and side-to-end anastomosis (SEA). Comparison of their functional outcomes in prospective, randomized, multi-center studies, including long-term assessments, is lacking.

Methods: Patients requiring TME for histologically proven rectal tumor, with or without neoadjuvant treatment, age ≥ 18 years, normal sphincter function without history of incontinence, any pretreatment staging or adenoma, expected R0-resection, were randomized for standardized SCA, CJP, or SEA procedures. Primary endpoint was comparison of composite evacuation scores 12 months after TME. Comparison of composite evacuation and incontinence scores at 6, 18 and 24 months after surgery, morbidity, and overall survival represented secondary endpoints. Analysis was based on "per protocol" (PP) population, fully complying with trial requirements, and intention-to treat (ITT) population.

Results: Three hundred thirty-six patients from 15 hospitals were randomized. PP population included 257 patients (JCP = 63; SEA = 95; SCA = 99). Composite evacuation scores of PP and ITT populations did not show statistically significant differences among the 3 groups at any time point. Similarly, composite incontinence scores for PP and ITT populations showed no statistically significant difference among the 3 trial arms at any time point.

Conclusions: Within boundaries of investigated procedures, surgeons in charge may continue to perform reconstruction of intestinal continuity following TME at their technical preference.
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http://dx.doi.org/10.1097/SLA.0000000000003057DOI Listing
May 2019

Structural basis for antibiotic resistance mediated by the ABCF ATPase VmlR.

Proc Natl Acad Sci U S A 2018 09 20;115(36):8978-8983. Epub 2018 Aug 20.

Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany;

Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In , the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient VmlR-EQ mutant in complex with a ErmDL-stalled ribosomal complex (SRC). The structure reveals that VmlR binds within the E site of the ribosome, with the antibiotic resistance domain (ARD) reaching into the peptidyltransferase center (PTC) of the ribosome and a C-terminal extension (CTE) making contact with the small subunit (SSU). To access the PTC, VmlR induces a conformational change in the P-site tRNA, shifting the acceptor arm out of the PTC and relocating the CCA end of the P-site tRNA toward the A site. Together with microbiological analyses, our study indicates that VmlR allosterically dissociates the drug from its ribosomal binding site and exhibits specificity to dislodge VgM, Lnc, and the pleuromutilin tiamulin (Tia), but not chloramphenicol (Cam), linezolid (Lnz), nor the macrolide erythromycin (Ery).
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http://dx.doi.org/10.1073/pnas.1808535115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6130385PMC
September 2018

Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1.

Nat Commun 2018 08 3;9(1):3053. Epub 2018 Aug 3.

Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.

During translation termination in bacteria, the release factors RF1 and RF2 are recycled from the ribosome by RF3. While high-resolution structures of the individual termination factors on the ribosome exist, direct structural insight into how RF3 mediates dissociation of the decoding RFs has been lacking. Here we have used the Apidaecin 137 peptide to trap RF1 together with RF3 on the ribosome and visualize an ensemble of termination intermediates using cryo-electron microscopy. Binding of RF3 to the ribosome induces small subunit (SSU) rotation and swivelling of the head, yielding intermediate states with shifted P-site tRNAs and RF1 conformations. RF3 does not directly eject RF1 from the ribosome, but rather induces full rotation of the SSU that indirectly dislodges RF1 from its binding site. SSU rotation is coupled to the accommodation of the GTPase domain of RF3 on the large subunit (LSU), thereby promoting GTP hydrolysis and dissociation of RF3 from the ribosome.
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http://dx.doi.org/10.1038/s41467-018-05465-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076264PMC
August 2018

Orthogonal Tip-to-Tip Nanocapillary Alignment Allows for Easy Detection of Fluorescent Emitters in Femtomolar Concentrations.

Nano Lett 2018 05 6;18(5):3165-3171. Epub 2018 Apr 6.

Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland.

Here we present the realization of a novel fluorescence detection method based on the electromigration of fluorescent molecules within a nanocapillary combined with the laser excitation through a platinum (Pt)-coated nanocapillary. By using the Pt nanocapillary assisted focusing of a laser beam, we completely remove the background scattering on the tip of the electrophoretic nanocapillary. In this excitation geometry, we demonstrate a 1000-fold sensitivity enhancement (1.0 nM to 1.0 pM) compared to the detection in microcapillaries with epifluorescence illumination and fluorescence spectrophotometry. Due to a significant electroosmotic flow, we observe a decelerating migration of DNA molecules close to the tip of the electrophoretic nanocapillary. The reduced DNA translocation velocity causes a two-step stacking process of molecules in the tip of the nanocapillary and can be used as a way to locally concentrate molecules. The sensitivity of our method is further improved by a continuous electrokinetic injection of DNA molecules followed by sample zone stacking on the tip of the nanocapillary. Concentrations ranging from 0.1 pM to 1.0 fM can be directly observed on the orifice of the electrophoretic nanocapillary. This is a 1000-fold improvement compared to traditional capillary electrophoresis with laser-induced fluorescence.
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http://dx.doi.org/10.1021/acs.nanolett.8b00831DOI Listing
May 2018

Electrical impedance tomography: Amplitudes of cardiac related impedance changes in the lung are highly position dependent.

PLoS One 2017 16;12(11):e0188313. Epub 2017 Nov 16.

Division of Paediatric Pulmonology, Department of Paediatrics, Inselspital, University Children's Hospital and University of Bern, Bern, Switzerland.

Background: Electrical impedance tomography (EIT) is used on the thorax to measure impedance changes due to the presence of air and blood in the lung. This experimental study was performed to investigate the effect of posture on cardiac and respiratory related impedance changes.

Methods: EIT measurements were performed on 14 healthy subjects in left-, right lateral, prone, supine and upright positions. Simultaneously, tidal volume was recorded with an ultrasonic flowmeter. For image reconstruction, the classic Sheffield back-projection and three variants of the modern GREIT algorithm were applied with two different reference frames. Amplitudes of cardiac- and respiratory impedance changes were extracted and compared between the positions.

Results: We found significant differences in both cardiac and respiratory amplitudes between postures. Especially, supine and upright positions showed dramatic changes in amplitude. These differences between postures were unaffected by the change of reference frames in all reconstruction methods except of the classic Sheffield back projection. Possible sources that explain the observed posture dependency are discussed.

Conclusion: Researchers and clinicians need to be aware of this phenomenon when comparing EIT amplitudes in different body positions.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188313PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690592PMC
December 2017

Spiral Modes and the Observation of Quantized Conductance in the Surface Bands of Bismuth Nanowires.

Sci Rep 2017 Nov 14;7(1):15569. Epub 2017 Nov 14.

Department of Physics, Boston College, Chestnut Hill, MA, 02467, USA.

When electrons are confined in two-dimensional materials, quantum-mechanical transport phenomena and high mobility can be observed. Few demonstrations of these behaviours in surface spin-orbit bands exist. Here, we report the observation of quantized conductance in the surface bands of 50-nm Bi nanowires. With increasing magnetic fields oriented along the wire axis, the wires exhibit a stepwise increase in conductance and oscillatory thermopower, possibly due to an increased number of high-mobility spiral surface modes based on spin-split bands. Surface high mobility is unexpected since bismuth is not a topological insulator and the surface is not suspended but in contact with the bulk. The oscillations enable us to probe the surface structure. We observe that mobility increases dramatically with magnetic fields because, owing to Lorentz forces, spiral modes orbit decreases in diameter pulling the charge carriers away from the surface. Our mobility estimates at high magnetic fields are comparable, within order of magnitude, to the mobility values reported for suspended graphene. Our findings represent a key step in understanding surface spin-orbit band electronic transport.
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http://dx.doi.org/10.1038/s41598-017-15476-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5686132PMC
November 2017

Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.

Mol Cell 2017 Nov;68(3):515-527.e6

Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany. Electronic address:

Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.
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http://dx.doi.org/10.1016/j.molcel.2017.10.014DOI Listing
November 2017

An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome.

Nat Struct Mol Biol 2017 Sep 24;24(9):752-757. Epub 2017 Jul 24.

Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.

Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a component of the antibacterial defense system of multicellular organisms, interfere with bacterial growth by inhibiting translation. Here we show that Api137, a derivative of the insect-produced antimicrobial peptide apidaecin, arrests terminating ribosomes using a unique mechanism of action. Api137 binds to the Escherichia coli ribosome and traps release factor (RF) RF1 or RF2 subsequent to the release of the nascent polypeptide chain. A high-resolution cryo-EM structure of the ribosome complexed with RF1 and Api137 reveals the molecular interactions that lead to RF trapping. Api137-mediated depletion of the cellular pool of free release factors causes the majority of ribosomes to stall at stop codons before polypeptide release, thereby resulting in a global shutdown of translation termination.
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http://dx.doi.org/10.1038/nsmb.3439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5589491PMC
September 2017

Proline-rich antimicrobial peptides targeting protein synthesis.

Nat Prod Rep 2017 07 24;34(7):702-711. Epub 2017 May 24.

Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M), University of Munich, 81377 Munich, Germany and Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.

Covering: up to 2017The innate immune system employs a broad array of antimicrobial peptides (AMPs) to attack invading microorganisms. While most AMPs act by permeabilizing the bacterial membrane, specific subclasses of AMPs have been identified that pass through membranes and inhibit bacterial growth by targeting fundamental intracellular processes. One such subclass is the proline-rich antimicrobial peptides (PrAMPs) that bind to the ribosome and interfere with the process of protein synthesis. A diverse range of PrAMPs have been identified in insects, such as bees, wasps and beetles, and crustaceans, such as crabs, as well as in mammals, such as cows, sheep, goats and pigs. Mechanistically, the best-characterized PrAMPs are the insect oncocins, such as Onc112, and bovine bactenecins, such as Bac7. Biochemical and structural studies have revealed that these PrAMPs bind within the ribosomal exit tunnel with a reverse orientation compared to a nascent polypeptide chain. The PrAMPs allow initiation but prevent the transition into the elongation phase of translation. Insight into the interactions of PrAMPs with their ribosomal target provides the opportunity to further develop these peptides as novel antimicrobial agents.
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http://dx.doi.org/10.1039/c7np00020kDOI Listing
July 2017

Single Mandibular Implant Study: Recruitment Considerations.

Int J Prosthodont 2017 Jan/Feb;30(1):43-46

Purpose: The aim of this multicenter single mandibular implant study was to compare the clinical outcome of an immediately loaded implant placed in the midline of an edentulous mandible with the clinical outcome when closed healing and delayed loading is chosen. Here, the patient recruitment period and the main reasons for exclusion were analyzed.

Materials And Methods: Patient recruitment was performed at nine German universities. Rather conservative inclusion and exclusion criteria, including denture satisfaction, denture status, a psychologic symptom checklist, and a defined bone height in the posterior mandible, had to be fulfilled. It was initially calculated that 230 persons would have to be screened within 13 months to include 180 persons in the trial.

Results: Within 13 months (December 2012 to December 2013), 201 patients were screened for possible inclusion in the trial and 148 met the inclusion criteria. Finally, after the recruitment period was extended by 2.5 months, 224 patients were screened and 169 were included. Of those screened, 55 (24.6%) did not meet the inclusion criteria and were excluded. Another 4 patients (1.8%) were excluded based on their psychologic symptom checklist score, while 5 others (2.8%) showed signs of noncompliance. A further 8 patients (4.4%) decided not to participate and withdrew their informed consent, and another 3 (1.3%) were no longer available after screening. Another 2 patients were excluded due to medical contraindications and 1 due to an insufficient mandibular denture. In 34 cases (15.2%), the residual bone height did not comply with McGarry type II or III.

Conclusion: Within the limitations of this patient recruitment period, it can be concluded that residual bone height is the most important factor when considering elderly edentulous patients for implant therapy. The psychologic symptom checklist score was less important.
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http://dx.doi.org/10.11607/ijp.4975DOI Listing
March 2017

Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea.

Archaea 2016 8;2016:7316725. Epub 2016 Dec 8.

Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700, USA.

Translation initiation factor 5A (IF5A) is essential and highly conserved in Eukarya (eIF5A) and Archaea (aIF5A). The activity of IF5A requires hypusine, a posttranslational modification synthesized in Eukarya from the polyamine precursor spermidine. Intracellular polyamine analyses revealed that agmatine and cadaverine were the main polyamines produced in in minimal medium, raising the question of how hypusine is synthesized in this halophilic Archaea. Metabolic reconstruction led to a tentative picture of polyamine metabolism and aIF5A modification in that was experimentally tested. Analysis of aIF5A from by LC-MS/MS revealed it was exclusively deoxyhypusinylated. Genetic studies confirmed the role of the predicted arginine decarboxylase gene in agmatine synthesis. The agmatinase-like gene was found to be essential, consistent with a role in aIF5A modification predicted by physical clustering evidence. Recombinant deoxyhypusine synthase (DHS) from was shown to transfer 4-aminobutyl moiety from spermidine to aIF5A from However, at least under conditions tested, this transfer was not observed with the DHS. Furthermore, the growth of was not inhibited by the classical DHS inhibitor GC7. We propose a model of deoxyhypusine synthesis in that differs from the canonical eukaryotic pathway, paving the way for further studies.
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http://dx.doi.org/10.1155/2016/7316725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5178350PMC
July 2017

Characterization of three pyranose dehydrogenase isoforms from the litter-decomposing basidiomycete Leucoagaricus meleagris (syn. Agaricus meleagris).

Appl Microbiol Biotechnol 2017 Apr 19;101(7):2879-2891. Epub 2016 Dec 19.

Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.

Multigenicity is commonly found in fungal enzyme systems, with the purpose of functional compensation upon deficiency of one of its members or leading to enzyme isoforms with new functionalities through gene diversification. Three genes of the flavin-dependent glucose-methanol-choline (GMC) oxidoreductase pyranose dehydrogenase (AmPDH) were previously identified in the litter-degrading fungus Agaricus (Leucoagaricus) meleagris, of which only AmPDH1 was successfully expressed and characterized. The aim of this work was to study the biophysical and biochemical properties of AmPDH2 and AmPDH3 and compare them with those of AmPDH1. AmPDH1, AmPDH2 and AmPDH3 showed negligible oxygen reactivity and possess a covalently tethered FAD cofactor. All three isoforms can oxidise a range of different monosaccarides and oligosaccharides including glucose, mannose, galactose and xylose, which are the main constituent sugars of cellulose and hemicelluloses, and judging from the apparent steady-state kinetics determined for these sugars, the three isoforms do not show significant differences pertaining to their reaction with sugar substrates. They oxidize glucose both at C2 and C3 and upon prolonged reaction C2 and C3 double-oxidized glucose is obtained, confirming that the A. meleagris genes pdh2 (AY753308.1) and pdh3 (DQ117577.1) indeed encode CAZy class AA3_2 pyranose dehydrogenases. While reactivity with electron donor substrates was comparable for the three AmPDH isoforms, their kinetic properties differed significantly for the model electron acceptor substrates tested, a radical (the 2,2'-azino-bis[3-ethylbenzothiazoline-6-sulphonic acid] cation radical), a quinone (benzoquinone) and a complexed iron ion (the ferricenium ion). Thus, a possible explanation for this PDH multiplicity in A. meleagris could be that different isoforms react preferentially with structurally different electron acceptors in vivo.
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http://dx.doi.org/10.1007/s00253-016-8051-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5352738PMC
April 2017