State-Dependent Fragmentation of Protonated Uracil and Uridine.

Action spectroscopy using photon excitation in the VUV range (photon energy 4.5-9 eV) was performed on protonated uracil (UraH+) and uridine (UrdH+). The precursor ions with m/ z 113 and m/ z 245, respectively, were produced by an electrospray ionization source and accumulated inside a quadrupole ion trap mass spectrometer. After irradiation with tunable synchrotron radiation, product ion mass spectra were obtained. Fragment yields as a function of excitation energy show several maxima that can be attributed to the photoexcitation into different electronic states. For uracil, vertically excited states were calculated using the equation-of-motion coupled cluster approach and compared to the observed maxima. This allows to establish correlations between electronic states and the resulting fragment masses and can thus help to disentangle the complex de-excitation and fragmentation pathways of nucleic acid building blocks. Photofragmentation of the nucleoside uridine shows a significantly lower variety of fragments, indicating stabilization of the nucleobase by the attached sugar.

Outcome of buccal mucosa graft urethroplasty: a detailed analysis of success, morbidity and quality of life in a contemporary patient cohort at a referral center.

BACKGROUND: To evaluate outcome of buccal mucosa graft urethroplasty (BMGU) for the treatment of urethral stricture disease, including a detailed analysis of success, morbidity and quality of life (QoL). METHODS: Between 12/05/2008 and 07/21/2010, 187 patients with urethral stricture disease, who were treated with BMGU at our University Medical Center, received a standardized questionnaire, evaluating postoperative success, morbidity and QoL. The primary endpoint was the success, i.e., stricture recurrence-free survival plus patients' satisfaction with surgery. Secondary endpoints included erectile function, voiding symptoms, pain and health-related QoL, which were assessed with a modified Urethral Stricture Surgery Patient Reported Outcome Measure (USS PROM), including the Erectile Function domain of the International Index of Erectile Function (IIEF-EF), Incontinence Questionnaire Male Lower Urinary Tract Symptoms Module (ICIQ-MLUTS) and EuroQol-5 dimensions (EQ-5D). RESULTS: In total, 83 patients (51.9%) completed the questionnaire. Bulbar, penile and panurethral strictures were found in 69 patients (83.1%), 13 patients (15.7%) and one patient (1.2%), respectively. The median length of the stricture was 5 cm (range: 1-16). At a median follow-up of 46 months (range: 36-54), 65 patients (78.3%) had no stricture recurrence and were satisfied with BMGU. Median scores for ICIQ-MLUTS, IIEF-EF and EQ-5D visual analogue scale were 6, 22 and 80, respectively. Based on USS PROM, postoperative improvement of QoL and satisfaction with BMGU was found in 67 patients (80.7%) and 68 patients (81.9%), respectively. CONCLUSIONS: In patients with urethral stricture disease, BMGU offers excellent success, morbidity and QoL.

Circular Dichroism in Fluorescence Emission Following the C 1s→π* Excitation and Resonant Auger Decay of Carbon Monoxide.

Dichroism in angle-resolved spectra of circularly polarized fluorescence from freely-rotating CO molecules was studied experimentally and theoretically. For this purpose, carbon monoxide in the gas phase was exposed to circularly polarized soft X-ray synchrotron radiation. The photon energy was tuned across the C 1s→π* resonant excitation, which decayed via the participator Auger transition into the CO⁺ A ²Π state. The dichroic parameter ß1 of the subsequent CO⁺ (A ²Π → X ²Σ⁺) visible fluorescence was measured by photon-induced fluorescence spectroscopy. Present experimental results are explained with the ab initio electronic structure and dynamics calculations performed by the single center method. Our results confirm the possibility to perform partial wave analysis of the emitted photoelectrons in closed-shell molecules.

Correction: Size and shape dependent photoluminescence and excited state decay rates of diamondoids.

Correction for 'Size and shape dependent photoluminescence and excited state decay rates of diamondoids' by Robert Richter et al., Phys. Chem. Chem. Phys., 2014, 16, 3070-3076.

Structure-based engineering of a minimal porin reveals loop-independent channel closure.

Porins, like outer membrane protein G (OmpG) of Escherichia coli, are ideal templates among ion channels for protein and chemical engineering because of their robustness and simple architecture. OmpG shows fast transitions between open and closed states, which were attributed to loop 6 (L6). As flickering limits single-channel-based applications, we pruned L6 by either 8 or 12 amino acids. While the open probabilities of both L6 variants resemble that of native OmpG, their gating frequencies were reduced by 63 and 81%, respectively. Using the 3.2 Å structure of the shorter L6 variant in the open state, we engineered a minimal porin (220 amino acids), where all remaining extramembranous loops were truncated. Unexpectedly, this minimized porin still exhibited gating, but it was 5-fold less frequent than in OmpG. The residual gating of the minimal pore is hence independent of L6 rearrangements and involves narrowing of the ion conductance pathway most probably driven by global stretching-flexing deformations of the membrane-embedded ß-barrel.

Histopathological characteristics of buccal mucosa transplants in humans after engraftment to the urethra: a prospective study.

PURPOSE: Histopathological changes in buccal mucosa transplants after engraftment to the urethra and exposure to urine remain nebulous. We investigated histopathological changes in buccal mucosa transplants integrated into the urethra in humans. MATERIALS AND METHODS: We prospectively evaluated 22 patients with recurrent urethral stricture after buccal mucosa urethroplasty between November 2012 and October 2013. All patients underwent repeat buccal mucosa urethroplasty performed by a single surgeon. Intraoperatively we harvested a sample of the integrated buccal mucosa transplant previously engrafted to the urethra, a sample of healthy urethra, a sample of freshly harvested buccal mucosa from the contralateral inner cheek and a sample of fibrotic tissue from the area of the current stricture. A dedicated uropathologist performed meticulous histopathological examination of all tissue samples using hematoxylin and eosin staining. Preoperative clinical data were also collected on all patients. RESULTS: The mean interval from previous to current buccal mucosa urethroplasty was 22.2 months (range 4.1 to 76.0). Mean stricture length at repeat urethroplasty was 52.7 mm (range 30.0 to 70.0). Histopathological characteristics of the integrated buccal mucosa transplants were completely preserved in all patients, consisting of thick sheets of stratified nonkeratinized squamous epithelium with a stratum spinosum. Transplants were not partially or entirely overgrown with urothelium. CONCLUSIONS: Buccal mucosa transplants retain their histopathological characteristics and are not overgrown with urothelium after urethral engraftment and urine exposure in humans. These findings may explain the superiority of buccal mucosa transplants on the outcome of substitution urethroplasty compared to that of other materials.

Ion-channels: goals for function-oriented synthesis.

Ion channels provide a conductance pathway for the passive transport of ions across membranes. These functional molecules perform key tasks in biological systems such as neuronal signaling, muscular control, and sensing. Recently, function-oriented synthesis researchers began to focus on ion channels with the goal of modifying the function of existing ion channels (ion selectivity, gating) or creating new channels with novel functions. Both approaches, ion channel engineering and de novo design, have involved synthetic chemists, biochemists, structural biologists, and neurochemists. Researchers characterize the function of ion channels by measuring their conductance in samples of biological membranes (patch clamp) or artificial membranes (planar lipid bilayers). At the single molecule level, these measurements require special attention to the purity of the sample, a challenge that synthetic chemists should be aware of. Ideally, researchers study the function of channels while also acquiring structural data (X-ray, NMR) to understand and predict how synthetic modifications alter channel function. Long-term oriented researchers would like to apply synthetic ion channels to single molecule sensing and to implantat these synthetic systems in living organisms as tools or for the treatment of channelopathies. In this Account, we discuss our own work on synthetic ion channels and explain the shift of our research focus from a de novo design of oligo-THFs and oligo-THF-amino acids to ion channel engineering. We introduce details about two biological lead structures for ion channel engineering: the gramicidin ß(6,3) helix as an example of a channel with a narrow ion conductance pathway and the outer membrane porins (OmpF, OmpG) with their open ß-barrel structure. The increase and the reversal of ion selectivity of these systems and the hydrophobic match/mismatch of the channel with the phospholipid bilayer are of particular interest. For engineering ion channels, we need to supplement the single-point attachment of a synthetic modulator with the synthesis of a more challenging two-point attachment. The successful function-oriented synthesis of ion channels will require interdisciplinary efforts that include new electrophysiology techniques, efficient synthesis (peptide/protein/organic), and good structural analysis.

Size and shape dependent photoluminescence and excited state decay rates of diamondoids.

We present photoluminescence spectra and excited state decay rates of a series of diamondoids, which represent molecular structural analogues to hydrogen-passivated bulk diamond. Specific isomers of the five smallest diamondoids (adamantane-pentamantane) have been brought into the gas phase and irradiated with synchrotron radiation. All investigated compounds show intrinsic photoluminescence in the ultraviolet spectral region. The emission spectra exhibit pronounced vibrational fine structure which is analyzed using quantum chemical calculations. We show that the geometrical relaxation of the first excited state of adamantane, exhibiting Rydberg character, leads to the loss of Td symmetry. The luminescence of adamantane is attributed to a transition from the delocalized first excited state into different vibrational modes of the electronic ground state. Similar geometrical changes of the excited state structure have also been identified in the other investigated diamondoids. The excited state decay rates show a clear dependence on the size of the diamondoid, but are independent of the particle geometry, further indicating a loss of particle symmetry upon electronic excitation.

Contemporary Outcomes after Transurethral Procedures for Bladder Neck Contracture Following Endoscopic Treatment of Benign Prostatic Hyperplasia.

OBJECTIVES: Bladder neck contracture (BNC) is a bothersome complication following endoscopic treatment for benign prostatic hyperplasia (BPH). The objective of our study was to give a more realistic insight into contemporary endoscopic BNC treatment and to evaluate and identify risk factors associated with inferior outcome. MATERIAL AND METHODS: We identified patients who underwent transurethral treatment for BNC secondary to previous endoscopic therapy for BPH between March 2009 and October 2016. Patients with vesico-urethral anastomotic stenosis after radical prostatectomy were excluded. Digital charts were reviewed for re-admissions and re-visits at our institutions and patients were contacted personally for follow-up. Our non-validated questionnaire assessed previous urologic therapies (including radiotherapy, endoscopic, and open surgery), time to eventual further therapy in case of BNC recurrence, and the modality of recurrence management. RESULTS: Of 60 patients, 49 (82%) and 11 (18%) underwent transurethral bladder neck resection and incision, respectively. Initial BPH therapy was transurethral resection of the prostate (TURP) in 54 (90%) and holmium laser enucleation of the prostate (HoLEP) in six (10%) patients. Median time from prior therapy was 8.5 (IQR 5.3-14) months and differed significantly in those with (6.5 months; IQR 4-10) and those without BNC recurrence (10 months; IQR 6-20; p = 0.046). Thirty-three patients (55%) underwent initial endoscopic treatment, and 27 (45%) repeated endoscopic treatment for BNC. In initially-treated patients, time since BPH surgery differed significantly between those with a recurrence (median 7.5 months; IQR 6-9) compared to those treated successfully (median 12 months; IQR 9-25; p = 0.01). In patients with repeated treatment, median time from prior BNC therapy did not differ between those with (4.5 months; IQR 2-12) and those without a recurrence (6 months; IQR 6-10; p = 0.6). Overall, BNC treatment was successful in 32 patients (53%). The observed success rate of BNC treatment was significantly higher after HoLEP compared to TURP (100% vs. 48%; p = 0.026). Type of BNC treatment, number of BNC treatment, and age at surgery did not influence the outcome. CONCLUSIONS: A longer time interval between previous BPH therapy and subsequent BNC incidence seems to favorably affect treatment success of endoscopic BNC treatment, and transurethral resection and incision appear equally effective. Granted the relatively small sample size, BNC treatment success seems to be higher after HoLEP compared to TURP, which warrants validation in larger cohorts.

Structural and functional characterization of a synthetically modified OmpG.

Chemical modification of ion channels has recently attracted attention due to their potential use in stochastic sensing and neurobiology. Among the available channel templates stable ß-barrel proteins have shown their potential for large scale chemical modifications due to their wide pore lumen. Ion-channel hybrids using the outer membrane protein OmpG were generated by S-alkylation with a synthetic modulator and functionally as well as structurally characterized. The dansyl moiety of the used modulator resulted in partial blockage of current though the OmpG channel with its gating characteristics mainly unaffected. The crystal structure of an OmpG-dansyl hybrid at 2.4Å resolution correlates this finding by showing that the modulator lines the inner walling of the OmpG pore. These results underline the suitability of OmpG as a structural base for the construction of stochastic sensors.

Expanding the scope of protein trans-splicing to fragment ligation of an integral membrane protein: towards modulation of porin-based ion channels by chemical modification.

It's raining, it's porin: Fragment ligation of OmpF ion channels was achieved by using the split Psp-GBD Pol intein; this allowed reconstitution of active trimeric porin. In combination with cysteine modification at an internal position, the porin's conductance properties were altered.

On the function and structure of synthetically modified porins.

The attachment of modulators to a trimeric porin ion channel was investigated (see picture of the trimer with a crown ether modulator (orange)). The interplay of modulator and protein is essential for the conformational heterogeneity of the hybrid channel. Single-site attachment in large pores is not sufficient to change the electrophysiological characteristics of the pores-such change requires additional noncovalent interactions or second-site attachments.

Differences in Recurrence Rate and De Novo Incontinence after Endoscopic Treatment of Vesicourethral Stenosis and Bladder Neck Stenosis.

OBJECTIVES: The objective of this study was to compare the recurrence rate and de novo incontinence after endoscopic treatment of vesicourethral stenosis (VUS) after radical prostatectomy (RP) and for bladder neck stenosis (BNS) after transurethral resection of the prostate (TURP). METHODS: Retrospective analysis of patients treated endoscopically for VUS after RP or for BNS after TURP at three German tertiary care centers between March 2009 and June 2016. Investigated endpoints were recurrence rate and de novo incontinence. Chi-squared tests and t-tests were used to model the differences between groups. RESULTS: A total of 147 patients underwent endoscopic therapy for VUS (59.2%) or BNS (40.8%). Mean age was 68.3 years (range 44-86), mean follow-up 27.1 months (1-98). Mean time to recurrence after initial therapy was 23.9 months (1-156), mean time to recurrence after prior endoscopic therapy for VUS or BNS was 12.0 months (1-159). Patients treated for VUS underwent significantly more often radiotherapy prior to endoscopic treatment (33.3 vs. 13.3%; p = 0.006) and the recurrence rate was significantly higher (59.8 vs. 41.7%; p = 0.031). The overall success rate of TUR for VUS was 40.2%, success rate of TUR for BNS was 58.3%. TUR for BNS is significantly more successful (p = 0.031). The mean number of TUR for BNS vs. TUR for VUS in successful cases was 1.5 vs. 1.8, which was not significantly different. The rate of de novo incontinence was significantly higher in patients treated for VUS (13.8 vs. 1.7%; p = 0.011). After excluding those patients with radiotherapy prior to endoscopic treatment, the recurrence rate did not differ significantly between both groups (60.3% for VUS vs. 44.2% for BNS; p = 0.091), whereas the rate of de novo incontinence (13.8 for VUS vs. 0% for BNS; p = 0.005) stayed significantly higher in patients treated for VUS. CONCLUSION: Most patients with BNS are successfully treated endoscopically. In patients with VUS, the success rate is lower. Both stenoses differ with respect to de novo incontinence. Patients must be counseled regarding the increased risk of de novo incontinence after endoscopic treatment of VUS, independent of prior radiotherapy. Longer follow-up is warranted to address long-term outcomes.

Optical Fluorescence Detected from X-ray Irradiated Liquid Water.

Despite its importance, the structure and dynamics of liquid water are still poorly understood in many apsects. Here, we report on the observation of optical fluorescence upon soft X-ray irradiation of liquid water. Detection of spectrally resolved fluorescence was achieved by a combination of the liquid microjet technique and fluorescence spectroscopy. We observe a genuine liquid-phase fluorescence manifested by a broad emission band in the 170-340 nm (4-7 eV) photon wavelength range. In addition, another narrower emission near 300 nm can be assigned to the fluorescence of OH (A state) in the gas phase, the emitting species being formed by Auger electrons escaping from liquid water. We argue that the newly observed broad-band emission of liquid water is relevant in search of extraterrestrial life, and we also envision the observed electron-ejection mechanism to find application for exploring solutes at liquid-vapor interfaces.

An asymmetric ion channel derived from gramicidin A. Synthesis, function and NMR structure.

The biological ion channel gramicidin A (gA) was modified by synthetic means to obtain the tail-to-tail linked asymmetric gA-derived dimer compound 3. Single-channel current measurements for 3 in planar lipid bilayers exhibit an Eisenman I ion selectivity for alkali cations. The structural asymmetry does not lead to an observable functional asymmetry. The structure of 3 in solution without and with Cs cations was investigated by 1H-NMR spectroscopy. In CDCl3/CD3OH (1 : 1, v/v), 3 forms a mixture of double-stranded beta-helices. Upon addition of excess CsCl, the double-stranded species are converted completely into one new conformer: the right-handed single-stranded beta-helix. A combination of DQF-COSY and TOCSY was used for the assignment of the 1H-NMR spectrum of the Cs-3 complex in CDCl3/CD3OH (1 : 1, v/v). A total of 69 backbone, 27 long-range, and 64 side-chain distance restraints were obtained from NOESY together with 25 phi and 14 chi1 torsion angles obtained from coupling constants. These data were used as input for structure calculation with dyana built in sybyl 6.8. A final set of 11 structures with an average rmsd for the backbone of 0.45 A was obtained (PDB: 1TKQ). The structure of the Cs-3 complex in solution is equivalent to the bioactive channel conformation in the membrane environment.

Flexibility of the N-terminal mVDAC1 segment controls the channel's gating behavior.

Since the solution of the molecular structures of members of the voltage dependent anion channels (VDACs), the N-terminal α-helix has been the main focus of attention, since its strategic location, in combination with its putative conformational flexibility, could define or control the channel's gating characteristics. Through engineering of two double-cysteine mVDAC1 variants we achieved fixing of the N-terminal segment at the bottom and midpoint of the pore. Whilst cross-linking at the midpoint resulted in the channel remaining constitutively open, cross-linking at the base resulted in an "asymmetric" gating behavior, with closure only at one electric field's orientation depending on the channel's orientation in the lipid bilayer. Additionally, and while the native channel adopts several well-defined closed states (S1 and S2), the cross-linked variants showed upon closure a clear preference for the S2 state. With native-channel characteristics restored following reduction of the cysteines, it is evident that the conformational flexibility of the N-terminal segment plays indeed a major part in the control of the channel's gating behavior.

Synthesis, characterization and properties of a new polymerisable surfactant: 12-methacryloyl dodecylphosphocholine.

A new polymerizable surfactant, 12-methacryloyl dodecylphosphocholine (MDPC), has been synthesized using a three-step procedure in moderate yield. Phase transitions were characterized by DSC and phase behavior in water was determined by surface tension and polarizing microscopy. MDPC showed typical surfactant behavior and self-aggregated to micelles above a distinct concentration. The critical micelle concentration (CMC) of MDPC was determined to be 5 x 10(-4)mol/L. MDPC showed mesomorphic properties between 75 and 86 degrees C as studied by differential scanning calorimetry (DSC). The formation of black lipid membranes was further investigated. The methacrylate functionalized MDPC could form a bilayer membrane (BLM) although it was very unstable (collapsed after 10-30s). However, it was possible to form stable BLMs in mixture with non-polymerizable two chain phospholipids, i.e. asolectin and diphytanoyl phosphatidylcholine (DPhPC). Stable bilayers could be obtained up to a MDPC content of 50 mol%. Gramicidin A was incorporated into MDPC/DPhPC membranes and exhibited ion-channel activity shown by single channel conductivity measurements.

Functional studies of synthetic gramicidin hybrid ion channels in CHO cells.

The function of a gramicidin hybrid ion channel in living Chinese hamster ovary (CHO) cells was investigated by the patch clamp method. The synthetic ion channel 1 consists of two cyclohexyl ether amino acids that link two mini-gramicidin strands. With 1 at a concentration of 1.0 microM, an increase in the whole-cell membrane conductance was observed after 1.37 min. The conductance showed larger currents when Cs(+) was used as charge carrier than when Na(+) and K(+) were used. In single-channel recordings with Cs(+) as charge carrier, the substance showed comparable single-channel amplitudes in the membrane of living cells and artificial black lipid bilayers. In addition to functioning as a cation channel, compound 1 appeared to be a water channel. Exposure of the CHO cells to an extracellular hypoosmotic solution did not substantially change the cell volume. Extracellular hypoosmotic conditions in the presence of 1 increased the cell size to 146.5 % that of the control. Thus, the synthetic hybrid channel 1 can function as a cation channel with some Cs(+) specificity, and as a water channel in CHO cells.