Patrick Jones

Histone Acetylation and Deacetylation Identification of Acetylation and Methylation Sites of HeLa Histone H4 by Mass Spectrometry

The acetylation isoforms of histone H4 from butyrate-treated HeLa cells were separated by C4 reverse-phase high pressure liquid chromatography and by polyacrylamide gel electrophoresis. Histone H4 bands were excised and digested in-gel with the endoprotease trypsin. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry was used to characterize the level of acetylation, and nanoelectrospray tandem mass spectrometric analysis of the acetylated peptides was used to determine the exact sites of acetylation. Although there are 15 acetylation sites possible, only four acetylated peptide sequences were actually observed. The tetra-acetylated form is modified at lysines 5, 8, 12, and 16, the tri-acetylated form is modified at lysines 8, 12, and 16, and the di-acetylated form is modified at lysines 12 and 16. The only significant amount of the mono-acetylated form was found at position 16. These results are consistent with the hypothesis of a “zip” model whereby acetylation of histone H4 proceeds in the direction of from Lys-16 to Lys-5, and deacetylation proceeds in the reverse direction. Histone acetylation and deacetylation are coordinated processes leading to a non-random distribution of isoforms. Our results also revealed that lysine 20 is di-methylated in all modified isoforms, as well as the non-acetylated isoform of H4.

General phase modulation method for stored waveform inverse fourier transform excitation for fourier transform ion cyclotron resonance mass spectrometry

A method for reducing the dynamic range of FT-ICR signal generated by the SWIFT technique includes the step of time shifting wave packets corresponding to segments of the Fourier spectral magnitude function to prevent coherent summing of the various frequency components of the excitation signal.

Egg case protein-1: A new class of silk proteins with fibroin-like properties from the spider, Latrodectus hesperus

Spiders produce multiple types of silk that exhibit diverse mechanical properties and biological functions. Most molecular studies of spider silk have focused on fibroins from dragline silk and capture silk, two important silk types involved in the survival of the spider. In our studies we have focused on the characterization of egg case silk, a third silk fiber produced by the black widow spider, Latrodectus hesperus. Analysis of the physical structure of egg case silk using scanning electron microscopy demonstrates the presence of small and large diameter fibers. By using the strong protein denaturant 8 m guanidine hydrochloride to solubilize the fibers, we demonstrated by SDS-PAGE and protein silver staining that an abundant component of egg case silk is a 100-kDa protein doublet. Combining matrix-assisted laser desorption ionization tandem time-of-flight mass spectrometry and reverse genetics, we have isolated a novel gene called ecp-1, which encodes for one of the protein components of the 100-kDa species. BLAST searches of the NCBInr protein data base using the primary sequence of ECP-1 revealed similarity to fibroins from spiders and silkworms, which mapped to two distinct regions within the ECP-1. These regions contained the conserved repetitive fibroin motifs poly(Ala) and poly(Gly-Ala), but surprisingly, no larger ensemble repeats could be identified within the primary sequence of ECP-1. Consistent with silk gland-restricted patterns of expression for fibroins, ECP-1 was demonstrated to be predominantly produced in the tubuliform gland, with lower levels detected in the major and minor ampullate glands. ECP-1 monomeric units were also shown to assemble into higher aggregate structures through the formation of disulfide bonds via a unique cysteine-rich N-terminal region. Collectively, our findings provide new insight into the components of egg case silk and identify a new class of silk proteins with distinctive molecular features relative to traditional members of the spider silk gene family.

Aciniform Spidroin, a Constituent of Egg Case Sacs and Wrapping Silk Fibers from the Black Widow Spider Latrodectus hesperus

Spiders produce high performance fibers with diverse mechanical properties and biological functions. Molecular and biochemical studies of spider egg case silk have revealed that the main constituent of the large diameter fiber contains the fibroin TuSp1. Here we demonstrate by SDS-PAGE and protein silver staining the presence of a distinct ∼300-kDa polypeptide that is found in solubilized egg case sacs. Combining matrix-assisted laser desorption ionization tandem time-of-flight mass spectrometry and reverse genetics, we have isolated a novel gene called AcSp1-like and demonstrate that its protein product is assembled into the small diameter fibers of egg case sacs and wrapping silks from the black widow spider, Latrodectus hesperus. BLAST searches of the NCBInr protein data base using the amino acid sequence of AcSp1-like revealed similarity to AcSp1, an inferred protein proposed to be a component of wrapping silk. However, the AcSp1-like protein was found to display more nonuniformity in its internal iterated repeat modules than the putative AcSp1 fibroin. Real time quantitative PCR analysis demonstrates that the AcSp1-like gene displays an aciniform gland-restricted pattern of expression. The amino acid composition of the fibroins extracted from the luminal contents of the aciniform glands was remarkably similar to the predicted amino acid composition of the AcSp1-like protein, which supports the assertion that AcSp1-like protein represents the major constituent stored within the aciniform gland. Collectively, our findings provide the first direct molecular evidence for the involvement of the aciniform gland in the production of a common fibroin that is assembled into the small diameter threads of egg case and wrapping silk of cob weavers.

Direct analysis in real time (DART) mass spectrometry of nucleotides and nucleosides: elucidation of a novel fragment [C5H5O]+ and its in-source adducts

Direct analysis in real time (DART) mass spectrometry is a recently developed innovative technology, which has shown broad applications for fast and convenient analysis of complex samples. Due to the ease of sample preparation, we have recently initiated an investigation of the feasibility of detecting nucleotides and nucleosides using the DART-AccuTOF instrument, which we will refer to as the DART mass spectrometer. Our experimental results reveal that the ions representing the intact molecules of nucleotides are not detectable in either positive-ion or negative-ion mode. Instead, all four natural nucleotides fragment in the DART ion source, and a common fragment ion, [C5H5O]+ (1), is observed, which is probably formed via multiple-elimination reactions. Interestingly, 1 can form adducts with nucleobases in different molar ratios in the DART ion source. In contrast to nucleotides, the ions representing the intact molecules of nucleosides are detected in both positive-ion and negative-ion mode using DART mass spectrometry. Surprisingly, the fragmentation pattern of nucleosides is different from that of nucleotides in the DART ion source. In the cases of nucleosides (under positive-ion conditions), the production of 1 is not observed, indicating that the phosphate group plays an important role for the multiple eliminations observed in the spectra of nucleotides. The in-source reactions described in the present work show the complexity of the conditions in the DART ion source, and we hope that our results illustrate a better understanding about DART mass spectrometry.

Worldwide Trends of Urinary Stone Disease Treatment Over the Last Two Decades: A Systematic Review

INTRODUCTION Numerous studies have reported on regional or national trends of stone disease treatment. However, no article has yet examined the global trends of intervention for stone disease. METHODS AND MATERIALS A systematic review of articles from 1996 to September 2016 for all English language articles reporting on trends of surgical treatment of stone disease was performed. Authors were contacted in the case of data not being clear. If the authors did not reply, data were estimated from graphs or tables. Results were analyzed using SPSS version 21, and trends were analyzed using linear regression. RESULTS Our systematic review yielded 120 articles, of which 8 were included in the initial review. This reflected outcomes from six countries with available data: United Kingdom, United States, New Zealand, Australia, Canada, and Brazil. Overall ureteroscopy (URS) had a 251.8% increase in total number of treatments performed with the share of total treatments increasing by 17%. While the share of total treatments for percutaneous nephrolithotomy (PCNL) remained static, the share for extracorporeal shockwave lithotripsy and open surgery fell by 14.5% and 12%, respectively. There was significant linear regression between rising trends of total treatments year on year for URS (p < 0.001). CONCLUSION In the last two decades, the share of total treatment for urolithiasis across the published literature has increased for URS, stable for PCNL, and decreased for lithotripsy and open surgery.

Current Status of Prostate Artery Embolization for Lower Urinary Tract Symptoms: Review of World Literature

Prostate artery embolization has emerged as a promising treatment for lower urinary tract symptoms secondary to benign prostatic hyperplasia. However, although it has gained increasing attention in radiology literature, it remains under-reported from a urologic perspective. We aim at providing an up-to-date review of this minimally invasive technique. Evidence suggests it is a promising and effective option for patients with large prostate volumes, multiple comorbidities, and suboptimal results from pharmacotherapy. Larger, randomized studies with longer follow-up periods are needed for this technique to be formally established in the urology community.

A theory for two‐dimensional Fourier‐transform ion cyclotron resonance mass spectrometry

A theoretical model, based on the Lorentz equations for ion motion and the mass action law, is developed for two‐dimensional Fourier‐transform mass spectrometry known as 2D FT–ICR or 2D FTMS. The theory illustrates that the modulation of 2D FT–ICR ion signals in the additional time dimension comes from the modulation of the primary ion speed by the 2D excitation pulses. The modulation of the primary ion speed is found not to be sinusoidal and the modulation of the ion signals in 2D FT–ICR spectra is found to be complicated even in the simplest chemical system. The complex modulation creates higher harmonic components in the spectra. Based on the model, a data processing algorithm is proposed. The results show that the Fourier transformation should be performed stepwise in order to obtain complete information, and that the phase portion of the frequency domain generated by the second Fourier transformation should not be discarded since it contains useful information.

Holmium laser enucleation versus simple prostatectomy for treating large prostates: Results of a systematic review and meta-analysis

Abstract Objective: To compare and evaluate the safety and efficacy of holmium laser enucleation of the prostate (HoLEP) and simple prostatectomy for large prostate burdens, as discussion and debate continue about the optimal surgical intervention for this common pathology. Materials and methods: A systematic search was conducted for studies comparing HoLEP with simple prostatectomy [open (OP), robot-assisted, laparoscopic] using a sensitive strategy and in accordance with Cochrane collaboration guidelines. Primary parameters of interest were objective measurements including maximum urinary flow rate (Qmax) and post-void residual urine volume (PVR), and subjective outcomes including International Prostate Symptom Score (IPSS) and quality of life (QoL). Secondary outcomes of interest included volume of tissue retrieved, catheterisation time, hospital stay, blood loss and serum sodium decrease. Data on baseline characteristics and complications were also collected. Where possible, comparable data were combined and meta-analysis was conducted. Results: In all, 310 articles were identified and after screening abstracts (114) and full manuscripts (14), three randomised studies (263 patients) were included, which met our pre-defined inclusion criteria. All these compared HoLEP with OP. The mean transrectal ultrasonography (TRUS) volume was 113.9 mL in the HoLEP group and 119.4 mL in the OP group. There was no statistically significant difference in Qmax, PVR, IPSS and QoL at 12 and 24 months between the two interventions. OP was associated with a significantly shorter operative time (P = 0.01) and greater tissue retrieved (P < 0.001). However, with HoLEP there was significantly less blood loss (P < 0.001), patients had a shorter hospital stay (P = 0.03), and were catheterised for significantly fewer hours (P = 0.01). There were no significant differences in the total number of complications recorded amongst HoLEP and OP (P = 0.80). Conclusion: The results of the meta-analysis have shown that HoLEP and OP possess similar overall efficacy profiles for both objective and subjective disease status outcome measures. This review shows these improvements persist to at least the 24 month follow-up point. Further randomised studies are warranted to fully determine the optimal surgical intervention for large prostate burdens.

Determination of the presence or absence of sulfur materials in drywall using direct analysis in real time in conjunction with an accurate-mass time-of-flight mass spectrometer.

Based on the concern about the presence of sulfur materials being in drywall (wallboard), a quick and reliable test to confirm the presence or absence of these materials using direct analysis in real time (DART) mass spectrometry in conjunction with an accurate-mass time-of-flight (TOF) mass spectrometer has been developed and is described here.