Does hydatid disease have protective effects against lung cancer?

We hypothesized that solid tumors rarely occur in patients with hydatid disease. We obtained the serum of 14 patients diagnosed with hydatid disease, the serum of 10 patients who did not have a history of hydatid disease, and the hydatid cyst fluid from six patients. These sera and fluid samples were added at different concentrations to NCI-H209/An1 human lung small cell carcinoma cells and L929 mouse fibroblasts as a control group. Sera of patients with hydatid diseases had cytotoxic effects on NCI-H209/An1 cells, but they did not have cytotoxic effects on fibroblast cells. Sera from healthy subjects did not have a cytotoxic effect on the tumor cell line or control fibroblasts. Cyst fluid, also, did not have toxic effects on the NCI-H209/An1 cell line, but was toxic to fibroblasts up to a 1:32 dilution. Sera from patients with hydatid disease had cytotoxic effects on human small cell lung cancer cells in vitro.     

The Effect of Chronic Long-Term Intermittent Hypobaric Hypoxia on Bone Mineral Density in Rats: Role of Nitric Oxide

Intermittent hypoxia is the most common pattern of hypoxic exposure in humans. The effect of chronic long-term intermittent hypobaric hypoxia (CLTIHH) on bone metabolism is not investigated. We examined the effect of CLTIHH on bone metabolism and the role of nitric oxide (NO) in this process. The rats were divided into three groups in this study. The animals in groups I and II have been exposed to CLTIHH. The animals in group II were also treated with nitric oxide synthase inhibitor NG-nitro-l-arginine methyl ester. To obtain CLTIHH, rats were placed in a hypobaric chamber (430 mm Hg; 5 h/day, 5 days/week, 5 weeks). The group III (control) rats breathed room air in the same environment. At the begining of the experiments, bone mineral density (BMD) of the animals were measured, and blood samples were collected from the tail vein. After the 5-week CLTIHH period, the same measurements were repeated. Parathyroid hormone, calcium, phosphate, bone alkaline phosphatase (b-ALP), NO, interleukin 1 beta, interleukin 6, and tumor necrosis factor alpha levels were determined. The cytokines, NO levels, and BMD in CLTIHH-induced rats were higher compared with baseline and control values. The cytokines, b-ALP, and BMD increased while NO levels decreased in the group II compared with baseline values. BMD values of group II were lower than group I but higher than control group. Our results suggested that CLTIHH has positive effects on bone density. Intermittent hypoxia protocols may be developed for treatment and prevention of osteopenia and osteoporosis.     

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics.With well-developed algorithms and computational tools for mass spectrometry (MS)¹ data analysis, peptide-based bottom-up proteomics has gained considerable popularity in the field of systems biology (1–9). Nevertheless, the bottom-up approach is suboptimal for the analysis of protein posttranslational modifications (PTMs) and sequence variants as a result of protein digestion (10). Alternatively, the protein-based top-down proteomics approach analyzes intact proteins, which provides a “bird''s eye” view of all proteoforms (11), including those arising from sequence variations, alternative splicing, and diverse PTMs, making it a disruptive technology for the comprehensive analysis of proteoforms (12–24). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for processing data from bottom-up proteomics experiments, the data analysis tools in top-down proteomics remain underdeveloped.The initial step in the analysis of top-down proteomics data is deconvolution of high-resolution mass and tandem mass spectra. Thorough high-resolution analysis of spectra by horn (THRASH), which was the first algorithm developed for the deconvolution of high-resolution mass spectra (25), is still widely used. THRASH automatically detects and evaluates individual isotopomer envelopes by comparing the experimental isotopomer envelope with a theoretical envelope and reporting those that score higher than a user-defined threshold. Another commonly used algorithm, MS-Deconv, utilizes a combinatorial approach to address the difficulty of grouping MS peaks from overlapping isotopomer envelopes (26). Recently, UniDec, which employs a Bayesian approach to separate mass and charge dimensions (27), can also be applied to the deconvolution of high-resolution spectra. Although these algorithms assist in data processing, unfortunately, the deconvolution results often contain a considerable amount of misassigned peaks as a consequence of the complexity of the high-resolution MS and MS/MS data generated in top-down proteomics experiments. Errors such as these can undermine the accuracy of protein identification and PTM localization and, thus, necessitate the implementation of visual components that allow for the validation and manual correction of the computational outputs.Following spectral deconvolution, a typical top-down proteomics workflow incorporates identification, quantitation, and characterization of proteoforms; however, most of the recently developed data analysis tools for top-down proteomics, including ProSightPC (28, 29), Mascot Top Down (also known as Big-Mascot) (30), MS-TopDown (31), and MS-Align+ (32), focus almost exclusively on protein identification. ProSightPC was the first software tool specifically developed for top-down protein identification. This software utilizes “shotgun annotated” databases (33) that include all possible proteoforms containing user-defined modifications. Consequently, ProSightPC is not optimized for identifying PTMs that are not defined by the user(s). Additionally, the inclusion of all possible modified forms within the database dramatically increases the size of the database and, thus, limits the search speed (32). Mascot Top Down (30) is based on standard Mascot but enables database searching using a higher mass limit for the precursor ions (up to 110 kDa), which allows for the identification of intact proteins. Protein identification using Mascot Top Down is fundamentally similar to that used in bottom-up proteomics (34), and, therefore, it is somewhat limited in terms of identifying unexpected PTMs. MS-TopDown (31) employs the spectral alignment algorithm (35), which matches the top-down tandem mass spectra to proteins in the database without prior knowledge of the PTMs. Nevertheless, MS-TopDown lacks statistical evaluation of the search results and performs slowly when searching against large databases. MS-Align+ also utilizes spectral alignment for top-down protein identification (32). It is capable of identifying unexpected PTMs and allows for efficient filtering of candidate proteins when the top-down spectra are searched against a large protein database. MS-Align+ also provides statistical evaluation for the selection of proteoform spectrum match (PrSM) with high confidence. More recently, Top-Down Mass Spectrometry Based Proteoform Identification and Characterization (TopPIC) was developed (http://proteomics.informatics.iupui.edu/software/toppic/index.html). TopPIC is an updated version of MS-Align+ with increased spectral alignment speed and reduced computing requirements. In addition, MSPathFinder, developed by Kim et al., also allows for the rapid identification of proteins from top-down tandem mass spectra (http://omics.pnl.gov/software/mspathfinder) using spectral alignment. Although software tools employing spectral alignment, such as MS-Align+ and MSPathFinder, are particularly useful for top-down protein identification, these programs operate using command line, making them difficult to use for those with limited knowledge of command syntax.Recently, new software tools have been developed for proteoform characterization (36, 37). Our group previously developed MASH Suite, a user-friendly interface for the processing, visualization, and validation of high-resolution MS and MS/MS data (36). Another software tool, ProSight Lite, developed recently by the Kelleher group (37), also allows characterization of protein PTMs. However, both of these software tools require prior knowledge of the protein sequence for the effective localization of PTMs. In addition, both software tools cannot process data from liquid chromatography (LC)-MS and LC-MS/MS experiments, which limits their usefulness in large-scale top-down proteomics. Thus, despite these recent efforts, a multifunctional software platform enabling identification, quantitation, and characterization of proteins from top-down spectra, as well as visual validation and data correction, is still lacking.Herein, we report the development of MASH Suite Pro, an integrated software platform, designed to incorporate tools for protein identification, quantitation, and characterization into a single comprehensive package for the analysis of top-down proteomics data. This program contains a user-friendly customizable interface similar to the previously developed MASH Suite (36) but also has a number of new capabilities, including the ability to handle complex proteomics datasets from LC-MS and LC-MS/MS experiments, as well as the ability to identify unknown proteins and PTMs using MS-Align+ (32). Importantly, MASH Suite Pro also provides visualization components for the validation and correction of the computational outputs, which ensures accurate and reliable deconvolution of the spectra and localization of PTMs and sequence variations.     

Simple and reliable detection of slime production of <Emphasis Type="Italic">Candida</Emphasis><Emphasis Type="Italic">spp</Emphasis>. directly from blood culture bottles: Comparison of visual tube method and transmission electron microscopy

Early detection of slime production may be useful for clinical decision because of its suggestive property for potential pathogenic capacity of a Candida strain especially in patients with a prosthetic device. In this study we aimed to compare the visual tube method (VTM) with transmission electron microscopy (TEM) in order to confirm the reliability of the former method. In order to demonstrate the reproducibility of the tube method and to determine the correct timing for the test, Candida isolates directly obtained from blood culture (DBC) bottles and their two subsequent subcultures were used. The results of this study showed that VTM is a simple and reliable method which can be used in every clinical mycology laboratory, provided that the test is applied on DBC isolates; as the ability of slime production is decreased or lost even after the first subculturing. We suggest that this simple method can be used and may have some contributions to the ongoing studies on the controversial issue concerning removal of biomaterials in candidemic patients.     

Interesting electrophysiological findings in a patient with coincidental right ventricular outflow tract and atrioventricular nodal reentrant tachycardia

Tachycardia induced tachycardias are not common in clinical practice, and it is believed that most cases of double tachycardia are coincidental. The existence of two different tachycardias in the same patient almost always poses problems in the electrophysiology laboratory. However, in rare instances, the emergence of a second tachycardia can actually provide invaluable information about the first one. In this report, we describe a 30-year-old woman who presented with palpitations. Electrophysiological study revealed that atrial programmed stimulation at baseline induced right ventricular outflow tract (RVOT) tachycardia and supraventricular tachycardia. The study also showed that each of the tachycardias was able to induce the other. A short run of RVOT tachycardia during supraventricular tachycardia was able to entrain the latter. This finding provided important information about the nature of the supraventricular tachycardia, which proved to be atrioventricular nodal reentrant tachycardia. Both of these tachycardias were successfully ablated, and the patient's palpitations disappeared.     

Bone quality and healing in a swine vascularized bone allotransplantation model using cyclosporine-based immunosuppression therapy

Although vascularized bone and joint allotransplantation is a promising new treatment option for reconstructing large bone defects, the need for immunosuppressive agents to prevent rejection in these procedures poses a major problem. This problem stems from the fact that several of these agents can cause harmful side effects, such as alterations in bone quality and healing. Therefore, the purpose of this study was to determine what effect the commonly used immunosuppressant regimen cyclosporine A-based combination therapy has on bone quality and healing. In 10 pigs, vascularized bone allografts with skin and muscle components (osteomyocutaneous free flaps) were transplanted from size-matched donor animals. Recipient animals received oral cyclosporine A/mycophenolate mofetil/prednisone therapy for 90 days. Bone quality was studied before and after transplantation by measuring the bone's acoustic velocity and density and calculating the bone's elastic coefficient. Bone healing was assessed using radiographic analysis. Four animals were lost as a result of graft rejection or immunosuppression-related complications before the 90-day endpoint of the study. Although bone specimens taken from the six animals that completed the 90-day protocol had histological signs of rejection, they all seemed to have normal bone healing. Posttransplant bone density values were significantly decreased (p < 0.05) (1544.7 +/- 47.5 kg/m3) as compared with pretransplant values (1722.7 +/- 44.1 kg/m3). Results of the acoustic velocity and elastic coefficients measurements showed a significant decrease (p < 0.05) in posttransplant values (from 3503.0 +/- 165.1 meters/sec to 2963.0 +/- 54.6 meters/sec and from 21.6 +/- 2.2 GPa to 13.6 +/- 0.5 GPa, respectively), indicating diminished bone quality. The findings indicate that cyclosporine A/mycophenolate mofetil/prednisone combination therapy is ineffective in preventing bone rejection, that it decreases bone quality, and that it is associated with systemic toxicity, suggesting that this immunosuppressive regimen at the doses used in this study is not ideal for vascularized bone allotransplantation procedures.     

Oxidative stress is decreased in off-pump versus on-pump coronary artery surgery

Oxidative stress occurs in patients undergoing coronary artery bypass operation. The aim of this study was to investigate the difference in oxidative stress in off-pump versus on-pump coronary artery bypass surgery. In the present study, in serial blood samples, plasma malondialdehyde (MDA) as index of lipid peroxidation, red blood cells glutathione peroxidase (GPx) and superoxide dismutase (SOD) were measured to compare the extent of oxidative stress in 30 patients undergoing OPCAB (off-pump coronary artery bypass grafting), 12 patients undergoing CABG (on-pump coronary artery bypass grafting) and 18 healthy controls. In CABG group, MDA levels increased significantly from 2.87 +/- 0.62 nmol/mL before anesthesia and 2.87 +/- 0.65 nmol/mL after anesthesia to 3.05 +/- 0.66 nmol/mL after ischemia (p < 0.05). Similarly, SOD levels also elevated significantly from 661.58 +/- 78.70 U/g Hb before anesthesia and 659.42 +/- 81.21 U/g Hb anesthesia induction to 678.08 +/- 75.80 U/g Hb after ischemia (p < 0.01, p < 0.01, respectively). In OPCAB group, only SOD levels increased from 581.73 +/- 86.24 U/g Hb anesthesia induction to 590.90 +/- 88.90 U/g Hb after reperfusion (p < 0.05). Glutathione peroxidase levels were not changed according to blood collection times in both of CABG group or OPCAB group (p > 0.05). Our results show that only mild signs of oxidative stress is found after reperfusion in OPCAB operation compared with CABG operation. Further studies are needed in order to confirm this hypothesis.     

Susceptibility profiles and resistance genes for carbapenems (cfiA) and metronidazole (nim) among Bacteroides species in a Turkish University Hospital

Sixty-six nonduplicate Bacteroides clinical isolates collected at Marmara University Hospital were tested to investigate carbapenem and metronidazole resistance profiles and to detect the resistance genes (cfiA and nim) and related insertion sequence (IS) elements. The study found that there were no strains resistant to metronidazole and nim genes were not detected in any of the strains. Five Bacteroides fragilis strains were resistant to meropenem, one of which was also resistant to imipenem. The cfiA gene was detected in 27% of strains, 32% of strains had the IS1187 element, and five strains harbored both gene cfiA and IS1187. These results indicate higher rates of carriage of the cfiA gene and IS1187 insertion elements than have been reported in other countries.