Mushroom Ganoderma lucidum Prevents Colitis-Associated Carcinogenesis in Mice.

Background Epidemiological studies suggest that mushroom intake is inversely correlated with gastric, gastrointestinal and breast cancers. We have recently demonstrated anticancer and anti-inflammatory activity of triterpene extract isolated from mushroom Ganoderma lucidum (GLT). The aim of the present study was to evaluate whether GLT prevents colitis-associated carcinogenesis in mice. Methods/Principal Findings Colon carcinogenesis was induced by the food-borne carcinogen (2-Amino-1-methyl-6-phenylimidazol[4,5-b]pyridine [PhIP]) and inflammation (dextran sodium sulfate [DSS]) in mice. Mice were treated with 0, 100, 300 and 500 mg GLT/kg of body weight 3 times per week for 4 months. Cell proliferation, expression of cyclin D1 and COX-2 and macrophage infiltration was assessed by immunohistochemistry. The effect of GLT on XRE/AhR, PXR and rPXR was evaluated by the reporter gene assays. Expression of metabolizing enzymes CYP1A2, CYP3A1 and CYP3A4 in colon tissue was determined by immunohistochemistry. GLT treatment significantly suppressed focal hyperplasia, aberrant crypt foci (ACF) formation and tumor formation in mice exposed to PhIP/DSS. The anti-proliferative effects of GLT were further confirmed by the decreased staining with Ki-67 in colon tissues. PhIP/DSS-induced colon inflammation was demonstrated by the significant shortening of the large intestine and macrophage infiltrations, whereas GLT treatment prevented the shortening of colon lengths, and reduced infiltration of macrophages in colon tissue. GLT treatment also significantly down-regulated PhIP/DSS-dependent expression of cyclin D1, COX-2, CYP1A2 and CYP3A4 in colon tissue. Conclusions Our data suggest that GLT could be considered as an alternative dietary approach for the prevention of colitis-associated cancer

A COMPARISON OF VARIOUS METHODS FOR THE ASSESSMENT OF VERTICAL JUMP HEIGHT

INTRODUCTION: The final result of the vertical jump (height of jump) is used both in research studies as well as in practice. The most frequent methods of assessing the height of a vertical jump are based on computations derived from the force-time curve (KISTLER, etc.). The comparison of the height of jump measured by KISTLER with the height of jumps measured and computed using other methods (e.g., Sargent jump, computation from time of non-contact phase, etc.) have resulted in differences among the values of the height of jump. The main goal of this paper is the comparison of various methods of computation of vertical jump height using kinetic and kinematic analysis. METHODS: A group of 51 male physical education students (age: 18-24 years, height: 1.78 ± 0.07 m, body mass: 75.11 ± 6.54 kg) was the subject of the research. A countermovement jump (CMJ) with an arm swing was performed on a KISTLER platform and registered with two videocameras. One camera registered the subject in the frontal plane and the second registered the detail view of the ankle and foot from the lateral plane. By using a 2D kinematic analysis the track of the center of mass and the ankle were computed, and the heights of these points at different phases of the jump were evaluated. The heights of three selected anatomical points were also computed at different phases of the CMJ. The forcetime function registered by the KISTLER platform was analyzed using software developed in our lab. The height of the jump, the height of the lift of the ankle and the time of the flight phase were evaluated. Ten different ways of computing the height of jump were used in this study. Statistical analysis was performed using the Statgraphics package (analysis of variance and correlation analysis). RESULTS: Statistical analysis confirmed significant differences among the various methods of height of jump measurement. The KISTLER measured height of jumps was approximately 0.13 m lower than those measured by kinematic analysis. The height of the ankle is the main factor influencing this difference. The vertical lift of the anatomical point fossa jugularis resulted in almost the same values as the height of jump of the center of gravity measured by the kinematic analysis (height: center of mass = 0.59 m, ankle = 0.58 m). A very high level of correlation dependence among the measured values (r = 0.88-0.97) indicated the height accuracy of the methods used for the measurement of the height of the jump. CONCLUSIONS: The results have shown that the measurement of the height of jump depends on the method used. The height of jump measured by the KISTLER platform is actually lower than in reality. The reason for these differences is the plantar flexion of the foot

Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers

Machine learning techniques for cancer prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. Recent “OMICS” studies which include a variety of cancer and normal tissue samples along with machine learning approaches have the potential to further accelerate such discovery. To demonstrate this potential, 2,175 gene expression samples from nine tissue types were obtained to identify gene sets whose expression is characteristic of each cancer class. Using random forests classification and ten-fold cross-validation, we developed nine single-tissue classifiers, two multi-tissue cancer-versus-normal classifiers, and one multi-tissue normal classifier. Given a sample of a specified tissue type, the single-tissue models classified samples as cancer or normal with a testing accuracy between 85.29% and 100%. Given a sample of non-specific tissue type, the multitissue bi-class model classified the sample as cancer versus normal with a testing accuracy of 97.89%. Given a sample of non-specific tissue type, the multi-tissue multiclass model classified the sample as cancer versus normal and as a specific tissue type with a testing accuracy of 97.43%. Given a normal sample of any of the nine tissue types, the multi-tissue normal model classified the sample as a particular tissue type with a testing accuracy of 97.35%. The machine learning classifiers developed in this study identify potential cancer biomarkers with sensitivity and specificity that exceed those of existing biomarkers and pointed to pathways that are critical to tissuespecific tumor development. This study demonstrates the feasibility of predicting the tissue origin of carcinoma in the context of multiple cancer classes

CancerDiscover: an integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data

Accurate identification of cancer biomarkers and classification of cancer type and subtype from High Throughput Sequencing (HTS) data is a challenging problem because it requires manual processing of raw HTS data from various sequencing platforms, quality control, and normalization, which are both tedious and timeconsuming. Machine learning techniques for cancer class prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. To date, great research efforts have been taken for cancer biomarker identification and cancer class prediction. However, currently available tools and pipelines lack flexibility in data preprocessing, running multiple feature selection methods and learning algorithms, therefore, developing a freely available and easy-to-use program is strongly demanded by researchers. Here, we propose CancerDiscover, an integrative opensource software pipeline that allows users to automatically and efficiently process large high-throughput raw datasets, normalize, and selects best performing features from multiple feature selection algorithms. Additionally, the integrative pipeline lets users apply different feature thresholds to identify cancer biomarkers and build various training models to distinguish different types and subtypes of cancer. The open-source software is available at https://github.com/HelikarLab/CancerDiscover and is free for use under the GPL3 license

Two-step Processing of Human Frataxin by Mitochondrial Processing Peptidase

We showed previously that maturation of the human frataxin precursor (p-fxn) involves two cleavages by the mitochondrial processing peptidase (MPP). This observation was not confirmed by another group, however, who reported only one cleavage. Here, we demonstrate conclusively that MPP cleaves p-fxn in two sequential steps, yielding a 18,826-Da intermediate (i-fxn) and a 17,255-Da mature (m-fxn) form, the latter corresponding to endogenous frataxin in human tissues. The two cleavages occur between residues 41–42 and 55–56, and both match the MPP consensus sequence RX ↓ (X/S). Recombinant rat and yeast MPP catalyze the pài step 4 and 40 times faster, respectively, than the i à m step. In isolated rat mitochondria, p-fxn undergoes a sequence of cleavages, p à i à m à d1 à d2, with d1 and d2 representing two C-terminal fragments of m-fxn produced by an unknown protease. The iàm step is limiting, and the overall rate of p à i à m does not exceed the rate of mà d1 à d2, such that the levels of m-fxn do not change during incubations as long as 3 h. Inhibition of the iàm step by a disease-causing frataxin mutation (W173G) leads to nonspecific degradation of i-fxn. Thus, the second of the two processing steps catalyzed by MPP limits the levels of mature frataxin within mitochondria

\u3ci\u3eIn Vitro\u3c/i\u3e Stable Isotope Labeling for Discovery of Novel Metabolites by Liquid Chromatography-Mass Spectrometry: Confirmation of γ-Tocopherol Metabolism in Human A549 Cell

A general approach for discovering novel catabolic metabolites from a parent biocompound was developed and validated on metabolism of γ-tocopherol in human A549 cell. Method is based on LC-MS analysis of in vitro stable isotope labeled metabolites and assumes that a parent compound and its metabolites share a common functional group that can be derivatized by well-documented reagents. In this method, two equal aliquots of extracted metabolites are separately derivatized with isotope-coded (heavy) and non-isotope-coded (light) form of derivatizing reagent, mixed at 1:1 ratio and analyzed using LC-MS. The metabolites with common functional group are then easily recognized by determination of a chromatographically co-eluted pair of isotopomers (MS doublet peaks) with similar peak intensities and mass difference corresponding to the mass difference between heavy and light form of derivatization reagent. The feasibility of this approach was demonstrated and validated by identification of products of γ-tocopherol catabolism in human A549 cell culture media using N-methyl-nicotinic acid N-hydroxysuccinimide ester (C1-NANHS) and Nmethyl- d3-nicotinic acid N-hydroxysuccinimide ester (C1-d3-NANHS) derivatizing reagent. Overall four γ-tocopherol metabolites were identified including 9\u27-COOH, 11\u27-COOH, 13\u27-COOH and 13\u27-OH. In addition, the developed LC-MS method can also be used for the fast and sensitive quantitative analysis of γ-tocopherol and other forms of vitamin E related compounds

Biomechanical assessment of various punching techniques

Punches without the use of instruments/objects are a common type of body violence and as such a frequent subject of medicolegal analyses. The assessment of the injuries occurred as well as of the potential of the assault to produce severe body harm is based on objective traces (especially the documented injuries of both parties involved) as well as the-often divergent-descriptions of the event. Quantitative data regarding the punching characteristics that could be used for the assessment are rare and originate mostly in sports science. The aim of this study was to provide physical data enabling/facilitating the assessment of various punching techniques. A total of 50 volunteers took part in our study (29 males and 21 females) and performed severe punches with the fist, with the small finger edge of the hand (karate chop), and with the open hand with both the dominant and the non-dominant hands in randomized order. The strikes were performed on a boxing pad attached to a KISTLER force plate (sampling frequency 10,000 Hz) mounted on a vertical wall. The punching velocity was defined as the hand velocity over the last 10 cm prior to the contact to the pad and ascertained by using a high-speed camera (2000 Hz). Apart from the strike velocity, the maximum force, the impulse (the integral of the force-time curve), the impact duration, and the effective mass of the punch (the ratio between the impulse and the strike velocity) were measured/calculated. The results show a various degree of dependence of the physical parameters of the strikes on the punching technique, gender, hand used, body weight, and other factors. On the other hand, a high degree of variability was observed that is likely attributable to individual punching capabilities. In a follow-up study, we plan to compare the \textquotedblordinary\textquotedbl persons with highly trained (boxers etc.) individuals. Even though the results must be interpreted with great caution and a direct transfer of the quantitative parameters to real-world situations is in general terms not possible, the study offers valuable insights and a solid basis for a qualified forensic medical/biomechanical assessment

Yeast and Human Frataxin Are Processed to Mature Form in Two Sequential Steps by the Mitochondrial Processing Peptidase

Frataxin is a nuclear-encoded mitochondrial protein which is deficient in Friedreich’s ataxia, a hereditary neurodegenerative disease. Yeast mutants lacking the yeast frataxin homologue (Yfh1p) show iron accumulation in mitochondria and increased sensitivity to oxidative stress, suggesting that frataxin plays a critical role in mitochondrial iron homeostasis and free radical toxicity. Both Yfh1p and frataxin are synthesized as larger precursor molecules that, upon import into mitochondria, are subject to two proteolytic cleavages, yielding an intermediate and a mature size form. A recent study found that recombinant rat mitochondrial processing peptidase (MPP) cleaves the mouse frataxin precursor to the intermediate but not the mature form (Koutnikova, H., Campuzano, V., and Koenig, M. (1998) Hum. Mol. Gen. 7, 1485–1489), suggesting that a different peptidase might be required for production of mature size frataxin. However, in the present study we show that MPP is solely responsible for maturation of yeast and human frataxin. MPP first cleaves the precursor to intermediate form and subsequently converts the intermediate to mature size protein. In this way, MPP could influence frataxin function and indirectly affect mitochondrial iron homeostasis

Yeast and Human Frataxin Are Processed to Mature Form in Two Sequential Steps by the Mitochondrial Processing Peptidase

Frataxin is a nuclear-encoded mitochondrial protein which is deficient in Friedreich’s ataxia, a hereditary neurodegenerative disease. Yeast mutants lacking the yeast frataxin homologue (Yfh1p) show iron accumulation in mitochondria and increased sensitivity to oxidative stress, suggesting that frataxin plays a critical role in mitochondrial iron homeostasis and free radical toxicity. Both Yfh1p and frataxin are synthesized as larger precursor molecules that, upon import into mitochondria, are subject to two proteolytic cleavages, yielding an intermediate and a mature size form. A recent study found that recombinant rat mitochondrial processing peptidase (MPP) cleaves the mouse frataxin precursor to the intermediate but not the mature form (Koutnikova, H., Campuzano, V., and Koenig, M. (1998) Hum. Mol. Gen. 7, 1485–1489), suggesting that a different peptidase might be required for production of mature size frataxin. However, in the present study we show that MPP is solely responsible for maturation of yeast and human frataxin. MPP first cleaves the precursor to intermediate form and subsequently converts the intermediate to mature size protein. In this way, MPP could influence frataxin function and indirectly affect mitochondrial iron homeostasis

Effect of Salts on the Co-Fermentation of Glucose and Xylose by a Genetically Engineered Strain of Saccharomyces Cerevisiae.

Background A challenge currently facing the cellulosic biofuel industry is the efficient fermentation of both C5 and C6 sugars in the presence of inhibitors. To overcome this challenge, microorganisms that are capable of mixed-sugar fermentation need to be further developed for increased inhibitor tolerance. However, this requires an understanding of the physiological impact of inhibitors on the microorganism. This paper investigates the effect of salts on Saccharomyces cerevisiae 424A(LNH-ST), a yeast strain capable of effectively co-fermenting glucose and xylose. Results In this study, we show that salts can be significant inhibitors of S. cerevisiae. All 6 pairs of anions (chloride and sulfate) and cations (sodium, potassium, and ammonium) tested resulted in reduced cell growth rate, glucose consumption rate, and ethanol production rate. In addition, the data showed that the xylose consumption is more strongly affected by salts than glucose consumption at all concentrations. At a NaCl concentration of 0.5M, the xylose consumption rate was reduced by 64.5% compared to the control. A metabolomics study found a shift in metabolism to increased glycerol production during xylose fermentation when salt was present, which was confirmed by an increase in extracellular glycerol titers by 4 fold. There were significant differences between the different cations. The salts with potassium cations were the least inhibitory. Surprisingly, although salts of sulfate produced twice the concentration of cations as compared to salts of chloride, the degree of inhibition was the same with one exception. Potassium salts of sulfate were less inhibitory than potassium paired with chloride, suggesting that chloride is more inhibitory than sulfate. Conclusions When developing microorganisms and processes for cellulosic ethanol production, it is important to consider salt concentrations as it has a significant negative impact on yeast performance, especially with regards to xylose fermentation