fMLC: fast multi-level clustering and visualization of large molecular datasets.

Motivation: Despite successful applications of data clustering and visualization techniques in molecular sequence identification, current technologies still do not scale to large biological datasets. Results: We address this problem by a new multi-threaded tool, fMLC, primarily developed to cluster DNA sequences, that is supplemented with an interactive web-based visualization component, DiVE. fMLC enabled to compare, cluster and visualize 350K ITS fungal sequences at the species level. It took less than two hours to compare and cluster the dataset, which is twelve times faster than the time reported previously. Availability and implementation: https://github.com/FastMLC/fMLC (doi: 10.5281/zenodo.926820). Contact: d.vu@westerdijkinstitute.nl or v.robert@westerdijkinstitute.nl.

Endophytic microorganisms--promising applications in bioremediation of greenhouse gases.

Bioremediation is a technique that uses microbial metabolism to remove pollutants. Various techniques and strategies of bioremediation (e.g., phytoremediation enhanced by endophytic microorganisms, rhizoremediation) can mainly be used to remove hazardous waste from the biosphere. During the last decade, this specific technique has emerged as a potential cleanup tool only for metal pollutants. This situation has changed recently as a possibility has appeared for bioremediation of other pollutants, for instance, volatile organic compounds, crude oils, and radionuclides. The mechanisms of bioremediation depend on the mobility, solubility, degradability, and bioavailability of contaminants. Biodegradation of pollutions is associated with microbial growth and metabolism, i.e., factors that have an impact on the process. Moreover, these factors have a great influence on degradation. As a result, recognition of natural microbial processes is indispensable for understanding the mechanisms of effective bioremediation. In this review, we have emphasized the occurrence of endophytic microorganisms and colonization of plants by endophytes. In addition, the role of enhanced bioremediation by endophytic bacteria and especially of phytoremediation is presented.

Infrared spectrum analysis of some flavonoids.

Infrared spectra of some flavonoids and quercetin and morin sulfonic derivatives were recorded. The spectral data of sodium salts of quercetin and morin sulfonic acids were interpreted as indicating the near position valency band of the carbonyl group in relation to its position in quercetin and morin. The distinct shift of this band in quercetin-5'-sulfonic acid (QSA) may probably be a result of the occurrence of an intramolecular proton transfer from the sulfonic -SO3H to the oxygen of -C=O group.

Effects of morin-5'-sulfonic acid sodium salt (NaMSA) on cyclophosphamide-induced changes in oxido-redox state in rat liver and kidney.

Cyclophosphamide (CPX) is an anticancer drug with immunosuppressive properties. Its adverse effects are partly connected to the induction of oxidative stress. Some studies indicate that water-soluble derivative of morin-morin-5'-sulfonic acid sodium salt (NaMSA) exhibits strong antioxidant activity. The aim of present study was to evaluate the effect of NaMSA on CPX-induced changes in oxido-redox state in rat. Experiment was carried out on Wistar rats divided in three experimental groups (N = 12) receiving: 0.9% saline, CPX (15 mg/kg) or CPX (15 mg/kg) + NaMSA (100 mg/kg), respectively, and were given intragastrically for 10 days. Malondialdehyde (MDA) and glutathione (GSH) concentrations and superoxide dismutase (SOD) activity were determined in liver and kidneys. Catalase (CAT) activity was assessed only in liver. Treatment with CPX resulted in significant decrease in MDA level in both tissues, which was completely reversed by NaMSA treatment only in liver. In comparison to the control group significant decrease in SOD activity were observed in both tissues of CPX receiving group. In kidneys this parameter was fully restored by NaMSA administration. CPX evoked significant decrease in GSH concentration in kidneys, which was completely reversed by NaMSA treatment. No significant changes were seen in GSH levels and CAT activity between all groups in liver. Results of our study suggest that CPX may exert significant impact on oxido-redox state in both organs. NaMSA fully reversed the CPX-induced changes, especially MDA level in liver, SOD activity and GSH concentration in kidneys and it may be done by enhancement of activity/concentration of endogenous antioxidants.

Analysis of antioxidant enzyme activity and magnesium level in chronic obstructive pulmonary disease (COPD).

There is an increasing interest in the relationship of hypomagnesemia and oxidative stress in pulmonary diseases. It seems to be clinically relevant to assess prooxidant/antioxidant balance and its correlation with magnesium level in COPD. In this study, there were investigated the antioxidant enzymes activity and magnesium plasma level in a group of patients with chronic obstructive pulmonary disease and in the control group. The study group consisted of 41 patients admitted to hospital for ambulatory medical treatment in pulmonary department of the Medical University of Lublin. The control group was made up of 20 patients who were admitted for control examinations. Superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) activity were assessed in red blood cells using kinetics methods. Significantly decreased activity of CAT in COPD, insignificantly decreased activity of GPX and insignificantly increased activity of SOD were detected. Patients with COPD also showed the lowered plasma magnesium level. The conclusion is that COPD is accompanied by a lowered magnesium level and an alteration in antioxidant status due to possible oxidative stress in this disease.

The changes in the antioxidant status of heart during experimental hypomagnesemia in balb/c mice.

The present experiment was performed to assess if hypomagnesemia can influence antioxidant status in mice heart. The results could explain possibly a free radical theory of heart damage in magnesium deficiency. We used a rodent model of hypomagnesemia. The magnesium sufficient group received a standard diet whereas a magnesium deficient group received the diet containing a trace amount of magnesium. The activities of the most important antioxidant enzymes--catalase, glutathione peroxidase and superoxide dismutase were assessed in mice heart and liver in a time dependent manner, on the 10th and the 20th day of experiment. The level of magnesium in plasma of animals receiving the magnesium deficient diet dropped twice after the 8th day and four times after the 13th day and then reached a plateau value. The activity of catalase in heart in the magnesium deficient group increased gradually and was significantly (P < 0.05) elevated by 27% on the 20th day of experiment whereas the superoxide dismutase activity was significantly decreased by 17% on the 20th day. Glutathione peroxidase activity was insignificantly elevated. The alterations of antioxidant enzyme activities in the heart indicate cardiomyocytes's exposure to oxidative stress, which can be responsible for the cardiac lesions observed during hypomagnesemia.

Developing an injectable formula containing an oxygen-sensitive drug: a case study of danofloxacin injectable.

The purpose of this study was to assess the impact of impurities in formulation components, antioxidants, formulation pH, and processing/packaging on the extent of color change associated with oxidation of danofloxacin injectable. The methods used in this study include reversed-phase HPLC, UV-VIS spectrophotometry, atomic absorption spectroscopy, visual observation, and iodimetric titration for quantification of the antioxidant. The results from this study revealed that trace impurities from two different excipients significantly contributed to color change associated with oxidation. Polyvinyl pyrrolidone (PVP) introduced trace levels of peroxides into the solution. A second excipient also had a significant impact on stability because it introduced trace metal impurities into the product. The minimization of oxygen levels alone in the solution and headspace was not sufficient to completely eliminate the product instability. The addition of an antioxidant, monothioglycerol (MTG), resulted in a formulation less sensitive to processing variables. The impact of pH on the performance of MTG was also studied. At pH 7.5, MTG resulted in significant improvement in stability; however, at pH 6.0 it was not effective as an antioxidant. Process modifications alone may not be sufficient to prevent oxidation. Chemical approaches, such as pH control, addition of an antioxidant, and control of components should be considered first as means of enhancing stability of oxygen-sensitive solutions.

Sustained in vivo activity of recombinant bovine granulocyte colony stimulating factor (rbG-CSF) using HEPES buffer.

The purpose of this study was to develop a long-acting injectable formulation of bG-CSF for veterinary use. However, in order to achieve sustained in vivo activity it was first necessary to stabilize the protein at the injection site. Preformulation studies, as well as literature, suggest that bG-CSF aggregates at neutral pH ranges (i.e., pH 6-8) and at temperatures of approximately 40 degrees C. Therefore, bG-CSF will not retain its activity for an extended period of time at the injection site. During this study we determined that HEPES buffer has a very significant impact on protein stability as well as on biological performance. Recombinant bovine granulocyte colony stimulating factor (rbG-CSF) was formulated in 1 M HEPES buffer for subcutaneous injection into cows. bG-CSF formulated in 1 M HEPES buffer resulted in sustained in vivo activity of bG-CSF compared to the "control" formulation (control formulation: 5% mannitol, 10 mM acetate buffer, 0.004% tween-80, pH 4). White blood cell (WBC) count was used as a marker to evaluate in vivo activity of the formulation. WBC numbers remained above a threshold value for only 24-30 h for the control formula. However, when bG-CSF was formulated in 1 M HEPES, the WBC remained above threshold for 3 days or 72 h. Formulating bG-CSF in 1 M HEPES at pH 7.5 also resulted in greater solution stability. This was surprising since bG-CSF is intrinsically not stable at neutral pH. The effect of 1 M HEPES on the T(M) (temperature at maximum heat flow on calorimetry scan) of bG-CSF was determined by microcalorimetry. In the absence of 1 M HEPES buffer the T(M) was 48 degrees C (onset approximately 40 degrees C), while bG-CSF formulated in 1 M HEPES buffer has a T(M) of 59 degrees C (onset approximately 50 degrees C). Similar organic buffers, such as MOPS, HEPPS, TES, and tricine, also resulted in improved solution stability as well as in sustained in vivo activity. The dramatic effect of these buffers on stability and biological performance of bG-CSF is not well understood. One hypothesis is that the electrostatic interaction between the zwitterionic form of these buffers and bG-CSF provides stabilization against denaturation.