Using minced horseradish roots and peroxides for the deodorization of swine manure: a pilot scale study

Enzymes that have proven to be capable of removing toxic compounds from water and soil may also be useful in the deodorization of animal manures. Considering that pork production in the US is a $40-billion industry with over half a million workers, odor control to protect air quality in the neighboring communities must be considered an essential part of managing livestock facilities. This pilot scale (20-120 L) study tested the use of minced horseradish (Armoracia rusticana L.) roots (1:10 roots to swine slurry ratio), with calcium peroxide (CaO(2) at 34 mM) or hydrogen peroxide (H(2)O(2) at 68 mM), to deodorize swine slurry taken from a 40,000-gallon storage pit at the Pennsylvania State University's Swine Center. Horseradish is known to contain large amounts of peroxidase, an enzyme that, in the presence of peroxides, can polymerize phenolic odorants and thus reduce the malodor. Twelve compounds commonly associated with malodor (seven volatile fatty acids or VFAs, three phenolic compounds and two indolic compounds) were used as odor indicators. Their concentration in swine slurry before and after treatment was determined by gas chromatography (GC) to assess the deodorization effect. The pilot scale testing demonstrated a complete removal of phenolic odorants (with a detection limit of 0.5 mg L(-1)) from the swine slurry, which was consistent with our previous laboratory experiments using 30-mL swine slurry samples. Horseradish could be recycled (reused) five times while retaining significant reduction in the concentration of phenolic odorants. In view of these findings, inexpensive plant materials, such as horseradish, represent a promising tool for eliminating phenolic odorants from swine slurry.     

Inferring phylogeny from whole genomes

MOTIVATION: Inferring species phylogenies with a history of gene losses and duplications is a challenging and an important task in computational biology. This problem can be solved by duplication-loss models in which the primary step is to reconcile a rooted gene tree with a rooted species tree. Most modern methods of phylogenetic reconstruction (from sequences) produce unrooted gene trees. This limitation leads to the problem of transforming unrooted gene tree into a rooted tree, and then reconciling rooted trees. The main questions are 'What about biological interpretation of choosing rooting?', 'Can we find efficiently the optimal rootings?', 'Is the optimal rooting unique?'. RESULTS: In this paper we present a model of reconciling unrooted gene tree with a rooted species tree, which is based on a concept of choosing rooting which has minimal reconciliation cost. Our analysis leads to the surprising property that all the minimal rootings have identical distributions of gene duplications and gene losses in the species tree. It implies, in our opinion, that the concept of an optimal rooting is very robust, and thus biologically meaningful. Also, it has nice computational properties. We present a linear time and space algorithm for computing optimal rooting(s). This algorithm was used in two different ways to reconstruct the optimal species phylogeny of five known yeast genomes from approximately 4700 gene trees. Moreover, we determined locations (history) of all gene duplications and gene losses in the final species tree. It is interesting to notice that the top five species trees are the same for both methods. AVAILABILITY: Software and documentation are freely available from http://bioputer.mimuw.edu.pl/~gorecki/urec     

Dynamics of estrogen-induced oxidative stress

The objective of this study was to assess the dynamics of oxidative damage to cellular macromolecules such as proteins, lipids and DNA under conditions of oxidative stress triggering early stages of estrogen-dependent carcinogenesis. A rodent model of carcinogenesis was used. Syrian hamsters were sacrificed after 1, 3, 5 h and one month from the initial implantation of estradiol. Matching control groups were used. Kidneys as target organs for estradiol-mediated oxidative stress were excised and homogenized for biochemical assays. Subcellular fractions were isolated. Carbonyl groups (as a marker of protein oxidation) and lipid hydroxyperoxides were assessed. DNA was isolated and 8-oxodGuo was assessed. Electron paramagnetic resonance spectroscopy was used to confirm the results for lipid peroxidation. Exposition to estradiol in the rodent model leads to damage of macromolecules of the cell, including proteins and DNA, but not lipids. Proteins appear to be the primary target of the damage but are closely followed by DNA. It has previously been speculated that protein peroxides can increase DNA modifications. This time sequence was observed in our study. Nevertheless, the direct relation between protein and DNA damage still remains unsolved.     

Dexamethasone stimulates leptin release from human adipocytes: Unexpected inhibition by insulin

In the present study we have examined the effect of dexamethasone on ob gene mRNA expression and leptin release from isolated human subcutaneous adipocytes. Dexamethasone stimulated leptin release from cultured adipocytes in a time- and dose-dependent manner. A two-fold increase in leptin release was detectable by 36 h of treatment with 10⁻⁷ M dexamethasone. Leptin release was preceded by a significant 83±30% increase in ob mRNA after 24 h exposure to the compound. Co-incubation of cells with dexamethasone (10⁷ M) and insulin (10⁻⁷ or 10⁻⁹ M) completely blocked the dexamethasone-stimulated increase in ob mRNA and leptin release. These data demonstrate that insulin and glucocorticoids regulate leptin synthesis and release from human adipocytes in vitro. J. Cell. Biochem. 65:254–258. © 1997 Wiley-Liss, Inc.     

NPY: its occurrence and relevance in the female reproductive system

Neuropeptide Y (NPY), an amidated peptide composed of 36 amino acid residues, is the most widely distributed neuropeptide that performs a broad spectrum of physiological functions in both the central and peripheral nervous systems. Among numerous other actions, this peptide is involved, at the periphery, in the neural regulation of blood pressure and blood flow through the organs, and also, acting via Y2 and/or Y5 receptors, in the regulation of angiogenesis. NPY influences blood vessels via its own Y receptors, predominantly of the Y1 subtype. As a sympathetic co-transmitter NPY causes vasoconstriction, stimulates vascular growth and potentiates the contractile activity of noradrenaline (NA), and as a parasympathetic neurotransmitter it is involved in the regulation of vasodilatation within e.g. the uterine artery. In the female reproductive system, NPY not only regulates the blood flow, but also the contractile activity of non-vascular smooth muscle cells of the uterus and oviduct, as well as the secretory function of the ovary. Both the concentration of NPY and its influence on the blood flow through the female reproductive organs are finely tuned by fluctuations in the concentration of ovarian steroid hormones. Thus, the present review was aimed at summarizing the current knowledge dealing with the physiological relevance of NPY in the regulation of female gonad and genital tract function, with a special regard to the pig as a model animal.     

Association Between Lipids, Lipoproteins Composition of HDL Particles and Triglyceride-Rich Lipoproteins, and LCAT and CETP Activity in Post-renal Transplant Patients

High-density lipoprotein (HDL) remodeling within the plasma compartment and the association between lecithin-cholesterol acyltransferase (LCAT) and cholesterol ester transfer protein (CETP) activity, and lipid, lipoprotein concentrations and composition were investigated. The aim was to examine the high sensitivity of C-reactive protein (hsCRP), lipid, apolipoprotein B (apoB), apoAI, total apoAII, apoAIInonB, apoB-containing apoAII (apoB:AII), total apoCIII, apoCIIInonB, apoB-containing apoCIII (apoB:CIII) concentration and LCAT and CETP activity to gain an insight into the association between them and LCAT and CETP, 57 post-renal transplant (Tx) patients with and without statin therapy and in 15 healthy subjects. Tx patients had moderate hypertriglyceridemia, hypercholesterolemia, and dyslipoproteinemia, disturbed triglyceride-rich lipoproteins (TRLs) and HDL composition, decreased LCAT, and slightly increased hsCRP but no CETP activity. Spearman’s correlation test showed the association between lipids and lipoproteins and LCAT or CETP, and multiple ridge stepwise forward regression showed that immunosuppressive therapy in Tx patients can disturb HDL and TRLs composition. The results suggest that inhibition or activation of LCAT is due, in part, to HDL-associated lipoprotein. Lipoprotein composition of apoAI, apoAIInonB, and apoCIIInonB in HDL particle and apoB:AII TRLs can contribute to decrease LCAT mass in Tx patients. Tx patients without statin and with lower triglycerides but higher HDL cholesterol concentration and disturbed lipoprotein composition of ApoAI and apoAII in HDL particle can decrease LCAT, increase LDL cholesterol, aggravate renal graft, and accelerate atherosclerosis and chronic heart diseases.     

Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors

The PglZ family of proteins belongs to the alkaline phosphatase superfamily, which consists of metallohydrolases with limited sequence identity but similar metal-coordination architectures in otherwise divergent active sites. Proteins with a well-defined PglZ domain are ubiquitous among prokaryotes as essential components of BREX phage defence systems and two-component systems (TCSs). Whereas other members of the alkaline phosphatase superfamily are well characterized, the activity, structure and biological function of PglZ family proteins remain unclear. We therefore investigated the structure and function of PorX, an orphan response regulator of the Porphyromonas gingivalis TCS containing a putative PglZ effector domain. The crystal structure of PorX revealed a canonical receiver domain, a helical bundle, and an unprecedented PglZ domain, similar to the general organization of the phylogenetically related BREX-PglZ proteins. The PglZ domain of PorX features an active site cleft suitable for large substrates. An extensive search for substrates revealed that PorX is a phosphodiesterase that acts on cyclic and linear oligonucleotides, including signalling molecules such as cyclic oligoadenylates. These results, combined with mutagenesis, biophysical and enzymatic analysis, suggest that PorX coordinates oligonucleotide signalling pathways and indirectly regulates gene expression to control the secretion of virulence factors.