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.     

Cross-kingdom signalling: exploitation of bacterial quorum sensing molecules by the green seaweed Ulva

The green seaweed Ulva has been shown to detect signal molecules produced by bacteria. Biofilms that release N-acylhomoserine lactones (AHLs) attract zoospores--the motile reproductive stages of Ulva. The evidence for AHL involvement is based on several independent lines of evidence, including the observation that zoospores are attracted to wild-type bacteria that produce AHLs but are not attracted to mutants that do not produce signal molecules. Synthetic AHL also attracts zoospores and the attraction is lost in the presence of autoinducer inactivation (AiiA) protein. The mechanism of attraction is not chemotactic but involves chemokinesis. When zoospores detect AHLs, the swimming rate is reduced and this results in accumulation of cells at the source of the AHL. It has been demonstrated that the detection of AHLs results in calcium influx into the zoospore. This is the first example of a calcium signalling event in a eukaryote in response to bacterial quorum sensing molecules. The role of AHLs in the ecology of Ulva is discussed. It is probable that AHLs act as cues for the settlement of zoospores, rather than being directly involved as a signalling mechanism.     

A comparative study of the prevalence of the metabolic syndrome and its components in type 2 diabetic patients in two Caribbean islands using the new International Diabetes Federation definition

BACKGROUND AND AIM: Tobago and Trinidad are two Caribbean islands with distinct genetic background and lifestyles; while Tobago is serene and a tourist centre, Trinidad is characterized by a hustling and bustling lifestyle. The study was aimed at determining and comparing the prevalence of the metabolic syndrome (MetS) and its critical components in type 2 diabetic patients using the new International Diabetes Federation (IDF) definition. METHODS: Four hundred and thirteen (166 Tobago, 247 Trinidad) type 2 diabetic patients visiting 10 lifestyle disease clinics were studied. Blood pressure, anthropometric parameters (height, weight, body mass index and waist circumference) and overnight fasting blood samples were taken. Plasma glucose and serum triglycerides, total cholesterol, LDL- and HDL-cholesterol, insulin, and adiponectin were determined. Insulin resistance (IR) was determined using the HOMA method. RESULTS: The patients in Tobago were significantly older than patients in Trinidad (p < 0.001) but the duration of diabetes (9.4 +/- 0.5 vs. 11.1 +/- 0.7 yr), medications, generalized (31.7 vs. 38.8%) and central (78.5 vs. 83.7%) obesity were similar (p > 0.05). In comparison with patients in Tobago, diabetic patients in Trinidad, irrespective of gender, had significantly higher prevalence of IDF critical components such as raised BP, raised triglycerides and reduced HDL-cholesterol (all, p < 0.001). Thus, while more patients in Trinidad were diagnosed with MetS based on three or four components, more patients in Tobago were diagnosed based on two components (p < 0.001). CONCLUSIONS: There were high prevalence rates of the components of the MetS in both the islands of Tobago and Trinidad. Quantitatively, the aggregation of the components is higher in patients in Trinidad, which constitute greater risk for adverse cardiovascular outcome. Controlling central obesity should be the target in preventing MetS in the two islands.     

A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database

mtcPTM is an online repository of human and mouse phosphosites in which data are hierarchically organized to preserve biologically relevant experimental information, thus allowing straightforward comparisons of phosphorylation patterns found under different conditions. The database also contains the largest available collection of atomic models of phosphorylatable proteins. Detailed analysis of this structural dataset reveals that phosphorylation sites are found in a heterogeneous range of structural and sequence contexts. mtcPTM is available on the web .     

Direct selection of human genomic loci by microarray hybridization

We applied high-density microarrays to the enrichment of specific sequences from the human genome for high-throughput sequencing. After capture of 6,726 approximately 500-base 'exon' segments, and of 'locus-specific' regions ranging in size from 200 kb to 5 Mb, followed by sequencing on a 454 Life Sciences FLX sequencer, most sequence reads represented selection targets. These direct selection methods supersede multiplex PCR for the large-scale analysis of genomic regions.     

Correction for light absorption in fluorescence studies of protein-ligand interactions

It is shown that absorption of the excitation light can lead to substantial systematic errors in fluorescence measurements of equilibrium constants for formation of protein-ligand complexes. The assumptions about the optical arrangement of the fluorescence spectrometer involved in the calculation of the correction of this absorption are discussed. A general semiempirical correction procedure which can be used for (calculated) absorbance values as high as 5 is described. The importance of choosing the excitation wavelength so as to minimize the necessity for these corrections is emphasized.     

Dissolved oxygen determination by electrocatalysed chemiluminescence with in-line solid phase media

Dissolved elemental oxygen is determined in a flowing aqueous stream using glucose oxidase to catalyse the reaction between D -glucose and O₂ to produce hydrogen peroxide. The levels of the resulting H₂O₂ are detected and quantified by luminol chemiluminescence using in-line solid phase media for pH adjustment of the reagent stream and for controlled release of the luminophore. The reaction is initiated by electrochemical catalysis. By the use of excess D -glucose in the reagent flow stream, the intensity of chemiluminescence is rendered proportional only to fluctuations in the dissolved O₂ concentration. The methodology provides a means for the detection of aqueous O₂ in the range 0–10 mg/L. © 1998 John Wiley & Sons, Ltd.     

Modulation of SF3B1 in the pre-mRNA spliceosome induces a RIG-I-dependent type I IFN response

Nucleic acid–sensing pathways play critical roles in innate immune activation through the production of type I interferon (IFN-I) and proinflammatory cytokines. These factors are required for effective antitumor immune responses. Pharmacological modulators of the pre-mRNA spliceosome splicing factor 3b subunit 1 (SF3B1) are under clinical investigation as cancer cytotoxic agents. However, potential roles of these agents in aberrant RNA generation and subsequent RNA-sensing pathway activation have not been studied. In this study, we observed that SF3B1 pharmacological modulation using pladienolide B (Plad B) induces production of aberrant RNA species and robust IFN-I responses via engagement of the dsRNA sensor retinoic acid–inducible gene I (RIG-I) and downstream interferon regulatory factor 3. We found that Plad B synergized with canonical RIG-I agonism to induce the IFN-I response. In addition, Plad B induced NF-κB responses and secretion of proinflammatory cytokines and chemokines. Finally, we showed that cancer cells bearing the hotspot SF3B1^K700E mutation, which leads to global aberrant splicing, had enhanced IFN-I response to canonical RIG-I agonism. Together, these results demonstrate that pharmacological modulation of SF3B1 in cancer cells can induce an enhanced IFN-I response dependent on RIG-I expression. The study suggests that spliceosome modulation may not only induce direct cancer cell cytotoxicity but also initiate an innate immune response via activation of RNA-sensing pathways.     

ARTHROPOD PHYLOGENY: A COMBINED APPROACH

Abstract— Ribosomal and ubiquitin protein coding sequence data are generated from 20 arthropods and five close relatives. These molecular data are combined with morphological characters derived from the literature to approach arthropod phylogenetics from the perspective of total evidence. Trilobita were included in the analysis through morphological comparison alone. The overall data strongly support arthropod monophyly. Recent molecular analyses which have yield different results are shown to have been based on few characters, few taxa or both. The most parsimonious explanation of the data is (Annelida + (Onychophora + (Trilobita + Chelicerata) + (Crustacea + (Myriapoda + Hexapoda))))). The data are largely concordant both internally among data sets and externally with previous cladistic anatomical analyses.     

How to approach the study of syndromes in macroevolution and ecology

Syndromes, wherein multiple traits evolve convergently in response to a shared selective driver, form a central concept in ecology and evolution. Recent work has questioned the existence of some classic syndromes, such as pollination and seed dispersal syndromes. Here, we discuss some of the major issues that have afflicted research into syndromes in macroevolution and ecology. First, correlated evolution of traits and hypothesized selective drivers is often relied on as the only evidence for adaptation of those traits to those hypothesized drivers, without supporting evidence. Second, the selective driver is often inferred from a combination of traits without explicit testing. Third, researchers often measure traits that are easy for humans to observe rather than measuring traits that are suited to testing the hypothesis of adaptation. Finally, species are often chosen for study because of their striking phenotypes, which leads to the illusion of syndromes and divergence. We argue that these issues can be avoided by combining studies of trait variation across entire clades or communities with explicit tests of adaptive hypotheses and that taking this approach will lead to a better understanding of syndrome‐like evolution and its drivers.