In situ proteolysis for protein crystallization and structure determination

We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.     

Bait traps remain attractive to euglossine bees even after two weeks: a report from Brazilian Atlantic forest

Bait traps are effective and commonly used method in the studies of orchid bees. Important questions in the context of this method, including those related to bait dispersion, how long baits remain attractive, the distance from which males are supposed to be attracted to lures and so on, are still open subjects. Data on the attractiveness of bait traps that have remained in the field during two weeks in a large Atlantic forest preserve are presented. Four main results emerge from the data: (i) the abundance of specimens collected per day decreased in all the attractants as the traps were left on the field; (ii) despite this decrease, the absolute number of individuals collected after eight and fifteen days is remarkably, mostly in eugenol and vanillin baits; (iii) the vast majority of species, 22 of 25, was already collected on the first sample day; (iv) a consistent variation in the relative abundance of individuals collected in each scent as collections were made. We urge that bait traps should not be left in the field beyond what is strictly necessary since there is a real possibility of collecting a significant number of individuals as these traps remain available.     

Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1

The Drosophila behaviour/human splicing (DBHS) proteins are a family of RNA/DNA binding cofactors liable for a range of cellular processes. DBHS proteins include the non-POU domain-containing octamer-binding protein (NONO) and paraspeckle protein component 1 (PSPC1), proteins capable of forming combinatorial dimers. Here, we describe the crystal structures of the human NONO and PSPC1 homodimers, representing uncharacterized DBHS dimerization states. The structures reveal a set of conserved contacts and structural plasticity within the dimerization interface that provide a rationale for dimer selectivity between DBHS paralogues. In addition, solution X-ray scattering and accompanying biochemical experiments describe a mechanism of cooperative RNA recognition by the NONO homodimer. Nucleic acid binding is reliant on RRM1, and appears to be affected by the orientation of RRM1, influenced by a newly identified ‘β-clasp’ structure. Our structures shed light on the molecular determinants for DBHS homo- and heterodimerization and provide a basis for understanding how DBHS proteins cooperatively recognize a broad spectrum of RNA targets.     

Determinants of Intestinal Detoxication of Lipid Hydroperoxides

It has long been recognized that hydroperoxides are agents of cytotoxicity. However, in recent years, it is increasingly apparent that lipid hydroperoxide may play an important role in mediating cellular and molecular events in degenerative pathophysiological processes that lead to intestinal disorders, such as cancer. Yet, surprisingly, little is known of the intestinal disposition of peroxidized lipids and of the metabolic factors that determine mucosal peroxide elimination. The present paper summarizes the evidence for the pivotal role of reductant (GSH and NADPH) availability in intestinal peroxide detoxication. This information will provide important insights into the relationship between luminal lipid hydroperoxides and intestinal GSH redox homeostasis, and is pertinent to understanding how dietary oxidants like lipid peroxides, can impact intestinal integrity with implications for genesis of gut pathology.     

Parasites of Pleurobrachia pileus Muller, 1776 (Ctenophora), from Galway Bay, western Ireland

Specimens of Pleurobrachia pileus Müller from Galway Bay,western Ireland, were found to be parasitised by three trematodes,one isopod and one nematode. Among these, the trematode, Opechonabacillaris Molin and didymozoid larvae were the most abundant,infecting over 17% of the Pleurobrachia population. Peak infectionwas during the summer of each year when >40% of P. - pileuswere parasitised. Serious infection was found to be either accompaniedor followed by a sharp decline in the abundance of the ctenophore.A close, but negative, correlation was established between theabundance of P. pileus and the percentage of parasitic infection.The percentage of infection in larger P. pileus was higher thanin small specimens. No parasites were detected from P. pileus1 mm or less in length.     

Biological kinetics evaluation of anaerobic stabilization pond treatment of palm oil mill effluent

Biological kinetic (bio-kinetic) study of the anaerobic stabilization pond treatment of palm oil mill effluent (POME) was carried out in a laboratory anaerobic bench scale reactor (ABSR). The reactor was operated at different feed flow-rates of 0.63, 0.76, 0.95, 1.27, 1.9 and 3.8 l of raw POME for a day. Chemical oxygen demand (COD) as influent substrates was selected for bio-kinetic study. The investigation showed that the growth yield (Y_G), specific biomass decay (b), maximum specific biomass growth rate (μ_max), saturation constant (K_s) and critical retention time (Θ_c) were in the range of 0.990 g VSS/g COD_removed day, 0.024 day⁻¹, 0.524 day⁻¹, 203.433 g COD l⁻¹ and 1.908 day, respectively.     

Sampling plan for Diaphania spp. (Lepidoptera: Pyralidae) and for hymenopteran parasitoids on cucumber

The objective of this work was to determine the best technique, sampling unit, and the number of samples to compose a conventional sampling plan for the cucurbit borers, Diaphania spp. (Lepidoptera: Pyralidae), and for hymenopteran parasitoids on cucumber. This research was carried out in 10 commercial cucumber crops fields from July to December 2000 in Tocantins, Minas Gerais State, Brazil (21 degrees 11' 15" S; 42 degrees 03' 45" W; altitude 363 m). The sampling methods studied were beating on a tray, direct counting of insects on the lower leaf surface, and whole leaf collection. Three sampling units also were studied: leaves from a branch located in the apical, median, or basal third of the canopy. The best sampling systems, which included the best technique and sampling unit, were determined based on the relative variance and the economic precision of the sampling. Once the best sampling systems were established, the numbers of samples to compose the conventional sampling plans were determined. The more suitable sampling system for the larvae of Diaphania spp. in cucumber plants was beating a leaf of the median third of the canopy on a plastic tray. One leaf must be sampled for every 50 plants in a crop. The more suitable sampling system for hymenopteran parasitoids in cucumber plants was to directly count the adults on one leaf of the median third of the canopy. One leaf must be sampled for every 74 plants in a crop.