Broad-host-range Yersinia phage PY100: genome sequence, proteome analysis of virions, and DNA packaging strategy

PY100 is a lytic bacteriophage with a broad host range within the genus Yersinia. The phage forms plaques on strains of the three human pathogenic species Yersinia enterocolitica, Y. pseudotuberculosis, and Y. pestis at 37°C. PY100 was isolated from farm manure and intended to be used in phage therapy trials. PY100 has an icosahedral capsid containing double-stranded DNA and a contractile tail. The genome consists of 50,291 bp and is predicted to contain 93 open reading frames (ORFs). PY100 gene products were found to be homologous to the capsid proteins and proteins involved in DNA metabolism of the enterobacterial phage T1; PY100 tail proteins possess homologies to putative tail proteins of phage AaΦ23 of Actinobacillus actinomycetemcomitans. In a proteome analysis of virion particles, 15 proteins of the head and tail structures were identified by mass spectrometry. The putative gene product of ORF2 of PY100 shows significant homology to the gene 3 product (small terminase subunit) of Salmonella phage P22 that is involved in packaging of the concatemeric phage DNA. The packaging mechanism of PY100 was analyzed by hybridization and sequence analysis of DNA isolated from virion particles. Newly replicated PY100 DNA is cut initially at a pac recognition site, which is located in the coding region of ORF2.     

Ndrg4 is required for normal myocyte proliferation during early cardiac development in zebrafish

NDRG4 is a novel member of the NDRG family (N-myc downstream-regulated gene). The roles of NDRG4 in development have not previously been evaluated. We show that, during zebrafish embryonic development, ndrg4 is expressed exclusively in the embryonic heart, the central nervous system (CNS) and the sensory system. Ndrg4 knockdown in zebrafish embryos causes a marked reduction in proliferative myocytes and results in hypoplastic hearts. This growth defect is associated with cardiac phenotypes in morphogenesis and function, including abnormal heart looping, inefficient circulation and weak contractility. We reveal that ndrg4 is required for restricting the expression of versican and bmp4 to the developing atrioventricular canal. This constellation of ndrg4 cardiac defects phenocopies those seen in mutant hearts of heartstrings (hst), the tbx5 loss-of-function mutants in zebrafish. We further show that ndrg4 expression is significantly decreased in hearts with reduced tbx5 activities. Conversely, increased expression of tbx5 that is due to tbx20 knockdown leads to an increase in ndrg4 expression. Together, our studies reveal an essential role of ndrg4 in regulating proliferation and growth of cardiomyocytes, suggesting that ndrg4 may function downstream of tbx5 during heart development and growth.     

Comparison of several traps for catching German cockroaches (Dictyoptera: Blattellidae) under laboratory conditions

German cockroach, Blattella germanica (L.) (Dictyoptera: Blattellidae), catch by five types of traps and modifications of each, were tested under controlled laboratory conditions. Cockroach catch differed significantly among traps. Lo-line trap caught the greatest number of cockroaches in the test arena for each size class (23% small nymphs, 39% of gravid females, and 60% of other size classes in the experimental arena). Jar traps caught the least number of cockroaches in the test arena for each size class (range, 7-23% of each size class trapped). Modifications of traps also altered catch of cockroaches. Food bait tablets increased catch significantly; however, increases were small (<10%). Size of traps did not affect catch; whole traps or half traps caught the same number of cockroaches. Jar traps were much less effective than sticky traps, catching only half the number of cockroaches as sticky traps. A thin layer of petrolatum was a more effective barrier in jar traps to cockroach escape than powdered Olancha clay. Traps with petrolatum caught about twice as many cockroaches as traps with clay. Trapping of any of six life stages was not significantly affected by catch of any of the other stages. Rather, trap catch of each life stage was dependent on the number of that life stage available in the experimental arenas. In conclusion, of the traps tested, the Lo-line trap was the most sensitive for measuring cockroach catch, whereas the Detector trap (one third of trap) was the most economical trap (greatest sensitivity for lowest cost).     

Conformation-opioid activity relationships of bicyclic guanidines from 3D similarity analysis

Conformation of bicyclic guanidines with kappa-opioid receptor activity derived in our laboratory from a positional scanning synthetic combinatorial library is presented in this work. We propose a common bioactive conformation and putative pharmacophoric features by means of 3D similarity methods. Our 'Y' shape molecular binding model explains structure-activity relationships and suggests that the guanidine functionality and a 4-methoxybenzyl group may be involved in key interactions with the receptor. Comparison of our model with known opiates suggest a similar binding mode showing that the bicyclic guanidines presented in this work are suitable scaffolds for further development of new opioid receptors ligands.     

Inositol polyphosphates regulate zebrafish left-right asymmetry

Vertebrate body plans have a conserved left-right (LR) asymmetry manifested in the position and anatomy of the heart, visceral organs, and brain. Recent studies have suggested that LR asymmetry is established by asymmetric Ca2+ signaling resulting from cilia-driven flow of extracellular fluid across the node. We report here that inositol 1,3,4,5,6-pentakisphosphate 2-kinase (Ipk1), which generates inositol hexakisphosphate, is critical for normal LR axis determination in zebrafish. Zebrafish embryos express ipk1 symmetrically during gastrulation and early segmentation. ipk1 knockdown by antisense morpholino oligonucleotide injection randomized LR-specific gene expression and organ placement, effects that were associated with reduced intracellular Ca2+ flux in cells surrounding the ciliated Kupffer's vesicle, a structure analogous to the mouse node. Our data suggest that the pathway for inositol hexakisphosphate production is a key regulator of asymmetric Ca(2+) flux during LR specification.     

Discontinuous carbon dioxide release in the German cockroach, Blattella germanica (Dictyoptera: Blattellidae), and its effect on respiratory transpiration

The discontinuous gas exchange cycle (DGC) was described in the German cockroach, Blattella germanica (L.) (Dictyoptera: Blattellidae) for the first time. Also, the effect of the DGC on water loss was investigated. The CO(2) emission pattern in both insecticide resistant and susceptible B. germanica varied with temperature. At 10, 15, and 20 degrees C the pattern was discontinuous. Cycle frequency increased at 25 and 30 degrees C, and at 35 degrees C the pattern became cyclic. In most DGCs, there was no clear distinction between the closed and flutter phases in both strains thus data for these phases were combined and analyzed as the interburst phase. The probability that B. germanica would breath discontinuously varied with temperature. Most cockroaches (62.8%) displayed DGCs at 10 degrees C, therefore measurement of metabolic rate and water loss was carried out at this temperature. Using repeated measures of analysis of variance, the interburst and burst V(.)(CO(2))(ml h(-1)) were not significantly different between the two strains. The variability in CO(2) emission during the interburst and burst phases over time was not significantly different from cycle to cycle or between strains. Overall metabolic rate during the entire recording was not significantly different between both strains. There was a significant difference in the duration of the interburst and burst phases between the strains. The susceptible strain had significantly longer interburst and burst phase durations during a complete DGC than the resistant strain. The interburst and burst phase durations were 5.01+/-0.19 and 6.21+/-0.13 min, respectively, for the resistant strain, whereas the durations were 7.16+/-0.37 and 6.73+/-0.17 min, respectively, for the susceptible strain. This resulted in a DGC of significantly longer duration (13.89+/-0.44 min) in the susceptible strain compared with the resistant strain (11.23+/-0.26 min). The duration of the interburst phase was significantly different from the open phase duration in the resistant strain such that during a single DGC lasting approximately 11.23 min, 43.5% consisted of the interburst phase while the burst phase made up 56.5% of the cycle. The cuticular permeability at 10 degrees C and 0% RH was 2.26 microg cm(-2) h(-1) mmHg(-1) for the resistant strain and 3.42 microg cm(-2) h(-1) mmHg(-1) for the susceptible strain. In both strains, cuticular transpiration accounted for approximately 95% of total water loss. The significantly longer duration of the interburst phase of the susceptible strain was not important in reducing water loss.     

Laboratory and field performance of an indoxacarb bait against German cockroaches (Dictyoptera: Blattellidae)

Experimental indoxacarb powder and gel baits were evaluated in the laboratory, and a gel bait was evaluated in subsequent field studies against the German cockroach, Blattella germanica (L.). In continuous exposure tests, LT50 values were 1.90 and 1.10 d for 0.25 and 1% indoxacarb powder baits, respectively. However, 0.25% indoxacarb gel bait had an LT50 value of 0.68 d, similar to a 0.05% abamectin gel bait formulated with the same bait base. There was no difference in toxicity between fresh and 7-d-old gel bait deposits. A pyrethroid-resistant strain of German cockroaches was significantly resistant to both abamectin and indoxacarb gel baits. Gel bait contained approximately 40% water, desiccated rapidly at 25-28 degrees C and 30-45% RH, but did not rehydrate when held at 56.7% RH for 3 d. Powder indoxacarb baits contained <1% water and did not desiccate or gain water. Indoxacarb gel bait (0.25%) was relatively nonrepellent (approximately 30%) and had positive maximum performance index values (approximately 100) in Ebeling choice box experiments. In field experiments in cockroach-infested kitchens, the 0.25% indoxacarb gel bait significantly reduced visual counts of German cockroaches approximately 74% at 3 d and >95% at 14 d. Indoxacarb baits are toxic, relatively nonrepellent, and can significantly reduce German cockroach populations.     

Delta-Notch signaling induces hypochord development in zebrafish

Different cell types that occupy the midline of vertebrate embryos originate within the Spemann-Mangold or gastrula organizer. One such cell type is hypochord, which lies ventral to notochord in anamniote embryos. We show that hypochord precursors arise from the lateral edges of the organizer in zebrafish. During gastrulation, hypochord precursors are closely associated with no tail-expressing midline precursors and paraxial mesoderm, which expresses deltaC and deltaD. Loss-of-function experiments revealed that deltaC and deltaD were required for her4 expression in presumptive hypochord precursors and for hypochord development. Conversely, ectopic, unregulated Notch activity blocked no tail expression and promoted her4 expression. We propose that Delta signaling from paraxial mesoderm diversifies midline cell fate by inducing a subset of neighboring midline precursors to develop as hypochord, rather than as notochord.     

Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry has become a valuable tool in proteomics. With the increasing acquisition rate of mass spectrometers, one of the major issues is the development of accurate, efficient and automatic peptide mass fingerprinting (PMF) identification tools. Current tools are mostly based on counting the number of experimental peptide masses matching with theoretical masses. Almost all of them use additional criteria such as isoelectric point, molecular weight, PTMs, taxonomy or enzymatic cleavage rules to enhance prediction performance. However, these identification tools seldom use peak intensities as parameter as there is currently no model predicting the intensities based on the physicochemical properties of peptides. In this work, we used standard datamining methods such as classification and regression methods to find correlations between peak intensities and the properties of the peptides composing a PMF spectrum. These methods were applied on a dataset comprising a series of PMF experiments involving 157 proteins. We found that the C4.5 method gave the more informative results for the classification task (prediction of the presence or absence of a peptide in a spectra) and M5' for the regression methods (prediction of the normalized intensity of a peptide peak). The C4.5 result correctly classified 88% of the theoretical peaks; whereas the M5' peak intensities had a correlation coefficient of 0.6743 with the experimental peak intensities. These methods enabled us to obtain decision and model trees that can be directly used for prediction and identification of PMF results. The work performed permitted to lay the foundations of a method to analyze factors influencing the peak intensity of PMF spectra. A simple extension of this analysis could lead to improve the accuracy of the results by using a larger dataset. Additional peptide characteristics or even PMF experimental parameters can also be taken into account in the datamining process to analyze their influence on the peak intensity. Furthermore, this datamining approach can certainly be extended to the tandem mass spectrometry domain or other mass spectrometry derived methods.