Wide Screening of Phage-Displayed Libraries Identifies Immune Targets in Planta

Microbe-Associated Molecular Patterns and virulence effectors are recognized by plants as a first step to mount a defence response against potential pathogens. This recognition involves a large family of extracellular membrane receptors and other immune proteins located in different sub-cellular compartments. We have used phage-display technology to express and select for Arabidopsis proteins able to bind bacterial pathogens. To rapidly identify microbe-bound phage, we developed a monitoring method based on microarrays. This combined strategy allowed for a genome-wide screening of plant proteins involved in pathogen perception. Two phage libraries for high-throughput selection were constructed from cDNA of plants infected with Pseudomonas aeruginosa PA14, or from combined samples of the virulent isolate DC3000 of Pseudomonas syringae pv. tomato and its avirulent variant avrRpt2. These three pathosystems represent different degrees in the specificity of plant-microbe interactions. Libraries cover up to 26107 different plant transcripts that can be displayed as functional proteins on the surface of T7 bacteriophage. A number of these were selected in a bio-panning assay for binding to Pseudomonas cells. Among the selected clones we isolated the ethylene response factor ATERF-1, which was able to bind the three bacterial strains in competition assays. ATERF-1 was rapidly exported from the nucleus upon infiltration of either alive or heat-killed Pseudomonas. Moreover, aterf-1 mutants exhibited enhanced susceptibility to infection. These findings suggest that ATERF-1 contains a microbe-recognition domain with a role in plant defence. To identify other putative pathogen-binding proteins on a genome-wide scale, the copy number of selected-vs.-total clones was compared by hybridizing phage cDNAs with Arabidopsis microarrays. Microarray analysis revealed a set of 472 candidates with significant fold change. Within this set defence-related genes, including well-known targets of bacterial effectors, are over-represented. Other genes non-previously related to defence can be associated through this study with general or strain-specific recognition of Pseudomonas.

A Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffold

Proteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a beta-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues.

Association between CASP8-652 6N Del Polymorphism (rs3834129) and Colorectal Cancer Risk: Results from a Multi-Centric Study

The common 2652 6N del variant in the CASP8 promoter (rs3834129) has been described as a putative low-penetrance risk factor for different cancer types. In particular, some studies suggested that the deleted allele (del) was inversely associated with CRC risk while other analyses failed to confirm this. Hence, to better understand the role of this variant in the risk of developing CRC, we performed a multi-centric case-control study. In the study, the variant 2652 6N del was genotyped in a total of 6,733 CRC cases and 7,576 controls recruited by six different centers located in Spain, Italy, USA, England, Czech Republic and the Netherlands collaborating to the international consortium COGENT (COlorectal cancer GENeTics). Our analysis indicated that rs3834129 was not associated with CRC risk in the full data set. However, the del allele was under-represented in one set of cases with a family history of CRC (per allele model OR = 0.79, 95% CI = 0.69-0.90) suggesting this allele might be a protective factor versus familial CRC. Since this multi-centric case-control study was performed on a very large sample size, it provided robust clarification of the effect of rs3834129 on the risk of developing CRC in Caucasians.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Length-weight relationship and the diets of Clarias lazera (Cuvier and Valenciennes), family Clariidae (Osteichthyes: Siluriformes) in Zaria, Nigeria

The length-weight relationship and the diets of Clarias lazera were investigated between July 1981 and June 1982. About 450 specimens were examined. The standard lengths of the fish ranged from 8.5 cm to 42.2 cm. Significant differences were found between the standard lengths of the males and females with the latter slightly shorter. Somatic weights varied between 10 g to 502 g. Length-weight regression analysis gave a "b" value of 3.02 for both males and females combined; thus indicating an isometric growth. Analysis of the food in the stomachs showed that the fish is an omnivore although, it fed more on insects and fish than other food items

MEASUREMENT OF SOLID SLURRY FLOW VIA CORRELATION OF ELECTROMAGNETIC FLOW METER, ELECTRICAL RESISTANCE TOMOGRAPHY AND MECHANISTIC MODELLING

The study presented here was carried out to obtain the actual solids flow rate by the combination of electrical resistance tomography and electromagnetic flow meter. A new in-situ measurement method based on measurements of the Electromagnetic Flow Meters (EFM) and Electrical Resistance Tomography (ERT) to study the flow rates of individual phases in a vertical flow was proposed. The study was based on laboratory experiments that were carried out with a 50 mm vertical flow rig for a number of sand concentrations and different mixture velocities. A range of sand slurries with median particle size from 212 mu m to 355 mu m was tested. The solid concentration by volume covered was 5% and 15%, and the corresponding density of 5% was 1078 kg/m(3) and of 15% was 1238 kg/m(3). The flow velocity was between 1.5 m/s and 3.0 m/s. A total of 6 experimental tests were conducted. The equivalent liquid model was adopted to validate in-situ volumetric solids fraction and calculate the slip velocity. The results show that the ERT technique can be used in conjunction with an electromagnetic flow meter as a way of measurement of slurry flow rate in a vertical pipe flow. However it should be emphasized that the EFM results must be treated with reservation when the flow pattern at the EFM mounting position is a non-homogenous flow. The flow rate obtained by the EFM should be corrected considering the slip velocity and the flow pattern.

Triploidy induction in Heterobranchus longifilis (Family: Clariidae) by cold shock

Triploid was induced in African Catfish (Heterobranchus longifilis) by cold shocking activated eggs at 5 degree C for forty minutes starting 3-4 minutes after fertilization. Triploidy was confirmed from mitotic chromosomes prepared from embryo which showed 100% triploidy in the cold shocking treatment and 100% diploidy in the control treatment

Los inicios de la vascología en Holanda: El Essai de grammaire de la langue basque de Willem J. van Eys (1865, 1867)

Ed. by Xabier Artiagoitia, Patxi Goenaga & Joseba A. Lakarra.

Effects of some environmental factors on the fecundity of Tilapia species (Family Cichlidae) in Kigera Reservoir, New Bussa

The effects of some environmental factors on the fecundity of Tilapia species (Family Cichilidae) was carried out at the Kigera dam. Four Tilapia species caught were Tilapia zilli, Hemichromis fasciatus, Sarotherodon galilaeus and Oreochromis niloticus while the environmental factors considered were water temperature, Dissolved Oxygen, pH value, level of rainfall and rate of sunshine and range of time. 43 fish comprising of 25 male with (58.1%) and 18 females having (41.9%) were studied with 74.42% been sexually matured. Both high levels of rainfall and dissolved oxygen favoured fecundity. The spawning peak occurred in (July), environmental factors monitored indicated that dissolved oxygen ranges from 3.7 to 4.45mg/lit rainfall ranges from (34.90mm to 237.80mm) sunshine ranges from (5hrs-8hrs) and pH ranges from (7.35-7.45). The spawning of these species in their natural or hatchery condition is therefore best achieved during the peak of raining season

Expression of eph-family receptor tyrosine kinases and ephrins in the tadpole of the frog Xenopus laevis, and possible roles in the development of retinotectal topography

Assembling a nervous system requires exquisite specificity in the construction of neuronal connectivity. One method by which such specificity is implemented is the presence of chemical cues within the tissues, differentiating one region from another, and the presence of receptors for those cues on the surface of neurons and their axons that are navigating within this cellular environment.

Connections from one part of the nervous system to another often take the form of a topographic mapping. One widely studied model system that involves such a mapping is the vertebrate retinotectal projection-the set of connections between the eye and the optic tectum of the midbrain, which is the primary visual center in non-mammals and is homologous to the superior colliculus in mammals. In this projection the two-dimensional surface of the retina is mapped smoothly onto the two-dimensional surface of the tectum, such that light from neighboring points in visual space excites neighboring cells in the brain. This mapping is implemented at least in part via differential chemical cues in different regions of the tectum.

The Eph family of receptor tyrosine kinases and their cell-surface ligands, the ephrins, have been implicated in a wide variety of processes, generally involving cellular movement in response to extracellular cues. In particular, they possess expression patterns-i.e., complementary gradients of receptor in retina and ligand in tectum- and in vitro and in vivo activities and phenotypes-i.e., repulsive guidance of axons and defective mapping in mutants, respectively-consistent with the long-sought retinotectal chemical mapping cues.

The tadpole of Xenopus laevis, the South African clawed frog, is advantageous for in vivo retinotectal studies because of its transparency and manipulability. However, neither the expression patterns nor the retinotectal roles of these proteins have been well characterized in this system. We report here comprehensive descriptions in swimming stage tadpoles of the messenger RNA expression patterns of eleven known Xenopus Eph and ephrin genes, including xephrin-A3, which is novel, and xEphB2, whose expression pattern has not previously been published in detail. We also report the results of in vivo protein injection perturbation studies on Xenopus retinotectal topography, which were negative, and of in vitro axonal guidance assays, which suggest a previously unrecognized attractive activity of ephrins at low concentrations on retinal ganglion cell axons. This raises the possibility that these axons find their correct targets in part by seeking out a preferred concentration of ligands appropriate to their individual receptor expression levels, rather than by being repelled to greater or lesser degrees by the ephrins but attracted by some as-yet-unknown cue(s).

Structure of the limbs and its significance for the ecology and systematics of the family Chydoridae. [Translation of: Voprosy Gidrobiologii, p385, 1965]

For an explanation of the dynamics of numbers of chydorids, appearing a massive group in the littoral of fresh water bodies, the structure of the limbs of 29 species was studied.

Key to the larvae of the genera of the sub-family Orthocladiinae from Larvae and Pupae of midges of the sub-family Orthocladiinae of the fauna of the USSR. [Translation from: Larvae and pupae of midges of the subfamily Orthocladiinae of the fauna of the USSR (Diptera, Chironomidae = Tendipedidae) (ed. Pankratova V.Ya.), 51-55. Leningrad, Nauka, 1970. ]

A key to the larvae of the genera of the sub-family Orthocladiinae from Larvae and Pupae of midges of the sub-family Orthocladiinae. Parts of the key refer to the rest of the publication which is not included in this partial translation.