Low codon bias and high rates of synonymous substitution in Drosophila hydei and D. melanogaster histone genes

We have evaluated codon usage bias in Drosophila histone genes and have obtained the nucleotide sequence of a 5,161-bp D. hydei histone gene repeat unit. This repeat contains genes for all five histone proteins (H1, H2a, H2b, H3, and H4) and differs from the previously reported one by a second EcoRI site. These D. hydei repeats have been aligned to each other and to the 5.0-kb (i.e., long) and 4.8-kb (i.e., short) histone repeat types from D. melanogaster. In each species, base composition at synonymous sites is similar to the average genomic composition and approaches that in the small intergenic spacers of the histone gene repeats. Accumulation of synonymous changes at synonymous sites after the species diverged is quite high. Both of these features are consistent with the relatively low codon usage bias observed in these genes when compared with other Drosophila genes. Thus, the generalization that abundantly expressed genes in Drosophila have high codon bias and low rates of silent substitution does not hold for the histone genes.      

Mass propagation techniques currently being used in the spawning and rearing of marine fish species

Propagation techniques for marine fish species, applicable to public aquariums, are reviewed based on work with ornamental tropicals and foodfish species. Adult conditioning, spawning procedures, incubation of eggs, larval rearing, larval food culture, and facilities are discussed with specific references to techniques used at Instant Ocean Hatcheries, Inc, for Anemonefish (Amphiprion spp) culture in synthetic seawater.     

An analysis of turbulent shear stresses in leakage flow through a bileaflet mechanical prostheses

In this work, estimates of turbulence were made from pulsatile flow laser Doppler velocimetry measurements using traditional phase averaging and averaging after the removal of cyclic variation. These estimates were compared with estimates obtained from steady leakage flow LDV measurements and an analytical method. The results of these studies indicate that leakage jets which are free and planar in shape may be more unstable than other leakage jets, and that cyclic variation does not cause a gross overestimation of the Reynolds stresses at large distances from the leakage jet orifice.     

Influence of stent configuration on cerebral aneurysm fluid dynamics

Embolic coiling is the most popular endovascular treatment available for cerebral aneurysms. Nevertheless, the embolic coiling of wide-neck aneurysms is challenging and, in many cases, ineffective. Use of highly porous stents to support coiling of wide-neck aneurysms has become a common procedure in recent years. Several studies have also demonstrated that high porosity stents alone can significantly alter aneurysmal hemodynamics, but differences among different stent configurations have not been fully characterized. As a result, it is usually unclear which stent configuration is optimal for treatment. In this paper, we present a flow study that elucidates the influence of stent configuration on cerebral aneurysm fluid dynamics in an idealized wide-neck basilar tip aneurysm model. Aneurysmal fluid dynamics for three different stent configurations (half-Y, Y and, cross-bar) were first quantified using particle image velocimetry and then compared. Computational fluid dynamics (CFD) simulations were also conducted for selected stent configurations to facilitate validation and provide more detailed characterizations of the fluid dynamics promoted by different stent configurations. In vitro results showed that the Y stent configuration reduced cross-neck flow most significantly, while the cross-bar configuration reduced velocity magnitudes within the aneurysmal sac most significantly. The half-Y configuration led to increased velocity magnitudes within the aneurysmal sac at high parent-vessel flow rates. Experimental results were in strong agreement with CFD simulations. Simulated results indicated that differences in fluid dynamic performance among the different stent configurations can be attributed primarily to protruding struts within the bifurcation region.     

Developmental toxicity of the cyanogenic glycoside linamarin in the golden hamster

Cassava, a staple food in many tropical countries, has been suspected as a cause of human congenital defects. Ingestion of the material during pregnancy has been reported to induce limb defects, microcephaly, open eye, and growth retardation in rats. Linamarin is a natural cyanogenic glycoside that occurs in high concentrations in cassava. In the present study, pregnant hamsters received an oral dose of 70,100, 120 or 140 mg/kg linamarin or an equivalent volume of isotonic saline during the early primitive streak stage of gestation. A dose of 120 or 140 mg/kg of the glycoside was associated with an increased incidence of vertebral and rib anomalies as well as the production of encephaloceles in the offspring. These larger doses of linamarin also resulted in obvious maternal toxicity. Linamarin treatment had no effect on fetal body weight, ossification of fetal skeletons, embryonic mortality, or litter size. Although ingestion of the cyanogenic glycoside was associated with a significant teratogenic response, the effects occurred only at doses that elicited signs of maternal intoxication.     

Identification of an alpha3-fucosyltransferase and a novel alpha2- fucosyltransferase activity in cercariae of the schistosome Trichobilharzia ocellata: biosynthesis of the Fucalpha1-->2Fucalpha1-- >3[Gal(NAc)beta1-->4]GlcNAc sequence

Fucose is a major constituent of the protein- and lipid-linked glycans of the various life-cycle stages of schistosomes. These fucosylated glycans are highly antigenic and seem to play a role in the pathology of schistosomiasis. In this article we describe the identification and characterization of two fucosyltransferases (FucTs) in cercariae of the avian schistosome Trichobilharzia ocellata, a GDP-Fuc:[Galbeta1-- >4]GlcNAcbeta-R alpha1-->3-FucT and a novel GDP-Fuc:Fucalpha-R alpha1-- >2-FucT. Triton X-100 extracts of cercariae were assayed for FucT activity using a variety of acceptor substrates. Type 1 chain (Galbeta1- ->3GlcNAc) based compounds were poor acceptors, whereas those based on a type 2 chain (Galbeta1-->4GlcNAc), whether alpha2'-fucosylated, alpha3'-sialylated, or unsubstituted, and whether present as oligosaccharide or contained in a glycopeptide or glycoprotein, all served as acceptor substrates. In this respect the schistosomal alpha3- FucT resembles human FucT V and VI rather than other known FucTs. N- ethylmaleimide, an inhibitor of several human FucTs, had no effect on the activity of the schistosomal alpha3-FucT, whereas GDP-beta-S was strongly inhibitory. Large scale incubations were carried out with Galbeta1-->4GlcNAc, GalNAcbeta1-->4GlcNAcbeta-O -(CH2)8COOCH3 and Fucalpha1-->3GlcNAcbeta1-->2Man as acceptor substrates and the products of the incubations were isolated using a sequence of chromatographic techniques. By methylation analysis and 2D-TOCSY and ROESY1H-NMR spectroscopy the products formed were shown to be Galbeta1-- >4[Fucalpha1-->2Fucalpha1-->3]GlcNAc, GalNAcbeta1-->4[Fucalpha1-- >2Fucalpha1-->3]GlcNAcbe ta-O-(CH2)8COOCH3, and Fucalpha1-->2Fucalpha1-- >3GlcNAcbeta1-->2Man, respectively. It is concluded that the alpha2- FucT and alpha3-FucT are involved in the biosynthesis of the (oligomeric) Lewisx sequences and the Fucalpha1-->2Fucalpha1-->3GlcNAc structural element that have been described on schistosomal glycoconjugates.      

Acceptor specificity of the human leukocyte alpha3 fucosyltransferase: role of FucT-VII in the generation of selectin ligands

The alpha3 fucosyltransferase, FucT-VII, is one of the key glycosyltransferases involved in the biosynthesis of the sialyl Lewis X (sLex) antigen on human leukocytes. The sialyl Lewis X antigen (NeuAcalpha(2-3)Galbeta(1-4)[Fucalpha(1-3)]GlcNAc-R) is an essential component of the recruitment of leukocytes to sites of inflammation, mediating the primary interaction between circulating leukocytes and activated endothelium. In order to characterize the enzymatic properties of the leukocyte alpha3 fucosyltransferase FucT-VII, the enzyme has been expressed in Trichoplusia ni insect cells. The enzyme is capable of synthesizing both sLexand sialyl-dimeric-Lexstructures in vitro , from 3'-sialyl-lacNAc and VIM-2 structures, respectively, with only low levels of fucose transfer observed to neutral or 3'-sulfated acceptors. Studies using fucosylated NeuAcalpha(2-3)-(Galbeta(1- 4)GlcNAc)3-Me acceptors demonstrate that FucT-VII is able to synthesize both di-fucosylated and tri-fucosylated structures from mono- fucosylated precursors, but preferentially fucosylates the distal GlcNAc within a polylactosamine chain. Furthermore, the rate of fucosylation of the internal GlcNAc residues is reduced once fucose has been added to the distal GlcNAc. These results indicate that FucT-VII is capable of generating complex selectin ligands, in vitro , however the order of fucose addition to the lactosamine chain affects the rate of selectin ligand synthesis.      

Single-step stereolithography of complex anatomical models for optical flow measurements

Transparent stereolithographic rapid prototyping (RP) technology has already demonstrated in literature to be a practical model construction tool for optical flow measurements such as digital particle image velocimetry (DPIV), laser doppler velocimetry (LDV), and flow visualization. Here, we employ recently available transparent RP resins and eliminate time-consuming casting and chemical curing steps from the traditional approach. This note details our methodology with relevant material properties and highlights its advantages. Stereolithographic model printing with our procedure is now a direct single-step process, enabling faster geometric replication of complex computational fluid dynamics (CFD) models for exact experimental validation studies. This methodology is specifically applied to the in vitro flow modeling of patient-specific total cavopulmonary connection (TCPC) morphologies. The effect of RP machining grooves, surface quality, and hydrodynamic performance measurements as compared with the smooth glass models are also quantified.     

Finite element modeling of embolic coil deployment: Multifactor characterization of treatment effects on cerebral aneurysm hemodynamics

Endovascular coiling is the most common treatment for cerebral aneurysms. During the treatment, a sequence of embolic coils with different stiffness, shapes, sizes, and lengths is deployed to fill the aneurysmal sac. Although coil packing density has been clinically correlated with treatment success, many studies have also reported success at low packing densities, as well as recurrence at high packing densities. Such reports indicate that other factors may influence treatment success. In this study, we used a novel finite element approach and computational fluid dynamics (CFD) to investigate the effects of packing density, coil shape, aneurysmal neck size, and parent vessel flow rate on aneurysmal hemodynamics. The study examines a testbed of 80 unique CFD simulations of post-treatment flows in idealized basilar tip aneurysm models. Simulated coil deployments were validated against in vitro and in vivo deployments. Among the investigated factors, packing density had the largest effect on intra-aneurysmal velocities. However, multifactor analysis of variance showed that coil shape can also have considerable effects, depending on packing density and neck size. Further, linear regression analysis showed an inverse relationship between mean void diameter in the aneurysm and mean intra-aneurysmal velocities, which underscores the importance of coil distribution and thus coil shape. Our study suggests that while packing density plays a key role in determining post-treatment hemodynamics, other factors such as coil shape, aneurysmal geometry, and parent vessel flow may also be very important.