Using the nucleotide substitution rate matrix to detect horizontal gene transfer

Background  

Horizontal gene transfer (HGT) has allowed bacteria to evolve many new capabilities. Because transferred genes perform many medically important functions, such as conferring antibiotic resistance, improved detection of horizontally transferred genes from sequence data would be an important advance. Existing sequence-based methods for detecting HGT focus on changes in nucleotide composition or on differences between gene and genome phylogenies; these methods have high error rates.     

Investigation of de novo cholesterol synthetic capacity in the gonads of goldfish (Carassius auratus) exposed to the phytosterol beta-sitosterol

Total and intra-mitochondrial gonadal cholesterol concentrations are decreased in fish exposed to the phytoestrogen beta-sitosterol (beta-sit). The present study examined the potential for beta-sit to disrupt de novo cholesterol synthesis in the gonads of goldfish exposed to 200 microgram/g beta-sit and 10 microgram/g 17beta-estradiol (E2; estrogenic control) by intra-peritoneal Silastic^® implants for 21 days. The de novo cholesterol synthetic capacity was estimated by incubating gonadal tissue with 14C-acetate for a period of 18 hours, followed by chloroform/methanol lipid extraction and thin layer chromatography (TLC) lipid separation. Lipid classes were confirmed using infrared spectroscopy. Plasma testosterone (T) and total cholesterol concentration were measured and gonadosomatic index (GSI) was calculated. Plasma T was significantly reduced in male beta-sit-treated fish compared to control and E2-treated fish (p < 0.001). 14C-Acetate incorporation into cholesterol and cholesterol esters was not significantly different among treatment groups for male and female fish, however, 14C-enrichment was higher than expected in both triglycerides (TG) and free fatty acids (FFA). FFA incorporation was significantly higher in male control fish than either beta-sit or E2 treatments (p = 0.005). Plasma cholesterol concentration was significantly increased in the male beta-sit treatment group compared to controls (p = 0.027). These results indicate gonadal de novo cholesterol biosynthetic capacity is not disrupted by beta-sit or E2 treatment in early recrudescing male or female goldfish, while plasma cholesterol and steroid concentrations are sensitive to beta-sit exposure.     

Split centromeric alpha-satellite FISH signals in a whole arm translocation 5p;10p: consequences and implications for interphase FISH studies

This is a case report of an apparently balanced whole arm translocation between the short arms of chromosomes 5 and 10 in which the centromeric alpha-satellite DNA is split between both derivative chromosomes for both probes, leading to abnormal signal patterns. The patient requested preimplantation genetic testing for the unbalanced products of the translocation. However, using centromeric alpha-satellite DNA probes as controls for the subtelomeric-specific probes in interphase was not informative because of the split signals. The ramifications of such variation in the alpha-satellite regions of chromosomes for other interphase FISH tests are discussed.     

Synthesis and characterization of multiblock copolymers based on spider dragline silk proteins

Spider dragline silk with its superlative tensile properties provides an ideal system to study the relationship between morphology and mechanical properties of a structural protein. Accordingly, we synthesized two hybrid multiblock copolymers by condensing poly(alanine) [(Ala)(5)] blocks of the structural proteins (spidroin MaSp1 and MaSp2) of spider dragline silk with different oligomers of isoprene (2200 and 5000 Da) having reactive end groups. The synthetic multiblock polymer displayed similar secondary structure to that of natural spidroin, the peptide segment forming a beta-sheet structure. These multiblock polymers showed a significant solubility in the component solvents. Moreover, the copolymer which contains the short polyisoprene segment would aggregate into a micellar-like structure, as observed by TEM.     

Pyrrolidine-5,5-trans-lactams as novel mechanism-based inhibitors of human cytomegalovirus protease. Part 3: potency and plasma stability

Mechanism-based inhibitors of HCMV protease, which are stable to human plasma (> or = 20 h) and have single-figure potency in the microM range against HCMV protease, have been developed based on the dansylproline alpha-methyl pyrrolidine-5,5-trans-lactam nucleus.     

Translocation of the 5-alkoxy substituent of 2,5-dialkoxyarylalkylamines to the 6-position: effects on 5-HT(2A/2C) receptor affinity

Positional modification of 2,5-dimethoxyamphetamine analogues has been studied. Specifically, the 5-alkoxy substituent was translocated to the 6-position of the phenyl nucleus. Methoxy groups were also constrained by incorporation into appended dihydrofuran and furan rings. 2,6-Dimethoxy-4-methylamphetamine had an approximately 3-fold lower affinity for the 5-HT(2A) receptor compared to the parent 2,5-dimethoxy-4-methylamphetamine (DOM). The rigid compound based on the 2,3,5,6-tetrahydrobenzo[1,2-b;5,4-b']difuran nucleus and the aromatic analogue containing the benzo[1,2-b;5,4-b']difuran nucleus possessed an approximate 7- and 27-fold increase in affinity, respectively, compared to 2,6-dimethoxy-4-methylamphetamine, the non-rigid, positional isomer.     

Modeling the relationship of Antarctic minke whales to major ocean boundaries

The population size of Antarctic minke whales Balaenoptera bonaerensis has been changing simultaneously with profound changes in the physics, i.e., mesopredator habitat features, of the Southern Ocean. Although the two trends may not be related, distinguishing among the factors responsible requires a better understanding of minke whale habitat preferences. For the first time at a large geographic scale, i.e., between 140° E and 35° W, we use data not constrained by vessels needing to avoid sea ice to model the habitat affinities of this pagophilic mesopredator. Using Maxent, we modeled minke whale proximity to the Antarctic Shelf Break Front (ASBF) and the southern boundary of Antarctic Circumpolar Current (sbACC), as well as association with sea ice, given that global climate change is altering the positions or intensity of these features. We also included water depth and chlorophyll (proxy for productivity) as variables. Minke whale presence data were gathered using strip and line census on 55 cruises on board icebreakers during late spring and summer, 1976–2005. The most important variable was distance to ASBF, followed by water depth and sea-ice concentration. That is, found principally in waters south of the sbACC during summer, minke whales were most abundant near the outer edge of the continental shelf (shallow depth), including areas heavily covered by sea ice. We propose that as the sbACC moves south and sea ice disappears, as projected by global climate models, minke whale habitat will shrink, and likely intra- and inter-specific competition will increase.     

The application of GIS and spatiotemporal analyses to investigations of unusual marine mammal strandings and mortality events

In 2006–2007, an unusually high number of harbor porpoises (Phocoena phocoena) stranded along the Washington and Oregon coastlines. Spatiotemporal analyses were used to examine their ability to detect clusters of porpoise strandings during an unusual mortality event (UME) in the Pacific Northwest using stranding location data. Strandings were evaluated as two separate populations, outer coast and inland waters. The presence of global clustering was evaluated using the Knox spatiotemporal test, and the presence of local clusters was investigated using a spatiotemporal scan statistic (space–time permutation). There was evidence of global clustering, but no local clustering, supporting the hypothesis that strandings were due to more varied etiologies instead of localized causes. Further analyses at subregional levels, and concurrently assessing environmental factors, might reveal additional geographic distribution patterns. This article describes the spatial analytical tools applied in this study and how they can help elucidate the spatiotemporal epidemiology of other UMEs and assist in determining their causes. More than one spatial analytical technique should be used if the study objective is to detect and describe clustering in time and space and to generate hypotheses regarding causation of marine mammal disease and stranding events.     

Cigarette smoke exposure induces CFTR internalization and insolubility, leading to airway surface liquid dehydration

Cigarette smoke (CS) exposure induces mucus obstruction and the development of chronic bronchitis (CB). While many of these responses are determined genetically, little is known about the effects CS can exert on pulmonary epithelia at the protein level. We, therefore, tested the hypothesis that CS exerts direct effects on the CFTR protein, which could impair airway hydration, leading to the mucus stasis characteristic of both cystic fibrosis and CB. In vivo and in vitro studies demonstrated that CS rapidly decreased CFTR activity, leading to airway surface liquid (ASL) volume depletion (i.e., dehydration). Further studies revealed that CS induced internalization of CFTR. Surprisingly, CS-internalized CFTR did not colocalize with lysosomal proteins. Instead, the bulk of CFTR shifted to a detergent-resistant fraction within the cell and colocalized with the intermediate filament vimentin, suggesting that CS induced CFTR movement into an aggresome-like, perinuclear compartment. To test whether airway dehydration could be reversed, we used hypertonic saline (HS) as an osmolyte to rehydrate ASL. HS restored ASL height in CS-exposed, dehydrated airway cultures. Similarly, inhaled HS restored mucus transport and increased clearance in patients with CB. Thus, we propose that CS exposure rapidly impairs CFTR function by internalizing CFTR, leading to ASL dehydration, which promotes mucus stasis and a failure of mucus clearance, leaving smokers at risk for developing CB. Furthermore, our data suggest that strategies to rehydrate airway surfaces may provide a novel form of therapy for patients with CB.