Genomic divergences among cattle,dog and human estimated from large-scale alignments of genomic sequences

Background

Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages.

Results

Optimal three-way multi-species global sequence alignments for 84 cattle clones or loci (each >50 kb of genomic sequence) were constructed using the human and dog genome assemblies as references. Genomic divergences and substitution rates were examined for each clone and for various sequence classes under different functional constraints. Analysis of these alignments revealed that the overall genomic divergences are relatively constant (0.32–0.37 change/site) for pairwise comparisons among cattle, dog and human; however substitution rates vary across genomic regions and among different sequence classes. A neutral mutation rate (2.0–2.2 × 10(-9) change/site/year) was derived from ancestral repetitive sequences, whereas the substitution rate in coding sequences (1.1 × 10(-9) change/site/year) was approximately half of the overall rate (1.9–2.0 × 10(-9) change/site/year). Relative rate tests also indicated that cattle have a significantly faster rate of substitution as compared to dog and that this difference is about 6%.

Conclusion

This analysis provides a large-scale and unbiased assessment of genomic divergences and regional variation of substitution rates among cattle, dog and human. It is expected that these data will serve as a baseline for future mammalian molecular evolution studies.

     

Alveolar macrophage activation is a key initiation signal for acute lung ischemia-reperfusion injury

Lung ischemia-reperfusion (I/R) injury is a biphasic inflammatory process. Previous studies indicate that the later phase is neutrophil-dependent and that alveolar macrophages (AMs) likely contribute to the acute phase of lung I/R injury. However, the mechanism is unclear. AMs become activated and produce various cytokines and chemokines in many inflammatory responses, including transplantation. We hypothesize that AMs respond to I/R by producing key cytokines and chemokines and that depletion of AMs would reduce cytokine/chemokine expression and lung injury after I/R. To test this, using a buffer-perfused, isolated mouse lung model, we studied the impact of AM depletion by liposome-clodronate on I/R-induced lung dysfunction/injury and expression of cytokines/chemokines. I/R caused a significant increase in pulmonary artery pressure, wet-to-dry weight ratio, vascular permeability, tumor necrosis factor (TNF)-alpha, monocyte chemoattractant protein (MCP)-1, and macrophage inflammatory protein (MIP)-2 expression, as well as decreased pulmonary compliance, when compared with sham lungs. After AM depletion, the changes in each of these parameters between I/R and sham groups were significantly attenuated. Thus AM depletion protects the lungs from I/R-induced dysfunction and injury and significantly reduces cytokine/chemokine production. Protein expression of TNF-alpha and MCP-1 are positively correlated to I/R-induced lung injury, and AMs are a major producer/initiator of TNF-alpha, MCP-1, and MIP-2. We conclude that AMs are an essential player in the initiation of acute lung I/R injury.     

Surface functionalization of gold nanoparticles using hetero-bifunctional poly(ethylene glycol) spacer for intracellular tracking and delivery

For the development of surface-functionalized gold nanoparticles as cellular probes and delivery agents, we have synthesized hetero-bifunctional poly(ethylene glycol) (PEG, MW 1500) having a thiol group on one terminus and a reactive functional group on the other for use as a flexible spacer. Coumarin, a model fluorescent dye, was conjugated to one end of the PEG spacer and gold nanoparticles were modified with coumarin-PEG-thiol. Surface attachment of coumarin through the PEG spacer decreased the fluorescence quenching effect of gold nanoparticles. The results of cellular cytotoxicity and fluorescence confocal analyses showed that the PEG spacer-modified nanoparticles were essentially non-toxic and could be efficiently internalized in the cells within 1 hour of incubation. Intracellular particle tracking using a Keck 3-D Fusion Microscope System showed that the functionalized gold nanoparticles were rapidly internalized in the cells and localized in the peri-nuclear region. Using the PEG spacer, the gold nano-platform can be conjugated with a variety of biologically relevant ligands such as fluorescent dyes, antibodies, etc in order to target, probe, and induce a stimulus at the target site.     

Cathemerality in the mongoose lemur, Eulemur mongoz

Results of a 10 month study of the mongoose lemur (Eulemur mongoz) at Anjamena are presented. The activity pattern is documented in detail for both wet and dry seasons based on observations conducted over the entire 24 h period. E. mongoz was found to be cathemeral throughout the year but exhibited shifts towards more diurnal activity in the wet season and more nocturnal activity in the dry season. The cathemeral activity pattern in the mongoose lemur appears to be coordinated with sunrise, sunset, and day length and modulated by an inhibitory effect of low nocturnal light intensity in the forest during the wet season, resulting in mainly diurnal activity. Temperature and rainfall may also influence the activity pattern. Few advantages to food-related behavior appear to derive from this activity pattern, although resource accessibility may be enhanced by nocturnal behavior in the dry season, leading to reduction in interspecific competition. Cathemerality may also represent a behavioral thermoregulatory mechanism allowing the mongoose lemur to conserve energy by being active during the cool nights of the dry season. In addition, nocturnal behavior in the dry season probably allows avoidance of predation by raptors at the time of year when least protection is afforded by vegetation.     

Attempted endocytosis of nano-environment produced by colloidal lithography by human fibroblasts

Control of the cells' nanoenvironment is likely to be important in the future of cell and tissue engineering. Microtopography has been shown to provide cues to cells that elicit a large range of cell responses, including control of adhesion, morphology, apoptosis and gene regulations. Now, researchers are focusing on nanotopography as techniques such as colloidal and electron beam lithography and polymer demixing have become available. In this study, human fibroblast response to nanocolumns (160-nm high, 100-nm diameter, 230-nm centre-centre spacing) produced by colloidal lithography are considered. Using electron microscopy and immunofluorescence to image the cytoskeleton, clathrin and dynamin, it was observed that the cells try to endocytose the nanocolumns. It also appeared that a small population of the cells changed to unusual morphologies with macrophage-like processes and highly disrupted cytoskeleton. These observations could have implications for nanomaterials science in areas such as cell transfection and drug delivery.