The effects of ultraviolet radiation on a freshwater prey fish: physiological stress response,club cell investment,and alarm cue production

Recent anthropogenic activities have caused deleterious effects to the stratospheric ozone layer, resulting in a global increase in the level of ultraviolet radiation (UVR). Understanding the way that organisms respond to such stressors is key to predicting the effects of anthropogenic activities on aquatic ecosystems and the species that inhabit them. The epidermal layer of the skin of fishes is not keratinized and acts as the primary interface between the fish and its environment. The skin of many species of fishes contains large epidermal club cells (ECCs) that are known to release chemicals (alarm cues) serving to warn other fishes of danger. However, the alarm role of the cells is likely secondary to their role in the immune system. Recent research suggests that ECCs in the epidermis may play a role in protecting the fish from damage caused by UVR. In the present study, we examined the effects of in vivo exposure to UVR on fathead minnows (Pimephales promelas), specifically investigating ECC investment, physiological stress responses, and alarm cue production. We found that fish exposed to UVR showed an increase in cortisol levels and a substantive decrease in ECC investment compared to non‐exposed controls. Unexpectedly, our subsequent analysis of the behavioural response of fish to alarm cues revealed no difference in the potency of the cues prepared from the skin of UV‐exposed or non‐exposed minnows. Our results indicate that, although nonlethal, UVR exposure may lead to secondary mortality by altering the fish immune system, although this same exposure may have little influence on chemically‐mediated predator–prey interactions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 832–841.     

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

Background

DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly advance the knowledge of disease mechanisms and be used to identify potential biomarkers. We developed an improved pipeline based on reduced representation bisulfite sequencing (RRBS) for cost-effective genome-wide quantification of DNA methylation at single base resolution. A selection of two restriction enzymes (Taq^αI and MspI) enables a more unbiased coverage of genomic regions of different CpG densities. We further developed a highly automated software package to analyze bisulfite sequencing results from the Solexa GAIIx system.

Results

With two sequencing lanes, we were able to quantify ~1.8 million individual CpG sites at a minimum sequencing depth of 10. Overall, about 76.7% of CpG islands, 54.9% of CpG island shores and 52.2% of core promoters in the human genome were covered with at least 3 CpG sites per region.

Conclusions

With this new pipeline, it is now possible to perform whole-genome DNA methylation analysis at single base resolution for a large number of samples for understanding how DNA methylation and its changes are involved in development, differentiation, and disease pathogenesis.     

High‐throughput species identification: from DNA isolation to bioinformatics

Ichthyoplankton collections provide a valuable means to study fish life histories. However, these collections are greatly underutilized, as larval fishes are frequently not identified to species due to their small size and limited morphological development. Currently, there is an effort underway to make species identification more readily available across a broad range of taxa through the sequencing of a standard gene. This effort requires the development of new methodologies to both rapidly produce and analyse large numbers of sequences. The methodology presented in this paper addresses these issues with a focus on the larvae of large pelagic fish species. All steps of the methodology are targeted towards high‐throughput identification using small amounts of tissue. To accomplish this, DNA isolation was automated on a liquid‐handling robot using magnetic bead technologies. Polymerase chain reaction and a unidirectional sequencing reaction followed standard protocols with all template cleanup and transferring also automated. Manual pipetting was thus reduced to a minimum. A character‐based bioinformatics program was developed to handle the large sequence output. This program incorporates base‐call quality scores in two types of sample to voucher sequence comparisons and provides suggested identifications and sequence information in an easily interpreted spreadsheet format. This technique when applied to tuna and billfish larvae collected in the Straits of Florida had an 89% success rate. A single species (Thunnus atlanticus) was found to dominate the catch of tuna larvae, while billfish larvae were more evenly divided between two species (Makaira nigricans and Istiophorus platypterus).     

PCR primers for polymorphic microsatellite loci in the plant‐ant Azteca ulei cordiae (Formicidae: Dolichoderinae)

Twelve microsatellite loci were isolated from the Peruvian tropical plant‐ant, Azteca ulei cordiae (Hymenoptera: Dolichoderinae). High levels of within‐population variation were observed at most loci, with number of alleles ranging from four to 18, and heterozygosity from 0.118 to 1 per population sample. Cross‐species amplification of these loci was also successfully tested in several other species of the same ant genus Azteca.     

Comparison of 5′-Nucleotidase Activities Among Cultured Murine Melanoma Cell Lines

The activity of 5′-nucleotidase and ouabain-sensitive Na/K ATPase was determined in seven different mouse melanoma cell lines. Ouabain-sensitive Na/K ATPase activity was found in NP40-treated cell homogenates of all cell lines. However, 5′-nucleotidase activity was found in only one mouse melanoma cell line—JB/RH. The absence of expression of 5′-nucleotidase activity in the other six cell lines is not associated with pigmentation in melanoma cells, nor is the gene switched off in all transformed melanocytes of C57BL/6 origin.     

Survival of Colonizing Wolves in the Northern Rocky Mountains of the United States, 1982–2004

Abstract: After roughly a 60-year absence, wolves (Canis lupus) immigrated (1979) and were reintroduced (1995-1996) into the northern Rocky Mountains (NRM), USA, where wolves are protected under the Endangered Species Act. The wolf recovery goal is to restore an equitably distributed metapopulation of ≥30 breeding pairs and 300 wolves in Montana, Idaho, and Wyoming, while minimizing damage to livestock; ultimately, the objective is to establish state-managed conservation programs for wolf populations in NRM. Previously, wolves were eradicated from the NRM because of excessive human killing. We used Andersen–Gill hazard models to assess biological, habitat, and anthropogenic factors contributing to current wolf mortality risk and whether federal protection was adequate to provide acceptably low hazards. We radiocollared 711 wolves in Idaho, Montana, and Wyoming (e.g., NRM region of the United States) from 1982 to 2004 and recorded 363 mortalities. Overall, annual survival rate of wolves in the recovery areas was 0.750 (95% CI = 0.728-0.772), which is generally considered adequate for wolf population sustainability and thereby allowed the NRM wolf population to increase. Contrary to our prediction, wolf mortality risk was higher in the northwest Montana (NWMT) recovery area, likely due to less abundant public land being secure wolf habitat compared to other recovery areas. In contrast, lower hazards in the Greater Yellowstone Area (GYA) and central Idaho (CID) likely were due to larger core areas that offered stronger wolf protection. We also found that wolves collared for damage management purposes (targeted sample) had substantially lower survival than those collared for monitoring purposes (representative sample) because most mortality was due to human factors (e.g., illegal take, control). This difference in survival underscores the importance of human-caused mortality in this recovering NRM population. Other factors contributing to increased mortality risk were pup and yearling age class, or dispersing status, which was related to younger age cohorts. When we included habitat variables in our analysis, we found that wolves having abundant agricultural and private land as well as livestock in their territory had higher mortality risk. Wolf survival was higher in areas with increased wolf density, implying that secure core habitat, particularly in GYA and CID, is important for wolf protection. We failed to detect changes in wolf hazards according to either gender or season. Maintaining wolves in NWMT will require greater attention to human harvest, conflict resolution, and illegal mortality than in either CID or GYA; however, if human access increases in the future in either of the latter 2 areas hazards to wolves also may increase. Indeed, because overall suitable habitat is more fragmented and the NRM has higher human access than many places where wolves roam freely and are subject to harvest (e.g., Canada and AK), monitoring of wolf vital rates, along with concomitant conservation and management strategies directed at wolves, their habitat, and humans, will be important for ensuring long-term viability of wolves in the region.     

Phagocytosis of degenerating myelin in transected feline optic nerve: an immunohistochemical study

The phagocytic activity of neuroglial cells in adult feline degenerating optic nerve was investigated by immunocytochemistry at both light and electron microscopy levels. Degeneration was initiated by unilateral eye enucleation and the segment distal to the transection showing true Wallerian degeneration was examined. Following enucleation, twelve adult domestic cats were examined over a period of seven to 215 days. All cases showed slow clearance of myelin debris and absence of proliferating monocytes throughout the post-enucleation period. All phagocytic cells present were neuroglial cells, and many of these cells expressed oligodendroglial antigens. These findings demonstrate the persistence of an active population of oligodendrocytes that might play an additional functional role during Wallerian degeneration of feline optic nerve.