We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Emerging infectious diseases (EIDs) of free-living wild animals can be classified into three major groups on the basis of key epizootiological criteria: (i) EIDs associated with “spill-over” from domestic animals to wildlife populations living in proximity; (ii) EIDs related directly to human intervention, via host or parasite translocations; and (iii) EIDs with no overt human or domestic animal involvement. These phenomena have two major biological implications: first, many wildlife species are reservoirs of pathogens that threaten domestic animal and human health; second, wildlife EIDs pose a substantial threat to the conservation of global biodiversity.

/pdf/emerging-infectious-diseases-of-wildlife-threats-to-4s3pc5irzv.pdf

Emerging Infectious Diseases of Wildlife-- Threats to Biodiversity and Human Health

By Matthew James Keelingand Pejman RohaniPrinceton, NJ: Princeton University Press,2008.408 pp., Illustrated. $65.00 (hardcover).Mathematical modeling of infectious dis-eases has progressed dramatically over thepast 3 decades and continues to ﬂourishat the nexus of mathematics, epidemiol-ogy, and infectious diseases research. Nowrecognized as a valuable tool, mathemat-ical models are being integrated into thepublic health decision-making processmore than ever before. However, despiterapid advancements in this area, a formaltraining program for mathematical mod-eling is lacking, and there are very fewbooks suitable for a broad readership. Tosupport this bridging science, a commonlanguage that is understood in all con-tributing disciplines is required.

Modeling Infectious Diseases in Humans and Animals

We live amid a global wave of anthropogenically driven biodiversity loss: species and population extirpations and, critically, declines in local species abundance. Particularly, human impacts on animal biodiversity are an under-recognized form of global environmental change. Among terrestrial vertebrates, 322 species have become extinct since 1500, and populations of the remaining species show 25% average decline in abundance. Invertebrate patterns are equally dire: 67% of monitored populations show 45% mean abundance decline. Such animal declines will cascade onto ecosystem functioning and human well-being. Much remains unknown about this “Anthropocene defaunation”; these knowledge gaps hinder our capacity to predict and limit defaunation impacts. Clearly, however, defaunation is both a pervasive component of the planet’s sixth mass extinction and also a major driver of global ecological change.

/pdf/defaunation-in-the-anthropocene-46k054u5cx.pdf

Defaunation in the Anthropocene

AIM: To investigate the initiating causes of cloacitis (inflammation of the cloaca) in kakapo (Strigops habroptilus).METHODS: Metagenomics using unbiased RNA or DNA sequencing was applied to faecal material from an 11-year-old female kakapo with exudative cloacitis, and a pool of eight birds (male and female aged 1–20 years) with no current signs or history of the disease. Faecal material from the diseased bird was collected pre- and post-treatment. For RNA sequencing, extracted RNA/DNA was subject to DNase, and the remaining RNA reverse transcribed to cDNA and subject to multiple displacement amplification prior to sequencing.RESULTS: No significant alignment to any known avian virus sequence was obtained from any faecal samples. However significant BLAST alignments to five bacteriophages known to infect enterobacteria were obtained. Strong evidence was obtained for the presence of the bacteriophage Escherichia phage TL-2011b, a bacteriophage known to occur in Escherichia coli causing outbreaks of foodbo...

Exudative cloacitis in the kakapo (Strigops habroptilus) potentially linked to Escherichia coli infection

Percutaneous Interdigital Injection of Mycobacterium bovis as a Model for Tuberculous Lesion Development in Wild Brushtail Possums (Trichosurus vulpecula)

1. Predicting outbreaks of Trichostrongylus tenuis in Red Grouse from larval counts has been hampered because of the poor recovery of the third-stage infective larvae from heather vegetation. Two possible explanations for this poor recovery were examined: (i) larvae are spatially aggregated; (ii) larvae exhibit temporal variability in abundance and may be missed by sampling at the wrong time.

2. Heather vegetation was intensively sampled and infective larvae were found to be spatially aggregated. The temporal distribution of T. tenuis also varied, with greater numbers of larvae present on heather sampled in the afternoon than the morning.

3. In a series of laboratory experiments the diurnal availability of T. tenuis larvae were examined on two plant species with differing physical structures: heather and wheat. These trials were tested against infective larvae of Haemonchus contortus, a related nematode known to exhibit diurnal migration patterns. Larvae were exposed to diurnal variations in light and temperature.

4. Infective larvae of both species were recovered in greater numbers during periods when the lights were on. Temperature did not have a significant influence on H. contortus larval availability but greater numbers of T. tenuis L3 were recovered at low temperature (10 °C) than at higher temperature (20 °C).

5. Both temporal variation in the presence of T. tenuis larvae on vegetation and the spatial variation in larval distribution may account for poor recovery of Trichostrongylus tenuis L3 in the field.

/pdf/spatial-aggregation-and-temporal-migration-of-free-living-1nu66kxr0m.pdf

Spatial aggregation and temporal migration of free-living stages of the parasitic nematode Trichostrongylus tenuis

Aims: To determine the presence of infection and co-infection of Plasmodium lineages in introduced birds at translocation sites for the North Island saddleback (Philesturnus rufusater), to investigate their role as Plasmodium spp. reservoirs.Methods: Blood samples were collected from introduced bird species, with a special focus on blackbirds (Turdus merula) and song thrushes (Turdus philomelos), at six locations in the North Island of New Zealand that were the origin, or translocation sites, for North Island saddleback. Where available, blood smears were examined, and blood samples were tested using nested PCR with subsequent sequence analysis, for the presence of Plasmodium spp.Results: Of the 55 samples tested using PCR analysis, 39 (71%) were positive for Plasmodium spp., and 28/40 (62%) blood smears were positive for Plasmodium spp. Overall, 31 blood samples were from blackbirds with 28/31 (90%) samples positive for Plasmodium spp. Six distinct avian Plasmodium lineages were identified, including three cosmopolitan lineages; Plasmodium vaughani SYAT05 was detected in 16 samples, Plasmodium matutinum Linn1 in 10 samples and Plasmodium elongatum GRW6 in eight samples. Mixed infections with more than one lineage were detected in 12 samples. Samples from two Australian magpies (Gymnorhina tibicen) were positive for Plasmodium. sp. lineage MYNA02, previously not identified in New Zealand.Conclusions and clinical relevance: This is the first report from New Zealand in which specific Plasmodium spp. mixed infections have been found in introduced birds. Co-infections with several cosmopolitan Plasmodium lineages were identified, as well as the first report in New Zealand of an exotic avian Plasmodium sp. lineage, in Australian magpies. Whilst the role of introduced birds in maintaining and spreading pathogenic avian malaria in New Zealand is unclear, there is a potential infection risk to native birds, especially where distributions overlap.

Presence and diversity of mixed avian Plasmodium spp. infections in introduced birds whose distribution overlapped with threatened New Zealand endemic birds

Whataroa virus, first detected in 1962 in bird populations around Whataroa township, is the only mosquito-borne virus circulating in New Zealand that has been isolated. Even though at least one other mosquito-borne pathogen (avian malaria) has greatly increased in prevalence in New Zealand in recent decades, no surveillance for Whataroa virus in its vertebrate hosts has been carried out for four decades. This is of concern since Whataroa virus may infect humans, possibly causing influenza-like symptoms. Here we reassess the status of Whataroa virus in the same bird species in the same area where it was detected previously. Molecular diagnostics identified Whataroa virus in three out of 95 non-native birds screened: two out of eight song thrushes Turdus philomelos, and one out of nine blackbirds Turdus merula. The detection of virus in birds, in contrast with recent screening of mosquitoes, highlights how wildlife surveillance for pathogens can be far more effective than vector surveillance. Results of this survey indicate the virus has not increased substantially in prevalence since last monitored, possibly because of little change in the local mosquito vector community. Finally, virus detection in the two Turdus species alone supports earlier claims that these non-native hosts act as reservoirs that maintain the virus, sourcing spillover infections in other native and non-native species. A similar role for the blackbird in avian malaria epidemiology in New Zealand has also recently been hypothesized.

Daniel M. Tompkins

Papers

Exudative cloacitis in the kakapo (Strigops habroptilus) potentially linked to Escherichia coli infection

Percutaneous Interdigital Injection of Mycobacterium bovis as a Model for Tuberculous Lesion Development in Wild Brushtail Possums (Trichosurus vulpecula)

Spatial aggregation and temporal migration of free-living stages of the parasitic nematode Trichostrongylus tenuis

Presence and diversity of mixed avian Plasmodium spp. infections in introduced birds whose distribution overlapped with threatened New Zealand endemic birds

Whataroa virus four decades on: emerging, persisting, or fading out?