Is the chimpanzee, Pan troglodytes, an endangered species? It depends on what “endangered” means

I review information on the status in the wild of the robust chimpanzee, Pan troglodytes, and consider whether this evidence is consistent with the designation of P. troglodytes as Endangered in the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List, and with public statements to the effect that great apes as a whole will be extinct within a few decades. Chimpanzees remain widespread in tropical Africa, occurring in a variety of forested habitats. Estimates of total surviving numbers have increased from about 200,000 in the 1980s to a maximum of almost 300,000 in 2003. However, this apparent increase comes about from new survey data, rather than representing a measured increase in actual population numbers. Infectious disease decimated several chimpanzee populations during the 1990s, and data from parts of Gabon, extrapolated to that country as a whole, suggest a major decline in great ape populations caused by disease and hunting. However, accurate data on population numbers are absent for the majority of wild chimpanzee populations. I found reports of the presence of Pan troglodytes in at least 51 national parks in at least 19 countries; some of these parks have been established very recently. Chimpanzees also occur in many non-park conservation areas. A set of large, well-protected parks could safeguard chimpanzees for the foreseeable future. Although many African parks do not function well at present, mechanisms to improve their function are understood and available. By a strict application of IUCN threat criteria, P. troglodytes can be considered Endangered, based on estimated rates of past decline and on the species long generation time. Relatively speaking, however, P. troglodytes is less endangered than are orangutans or gorillas, and the species is unlikely to go extinct by the year 2100, especially if existing conservation measures improve. The IUCN threat-rating system has become overly complex; the system can produce results that do not accord with common sense and these results must therefore be interpreted with care.     

Morphology and phylogeny of Sainouron acronematica sp. n. and the ultrastructural unity of Cercozoa

Sainouron are soil zooflagellates of obscure taxonomy. We studied the ultrastructure of S. acronematica sp. n. and sequenced its extremely divergent 18S rDNA and that of Cholamonas cyrtodiopsidis (here grouped as new family Sainouridae) to clarify their phylogeny. Ultrastructurally similar, they weakly group together, deeply within Monadofilosa. Sainouron has three cytoplasmic microtubules; all organelles specifically link to them or the nucleus. Mature centrioles have fibrous rhizoplasts. The posterior centriole bearing the motile cilium (with cortical filaments) has a transitional hub-lattice; a dense spiral fibre links its thicker rhizoplast and triplets; its ciliary root has two microtubules: mt1, underlying the plasma membrane, initiates at the spiral fibre; mt2, laterally attached to mt1 and nucleus, initiates in the amorphous centrosomal region. The anterior younger cilium, an immotile stub with submembrane skeleton as in Cholamonas, lacks axoneme, microtubular root, rhizoplasts and spiral fibre, but becomes the posterior one every cell cycle. The nuclear envelope donates coated vesicles directly to the Golgi, which makes kinetocyst-type extrusomes, concentrated at the cell anterior for extrusion into phagosomes. Ciliary transition region proximal hub-lattices (postulated to contain centrin) and distal nonagonal fibres are cercozoan synapomorphies, found with slight structural variation in all flagellate Cercozoa, but not in outgroups.     

The diet of the olive colobus monkey,Procolobus verus,in Sierra Leone

Observations of the feeding behavior of wild olive colobus monkeys (Procolobus verus)were made in southern Sierra Leone, West Africa. Most data came from systematically sampling one habituated social group, which inhabited old secondary rain forest on Tiwai Island. Olive colobus at Tiwai were highly selective feeders, obtaining most of their food from a small number of uncommon middle-canopy trees, from the forest understory, and from climbers. Mature leaf blades were largely ignored; young foliage (particularly of climbers) was a year-round dietary staple, while seeds, flowers, and mature leaf petioles were seasonally important. It is argued that this diet results largely from selection for two different attributes of food: high digestibility and physical location. Preferred foods had low fiber and tannin contents, while preferred feeding sites were in thick low growth and climber tangles. P. verusis the smallest extant primate species using a foregut fermentation system. Observations of its diet accord with inferences drawn from dental anatomy, digestive physiology, and considerations of body size.     

PGH2-derived levuglandin adducts increase the neurotoxicity of amyloid beta1-42

The body of evidence indicating that oligomers of amyloid beta(1-42) (Abeta(1-42)) produce toxicity to neurons, together with our demonstration that prostaglandin H(2) (PGH(2)) oligomerizes amyloid beta(1-42), led to the examination of the neurotoxicity of amyloid beta(1-42) treated with PGH(2). The neurotoxic effects of Abeta(1-42) incubated with PGH(2) was examined in primary cultures of cerebral neurons of mice, monitoring the reduction of 3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyltetrazolium bromide (MTT) as an indicator of cell toxicity. Whereas Abeta(1-42) itself, incubated for 24 h, has little or no effect on MTT reduction, Abeta(1-42) 24 h after exposure to PGH(2) produced a marked inhibition of MTT reduction, comparable with the inhibition resulting from Abeta(1-42) that has been oligomerized by incubation for 6 days. Similar results were obtained when Abeta(1-42) was incubated with levuglandin E(2) (LGE(2)), a reactive aldehyde formed by spontaneous rearrangement of PGH(2). The oligomers formed from reaction of Abeta(1-42) with LGE(2) exhibit immunochemical similarity with amyloid-derived diffusible ligands (ADDLs), as determined by analysis of the products of reaction of Abeta(1-42) with LGE(2) using western blotting with an antibody that is selective for ADDLs.     

在中国应用垂直波束雷达监测褐飞虱和其他水稻害虫迁飞的可行性

近年来,可用于昆虫迁飞研究且可自动运行的垂直波束雷达(vertical-looking radar,VLR)的发展使得对迁飞性害虫的周年长期自动监测成为可能。本文提供了我们对能否将这种雷达应用于中国的褐飞虱和其他水稻害虫的监测与预测体系以改善其综合治理的可行性研究结果。以往的研究已经表明,这些害虫一般在300—2000m高度迁飞;而我们根据褐飞虱的雷达和射有效截面的计算结果表明,目前使用的3．2cm波长的VLR对褐飞虱个体目标的最大可检测高度仅约240m;虽然建造一部8．8mm波长的VLR即可覆盖褐飞虱迁飞高度的绝大部分,但其造价和维护费用均过于昂贵。为此,一个更可行的解决方案是,以3．2cm波长的VLR作为包括大多数水稻害虫在内的个体较大的迁飞性害虫的监测工具。     

Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth

Background

The use of biological annotation such as genes and pathways in the analysis of gene expression data has aided the identification of genes for follow-up studies and suggested functional information to uncharacterized genes. Several studies have applied similar methods to genome wide association studies and identified a number of disease related pathways. However, many questions remain on how to best approach this problem, such as whether there is a need to obtain a score to summarize association evidence at the gene level, and whether a pathway, dominated by just a few highly significant genes, is of interest.

Methods

We evaluated the performance of two pathway-based methods (Random Set, and Binomial approximation to the hypergeometric test) based on their applications to three data sets of Crohn's disease. We consider both the disease status as a phenotype as well as the residuals after conditioning on IL23R, a known Crohn's related gene, as a phenotype.

Results

Our results show that Random Set method has the most power to identify disease related pathways. We confirm previously reported disease related pathways and provide evidence for IL-2 Receptor Beta Chain in T cell Activation and IL-9 signaling as Crohn's disease associated pathways.

Conclusions

Our results highlight the need to apply powerful gene score methods prior to pathway enrichment tests, and that controlling for genes that attain genome wide significance enable further biological insight.     

Characterization of the induction and cellular role of the BaeSR two-component envelope stress response of Escherichia coli

The bacterial cell envelope is the interface between a bacterium and its environment and is constantly exposed to environmental changes. The BaeSR two-component system regulates one of six envelope stress responses in Escherichia coli and is induced by spheroplasting, overexpression of the pilin subunit PapG, and exposure to indole. The known BaeR regulon is small, consisting of eight genes, mdtABCD-baeSR, acrD, and spy, two of which encode the BaeSR two-component system itself. In this study, we investigated the molecular nature of the BaeS-inducing cue and the cellular role of the BaeSR envelope stress response. We demonstrated that at least two flavonoids and sodium tungstate are novel inducers of the BaeSR response. Interestingly, flavonoids and sodium tungstate led to much stronger induction of the BaeSR response in an mdtA efflux pump mutant, while indole did not. These findings are consistent with the hypothesis that flavonoids and sodium tungstate are natural substrates of the MdtABC efflux pump. Indole has recently been implicated in cell-cell signaling and biofilm repression through a putative interaction with the LuxR homologue SdiA. Using genetic analyses, we found that induction of the BaeSR response by indole occurs via a pathway separate from the SdiA biofilm pathway. Further, we demonstrated that the BaeSR response does not influence biofilm formation, nor is it involved in indole-mediated inhibition of biofilm formation. We hypothesize that the main function of the Bae response is to upregulate efflux pump expression in response to specific envelope-damaging agents.