Paralogous mitochondrial control region in the giant tiger shrimp, Penaeus monodon (F.) affects population genetics inference: A cautionary tale

The mitochondrial control region (mtCR) is a widely used genetic marker for phylogenetic, phylogeographic and population genetic inference. The analysis of mtCR in 115 Indonesian specimens of the giant tiger shrimp, Penaeus monodon, revealed 26 individuals yielding a second - apparently paralogous - sequence in addition to the putatively authentic mitochondrial haplotype. The paralogous haplotypes fell into two major haplogroups that are highly diverged with respect to the authentic mitochondrial haplotypes (average pairwise sequence divergence of 12.5% and 5.0%, respectively). A comparison with published mtCR sequences of P. monodon showed that the paralogous contaminant sequences were inadvertently included in a series of recent population genetic studies, leading to seriously compromised conclusions about genetic diversity and differentiation. The prevalence of the paralogous haplotypes throughout the sampled Indo-Pacific populations is highly skewed: From African and Indian individuals only paralogs have been sequenced, while they are completely absent from Australian individuals. This suggests that geographically unequally distributed allelic variants at binding sites of the primer pair ordinarily used to amplify mtCR in P. monodon suppressed the amplification of authentic mtCR in a wide range of samples.     

Effects of overexpression of membrane-bound transferrin-like protein (MTf) on chondrogenic differentiation in Vitro

Membrane-bound transferrin-like protein (MTf) is expressed in parallel with the expression of cartilage-characteristic genes during differentiation of chondrocytes, and the MTf level is much higher in cartilage than in other tissues. To investigate the role of MTf in cartilage, we examined the effects of growth factors on MTf expression in mouse prechondrogenic ATDC5 cells and the effect of MTf overexpression on differentiation of ATDC5 and mouse pluripotent mesenchymal C3H10T1/2 cells. In ATDC5 cultures, bone morphogenetic protein-2 and transforming growth factor-beta as well as insulin induced MTf mRNA expression when these peptides induced chondrogenic differentiation. Forced expression of rabbit MTf in ATDC5 cells induced aggrecan, type II collagen, matrilin-1, type X collagen mRNAs, and cell-shape changes from fibroblastic cells to spherical chondrocytes. Accordingly, the synthesis and accumulation of proteoglycans were higher in MTf-expressing cultures than in control cultures. These effects of MTf overexpression correlated with the MTf protein level on the cell surface and decreased in the presence of anti-MTf antibody. However, the aggrecan mRNA level in the ATDC5 cells overexpressing MTf was lower than that in wild type ATDC5 cells exposed to 10 microg/ml insulin. MTf overexpression in C3H10T1/2 cells also induced aggrecan and/or type II collagen mRNA but not the spherical phenotype. These findings suggest that the expression of MTf on the cell surface facilitates the differentiation of prechondrogenic cells, although MTf overexpression alone seems to be insufficient to commit pluripotent mesenchymal cells to the chondrocyte lineage.     

Estimation of Transmission Parameters of H5N1 Avian Influenza Virus in Chickens

Despite considerable research efforts, little is yet known about key epidemiological parameters of H5N1 highly pathogenic influenza viruses in their avian hosts. Here we show how these parameters can be estimated using a limited number of birds in experimental transmission studies. Our quantitative estimates, based on Bayesian methods of inference, reveal that (i) the period of latency of H5N1 influenza virus in unvaccinated chickens is short (mean: 0.24 days; 95% credible interval: 0.099–0.48 days); (ii) the infectious period of H5N1 virus in unvaccinated chickens is approximately 2 days (mean: 2.1 days; 95%CI: 1.8–2.3 days); (iii) the reproduction number of H5N1 virus in unvaccinated chickens need not be high (mean: 1.6; 95%CI: 0.90–2.5), although the virus is expected to spread rapidly because it has a short generation interval in unvaccinated chickens (mean: 1.3 days; 95%CI: 1.0–1.5 days); and (iv) vaccination with genetically and antigenically distant H5N2 vaccines can effectively halt transmission. Simulations based on the estimated parameters indicate that herd immunity may be obtained if at least 80% of chickens in a flock are vaccinated. We discuss the implications for the control of H5N1 avian influenza virus in areas where it is endemic.     

Sex pheromone components of the rice leaffolder,Cnaphalocrocis medinalis (Lepidoptera: Crambidae), in Indonesia

Field tests of three synthetic sex pheromone blends (Japanese blend: Z11–18:Ald (55 μg), Z13–18:Ald (500 μg), Z11–18:OH (120 μg) and Z13–18:OH (180 μg), Indian blend: Z11–16:Ac (50 μg) and Z13–18:Ac (500 μg) and Philippine blend: Z11–16:Ac (500 μg) and Z13–18:Ac (10 μg) based on geographic variations in sex pheromones) of the rice leaffolder moth, Cnaphalocrocis medinalis Guenée (Lepidoptera: Crambidae), were conducted at Yogyakarta (Java), and at Sempidi and Penatih (Bali), Indonesia. Only the Japanese blend attracted significant numbers of male C. medinalis, while neither the Indian nor the Philippine blend showed any attractiveness to the males. In the GC–MS analysis of a crude extract from pheromone glands of female C. medinalis collected at Sanur, Bali. Indonesia, Z11–18:Ald, Z13–18:Ald, Z11–18:OH and Z13–18:OH were detected at a ratio of 10:100:26:37, and the total amount was approximately 0.8 ng/female. Neither Z11–16:Ac nor Z13–18:Ac were detected. These results suggest that C. medinalis that respond to the Japanese blend are widely distributed from Eastern Asia through Southeast Asia.     

Histopathological and ultrastructural features of enlarged cells of humpback grouper Cromileptes altivelis challenged with Megalocytivirus (family Iridoviridae) after vaccination

The genus Megalocytivirus in the family Iridoviridae encompasses isolates of red sea bream iridovirus (RSIV) and grouper sleepy disease iridovirus (GSDIV). In the present study, humpback grouper Cromileptes altivelis juveniles were challenged with GSDIV after vaccination with a commercial RSIV vaccine. The unvaccinated group (in duplicate) showed higher mortalities (59.3 to 66.7%) than the vaccination group (0% mortalitiy, in duplicate). Surviving fish in the vaccinated group displayed masses of enlarged cells in the spleen. Electron microscopy revealed that they contained hemosiderin granules within the cytoplasm. In contrast, moribund fish from the unvaccinated group exhibited large numbers of inclusion body-bearing cells (IBCs) in the spleen, while surviving fish displayed masses of enlarged cells in which a small number of GSDIV virions were assembled.     

Le site de Tögi Ndrawa, île de Nias, Sumatra nord : les premières traces d'une occupation hoabinhienne en grotte en Indonésie

The site of Tögi Ndrawa, Island of Nias, North Sumatra: The first record of a Hoabinhian cave occupation in Indonesia. Although in Indonesia, Hoabinhian sites usually refer to large shell midden dated back from the Holocene period, the Tögi Ndrawa cave in the Island of Nias (North Sumatra) has revealed a thick shell accumulation, sealed in a cavity, and beginning with the end of the Late Pleistocene. Excavations have produced classical Hoabinhian pebble artefacts, a forest and coastal fauna, and human bones. Beyond the new chronological landmarks provided by these findings, they question the extension of the Hoabinhian phenomenon originating from continental Asia, and provide hints about human settlement and use of the environment at this period of prehistory. Pour citer cet article : H. Forestier et al., C. R. Palevol 4 (2005).     

Complexity within an oil palm monoculture: The effects of habitat variability and rainfall on adult dragonfly (Odonata) communities

Recent expansion of oil palm agriculture has resulted in loss of forest habitat and forest-dependent species. However, large numbers of species—particularly insects—can persist within plantations. This study focuses on Odonata (dragonflies and damselflies): a charismatic indicator taxon and a potentially valuable pest control agent. We surveyed adult Odonata populations biannually over three years within an industrial oil palm plantation in Sumatra, Indonesia. We assessed the effects of rainfall (including an El Niño Southern Oscillation-associated drought), the role of roadside ditches, and the importance of understory vegetation on Odonata populations. To assess the impacts of vegetation, we took advantage of a long-term vegetation management experiment that is part of the Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) Programme. We found 41 Odonata species, and communities varied between plantation core and roadside edge microhabitats, and between seasons. Abundance was significantly related to rainfall levels four months before surveys, probably indicating the importance of high water levels in roadside ditches for successful larval development. We found no significant effect of the BEFTA understory vegetation treatments on Odonata abundance, and only limited effects on community composition, suggesting that local understory vegetation structure plays a relatively unimportant role in determining communities. Our findings highlight that there are large numbers of Odonata species present within oil palm plantations and suggest that their abundance could potentially be increased by maintaining or establishing waterbodies. As Odonata are predators, this could bring pest control benefits, in addition to enhancing biodiversity within intensive agricultural landscapes.