Big cats at large: Density,structure, and spatio-temporal patterns of a leopard population free of anthropogenic mortality

Human impact is near pervasive across the planet and studies of wildlife populations free of anthropogenic mortality are increasingly scarce. This is particularly true for large carnivores that often compete with and, in turn, are killed by humans. Accordingly, the densities at which carnivore populations occur naturally, and their role in shaping and/or being shaped by natural processes, are frequently unknown. We undertook a camera-trap survey in the Sabi Sand Game Reserve (SSGR), South Africa, to examine the density, structure and spatio-temporal patterns of a leopard Panthera pardus population largely unaffected by anthropogenic mortality. Estimated population density based on spatial capture–recapture models was 11.8 ± 2.6 leopards/100 km². This is likely close to the upper density limit attainable by leopards, and can be attributed to high levels of protection (particularly, an absence of detrimental edge effects) and optimal habitat (in terms of prey availability and cover for hunting) within the SSGR. Although our spatio-temporal analyses indicated that leopard space use was modulated primarily by “bottom-up” forces, the population appeared to be self-regulating and at a threshold that is unlikely to change, irrespective of increases in prey abundance. Our study provides unique insight into a naturally-functioning carnivore population at its ecological carrying capacity. Such insight can potentially be used to assess the health of other leopard populations, inform conservation targets, and anticipate the outcomes of population recovery attempts.     

A Change in the Ion Selectivity of Ligand-Gated Ion Channels Provides a Mechanism to Switch Behavior

Behavioral output of neural networks depends on a delicate balance between excitatory and inhibitory synaptic connections. However, it is not known whether network formation and stability is constrained by the sign of synaptic connections between neurons within the network. Here we show that switching the sign of a synapse within a neural circuit can reverse the behavioral output. The inhibitory tyramine-gated chloride channel, LGC-55, induces head relaxation and inhibits forward locomotion during the Caenorhabditis elegans escape response. We switched the ion selectivity of an inhibitory LGC-55 anion channel to an excitatory LGC-55 cation channel. The engineered cation channel is properly trafficked in the native neural circuit and results in behavioral responses that are opposite to those produced by activation of the LGC-55 anion channel. Our findings indicate that switches in ion selectivity of ligand-gated ion channels (LGICs) do not affect network connectivity or stability and may provide an evolutionary and a synthetic mechanism to change behavior.     

Life history of the silvertip shark Carcharhinus albimarginatus from Papua New Guinea

Coral Reefs - Growth and maturity of the silvertip shark Carcharhinus albimarginatus from Papua New Guinea were estimated to form the basis of future population assessments. Samples were collected...     

Effects of Including Misidentified Sharks in Life History Analyses: A Case Study on the Grey Reef Shark Carcharhinus amblyrhynchos from Papua New Guinea

Fisheries observer programs are used around the world to collect crucial information and samples that inform fisheries management. However, observer error may misidentify similar-looking shark species. This raises questions about the level of error that species misidentifications could introduce to estimates of species’ life history parameters. This study addressed these questions using the Grey Reef Shark Carcharhinus amblyrhynchos as a case study. Observer misidentification rates were quantified by validating species identifications using diagnostic photographs taken on board supplemented with DNA barcoding. Length-at-age and maturity ogive analyses were then estimated and compared with and without the misidentified individuals. Vertebrae were retained from a total of 155 sharks identified by observers as C. amblyrhynchos. However, 22 (14%) of these were sharks were misidentified by the observers and were subsequently re-identified based on photographs and/or DNA barcoding. Of the 22 individuals misidentified as C. amblyrhynchos, 16 (73%) were detected using photographs and a further 6 via genetic validation. If misidentified individuals had been included, substantial error would have been introduced to both the length-at-age and the maturity estimates. Thus validating the species identification, increased the accuracy of estimated life history parameters for C. amblyrhynchos. From the corrected sample a multi-model inference approach was used to estimate growth for C. amblyrhynchos using three candidate models. The model averaged length-at-age parameters for C. amblyrhynchos with the sexes combined were L¯∞ = 159 cm TL and L¯0 = 72 cm TL. Females mature at a greater length (l₅₀ = 136 cm TL) and older age (A₅₀ = 9.1 years) than males (l₅₀ = 123 cm TL; A₅₀ = 5.9 years). The inclusion of techniques to reduce misidentification in observer programs will improve the results of life history studies and ultimately improve management through the use of more accurate data for assessments.     

BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

Background

Recently in a number of studies, it has been demonstrated that the innate immune system doesn't merely acts as the first line of defense but provides critical signals for the development of specific adaptive immune response. Innate immune system employs a set of receptors called pattern recognition receptors (PRRs) that recognize evolutionarily conserved patterns from pathogens called pathogen associated molecular patterns (PAMPs). In order to assist scientific community, a database PRRDB has been developed that provides extensive information about pattern recognition receptors and their ligands.

Results

The current version of database contains around 500 patterns recognizing receptors from 77 distinct organisms ranging from insects to human. This includes 177 Toll-like receptors, 124 are Scavenger receptors and 67 are Nucleotide Binding Site-Leucine repeats rich receptors. The database also provides information about 266 ligands that includes carbohydrates, proteins, nucleic acids, glycolipids, glycoproteins, lipopeptides. A number of web tools have been integrated in PRRDB in order to provide following services: i) searching on any field; ii) database browsing; and iii) BLAST search against the pattern-recognition receptors. PRRDB also provides external links to standard databases like Swiss-Prot and Pubmed.

Conclusion

PRRDB is a unique database of its kind, which provides comprehensive information about innate immunity. This database will be very useful in designing effective adjuvant for subunit vaccine and in understanding role of innate immunity. The database is available from the URL's in the Availabiltiy and requirements section.     

Challenges of a transition to a sustainably managed shrimp culture agro-ecosystem in the Mahakam delta,East Kalimantan,Indonesia

Around 1990, when in other countries mangrove protection took off, massive conversion of mangrove forest into shrimp ponds started in the Mahakam delta. To identify constraints to and options for sustainable management we analysed institutions and constraints with stakeholders. In 3 sites we used participatory tools and a complementary survey to assess the livelihood framework. Since 1970, ponds for shrimp farming gradually replaced 75% of mangrove forested area. After 2004, recovery of mangrove took off, as, mainly due to low shrimp yields, ponds were abandoned. In 2008, 54% of the delta was dedicated to ponds for shrimp production. Around 80% of livelihood activities of pond-farmers, pond caretakers, and fishermen was related to mangroves. The involvement of men and women in these activities varied between sites and types. Poor households depended more on mangroves. Most activities resulted in seasonal income peaks; only a few activities resulted in a full daily livelihood. Ponds, on the other hand, provide 50% of households’ livelihood, but this remains vulnerable in the context of the risky shrimp production. Skewed land holding, unequal sharing of benefits, competing claims and vested interests of stakeholders pose a great challenge to a transition to a more sustainable use of the mangrove area. In particular, ponds located on peat soils are non-sustainable and would require full restoration into mangrove; ponds on other soils could best be transformed into a mixed mangrove-pond system using a ‘green-water’ technology.     

Progress toward Global Reduction in Under-Five Mortality: A Bootstrap Analysis of Uncertainty in Millennium Development Goal 4 Estimates

Background

Millennium Development Goal 4 calls for an annual rate of reduction (ARR) of the under-five mortality rate (U5MR) of 4.4% between 1990 and 2015. Progress is measured through the point estimates of the United Nations Inter-agency Group for Child Mortality Estimation (UN IGME). To facilitate evidence-based conclusions about progress toward the goal, we assessed the uncertainty in the estimates arising from sampling errors and biases in data series and the inferior quality of specific data series.

Methods and Findings

We implemented a bootstrap procedure to construct 90% uncertainty intervals (UIs) for the U5MR and ARR to complement the UN IGME estimates. We constructed the bounds for all countries without a generalized HIV epidemic, where a standard estimation approach is carried out (174 countries). In the bootstrap procedure, potential biases in levels and trends of data series of different source types were accounted for. There is considerable uncertainty about the U5MR, particularly for high mortality countries and in recent years. Among 86 countries with a U5MR of at least 40 deaths per 1,000 live births in 1990, the median width of the UI, relative to the U5MR level, was 19% for 1990 and 48% for 2011, with the increase in uncertainty due to more limited data availability. The median absolute width of the 90% UI for the ARR from 1990 to 2011 was 2.2%. Although the ARR point estimate for all high mortality countries was greater than zero, for eight of them uncertainty included the possibility of no improvement between 1990 and 2011. For 13 countries, it is deemed likely that the ARR from 1990 to 2011 exceeded 4.4%.

Conclusions

In light of the upcoming evaluation of Millennium Development Goal 4 in 2015, uncertainty assessments need to be taken into account to avoid unwarranted conclusions about countries'' progress based on limited data. Please see later in the article for the Editors'' Summary     

Mice doubly deficient for the Polycomb Group genes Mel18 and Bmi1 reveal synergy and requirement for maintenance but not initiation of Hox gene expression

Polycomb group genes were identified as a conserved group of genes whose products are required in multimeric complexes to maintain spatially restricted expression of Hox cluster genes. Unlike in Drosophila, in mammals Polycomb group (PcG) genes are represented as highly related gene pairs, indicative of duplication during metazoan evolution. Mel18 and Bmi1 are mammalian homologs of Drosophila Posterior sex combs. Mice deficient for Mel18 or Bmi1 exhibit similar posterior transformations of the axial skeleton and display severe immune deficiency, suggesting that their gene products act on overlapping pathways/target genes. However unique phenotypes upon loss of either Mel18 or Bmi1 are also observed. We show using embryos doubly deficient for Mel18 and Bmi1 that Mel18 and Bmi1 act in synergy and in a dose-dependent and cell type-specific manner to repress Hox cluster genes and mediate cell survival of embryos during development. In addition, we demonstrate that Mel18 and Bmi1, although essential for maintenance of the appropriate expression domains of Hox cluster genes, are not required for the initial establishment of Hox gene expression. Furthermore, we show an unexpected requirement for Mel18 and Bmi1 gene products to maintain stable expression of Hox cluster genes in regions caudal to the prospective anterior expression boundaries during subsequent development.