Combining camera trap surveys and IUCN range maps to improve knowledge of species distributions.

Reliable maps of species distributions are fundamental for biodiversity research and conservation. The International Union for Conservation of Nature (IUCN) range maps are widely recognized as authoritative representations of species' geographic limits, yet they might not always align with actual occurrence data. In recent area of habitat (AOH) maps, areas that are not habitat have been removed from IUCN ranges to reduce commission errors, but their concordance with actual species occurrence also remains untested. We tested concordance between occurrences recorded in camera trap surveys and predicted occurrences from the IUCN and AOH maps for 510 medium- to large-bodied mammalian species in 80 camera trap sampling areas. Across all areas, cameras detected only 39% of species expected to occur based on IUCN ranges and AOH maps; 85% of the IUCN only mismatches occurred within 200 km of range edges. Only 4% of species occurrences were detected by cameras outside IUCN ranges. The probability of mismatches between cameras and the IUCN range was significantly higher for smaller-bodied mammals and habitat specialists in the Neotropics and Indomalaya and in areas with shorter canopy forests. Our findings suggest that range and AOH maps rarely underrepresent areas where species occur, but they may more often overrepresent ranges by including areas where a species may be absent, particularly at range edges. We suggest that combining range maps with data from ground-based biodiversity sensors, such as camera traps, provides a richer knowledge base for conservation mapping and planning.

Combinación de censos con fototrampas y mapas de extensión de la UICN para incrementar el conocimiento sobre la distribución de las especies Resumen Los mapas confiables de la distribución de las especies son fundamentales para la investigación y conservación de la biodiversidad. Los mapas de distribución de la Unión Internacional para la Conservación de la Naturaleza (UICN) están reconocidos como representaciones de autoridad de los límites geográficos de las especies, aunque no siempre se alinean con los datos actuales de su presencia. En los mapas recientes de área de hábitat (ADH), las áreas que no son hábitat han sido eliminadas de la distribución de la UICN para reducir los errores de comisión, pero su concordancia con la presencia actual de las especies tampoco ha sido analizada. Analizamos la concordancia entre la presencia registrada por los censos de fototrampas y pronosticamos la presencia a partir de los mapas de la UICN y de ADH de 510 especies de mamíferos de talla mediana a grande en 80 áreas de muestreo de fototrampas. Las cámaras detectaron sólo el 39% de las especies esperadas con base en la distribución de la UICN y los mapas de ADH en todas las áreas; el 85% de las disparidades con la UICN ocurrieron dentro de los 200 km a partir del borde de la distribución. Sólo el 4% de la presencia de las especies fue detectada por las cámaras ubicadas fuera de la distribución de la UICN. La probabilidad de disparidad entre las cámaras y la UICN fue significativamente mayor para los mamíferos de talla pequeña y para los especialistas de hábitat en las regiones Neotropical e Indomalaya y en áreas con doseles forestales más bajos. Nuestros hallazgos sugieren que los mapas de distribución y ADH pocas veces subrepresentan las áreas con presencia de las especies, pero con frecuencia pueden sobrerrepresentar la distribución al incluir áreas en donde las especies pueden estar ausentes, en particular los bordes de la distribución. Sugerimos que la combinación de los mapas de distribución con los sensores de biodiversidad en tierra, como las fototrampas, proporciona una base más rica de conocimiento para el mapeo y la planeación de la conservación.

Neutralizing Antibody Validation Testing and Reporting Harmonization.

Evolving immunogenicity assay performance expectations and a lack of harmonized neutralizing antibody validation testing and reporting tools have resulted in significant time spent by health authorities and sponsors on resolving filing queries. A team of experts within the American Association of Pharmaceutical Scientists' Therapeutic Product Immunogenicity Community across industry and the Food and Drug Administration addressed challenges unique to cell-based and non-cell-based neutralizing antibody assays. Harmonization of validation expectations and data reporting will facilitate filings to health authorities and are described in this manuscript. This team provides validation testing and reporting strategies and tools for the following assessments: (1) format selection; (2) cut point; (3) assay acceptance criteria; (4) control precision; (5) sensitivity including positive control selection and performance tracking; (6) negative control selection; (7) selectivity/specificity including matrix interference, hemolysis, lipemia, bilirubin, concomitant medications, and structurally similar analytes; (8) drug tolerance; (9) target tolerance; (10) sample stability; and (11) assay robustness.

Efficacy of extracting indices from large-scale acoustic recordings to monitor biodiversity.

Passive acoustic monitoring could be a powerful way to assess biodiversity across large spatial and temporal scales. However, extracting meaningful information from recordings can be prohibitively time consuming. Acoustic indices (i.e., a mathematical summary of acoustic energy) offer a relatively rapid method for processing acoustic data and are increasingly used to characterize biological communities. We examined the relationship between acoustic indices and the diversity and abundance of biological sounds in recordings. We reviewed the acoustic-index literature and found that over 60 indices have been applied to a range of objectives with varying success. We used 36 of the most indicative indices to develop a predictive model of the diversity of animal sounds in recordings. Acoustic data were collected at 43 sites in temperate terrestrial and tropical marine habitats across the continental United States. For terrestrial recordings, random-forest models with a suite of acoustic indices as covariates predicted Shannon diversity, richness, and total number of biological sounds with high accuracy (R2  ≥ 0.94, mean squared error [MSE] ≤170.2). Among the indices assessed, roughness, acoustic activity, and acoustic richness contributed most to the predictive ability of models. Performance of index models was negatively affected by insect, weather, and anthropogenic sounds. For marine recordings, random-forest models poorly predicted Shannon diversity, richness, and total number of biological sounds (R2 ≤ 0.40, MSE ≥ 195). Our results suggest that using a combination of relevant acoustic indices in a flexible model can accurately predict the diversity of biological sounds in temperate terrestrial acoustic recordings. Thus, acoustic approaches could be an important contribution to biodiversity monitoring in some habitats.

The Effect of Chemical Treatments on Lampenflora and a Collembola Indicator Species at a Popular Tour Cave in California, USA.

Growth of invasive, opportunistic plants (i.e. lampenflora) in popular tour caves is a significant concern for land managers worldwide. Numerous chemicals at various concentrations have been utilized to remove phototrophic lampenflora colonizing artificially lit surfaces within these caves; however formulations, effectiveness, and impacts appear anecdotal and temporally limited. At Crystal Cave, Sequoia National Park, California, we study lampenflora and cave springtail (Tomocerus celsus) response to a single 0.05 ml/cm2 dose of 1.0% sodium hypochlorite, 0.5% sodium hypochlorite, and 15.0% hydrogen peroxide compared to no treatment over the course of one year. Additionally, we explore potential food web impacts resulting from invasive lampenflora in naturally oligotrophic caves by utilizing stable isotope analysis of T. celsus found on and off lampenflora. Time-effect decay models indicate 1.0 and 0.5% sodium hypochlorite effectively eliminate lampenflora in 11 and 21 days, respectively, while lampenflora decay projections exceed 600 days with 15.0% hydrogen peroxide treatment. Repeat surveys of T. celsus indicate a negative response to 1.0% sodium hypochlorite (P = 0.02), and the probability of observing T. celsus was inversely related to the effectiveness of each treatment. Further, T. celsus had similar diets regardless of their lampenflora association (P = 0.92). We conclude that treatments of sodium hypochlorite at or below 0.5% achieve management goals with limited impacts to the presence or diet of a common cave-adapted indicator species.

Inhibition of interleukin-5 induced false positive anti-drug antibody responses against mepolizumab through the use of a competitive blocking antibody.

Mepolizumab, a humanized IgG1 monoclonal antibody that blocks native homodimeric interleukin-5 (IL-5) from binding to the IL-5 receptor, has recently been approved for treatment of severe eosinophilic asthma. Our initial immunogenicity assay method for phase I and II studies utilized a bridging electrochemiluminescence format with biotin and ruthenium-labelled mepolizumab linked by anti-drug antibodies (ADA). We discovered that IL-5 significantly increased in dosed subjects from a phase II study and that the increased IL-5 was in the form of a drug-bound complex. We demonstrated that the elevated drug-bound IL-5 produced false-positive response in the in vitro ADA assay, in which drug-bound IL-5 dissociated and then bridged mepolizumab conjugates to yield positive signal. To eliminate the IL-5 interference, we compared two strategies: a solid-phase immunodepletion of IL-5 and an in-solution IL-5 immunocompetition. We identified the best competitive antibody for each purpose. We found both methods demonstrated similar effectiveness in reducing the false positive signal in IL-5 spiked samples; however, the in-solution immunocompetition for IL-5 had fewer false positives in study samples. Additionally, the in-solution immunocompetition method was experimentally simpler to execute. We modified the ADA assay by adding a pre-treatment step with a mepolizumab competitive anti- IL-5 antibody. Using this new method, we retested clinical samples from two phase II studies (MEA112997 and MEA114092). The confirmed ADA positive incidence was reduced from 29% and 61% to 1% and 8% with the modified in-solution immune inhibition method. Target interference is a fairly common problem facing immunogenicity testing, and target-induced false positive cannot be distinguished from true ADA response by the commonly used drug competitive confirmation assay. The approach and method used here for resolving target interference in ADA detection will be useful for differentiating between a true ADA response and target induced false positive as well as similar challenges in other programs.

Organic contaminants in western pond turtles in remote habitat in California.

Remote aquatic ecosystems are exposed to an assortment of semivolatile organic compounds (SOCs) originating from current and historic uses, of local and global origin. Here, a representative suite of 57 current- and historic-use pesticides, polychlorinated biphenyls, and polycyclic aromatic hydrocarbons were surveyed in the plasma of the western pond turtle (Emys marmorata) and their potential prey items and habitat. California study sites included Sequoia National Park, Whiskeytown National Recreation Area, and Six Rivers National Forest. Each was downstream of undeveloped watersheds and varied in distance from agricultural and urban pollution sources. SOCs were detected frequently in all sites with more found in turtle plasma and aquatic macroinvertebrates in the two sites closest to agricultural and urban sources. Summed PCBs were highest in Whiskeytown National Recreation Area turtle plasma (mean; 1.56 ng/g ww) compared to plasma from Sequoia National Park (0.16 ng/g ww; p = 0.002) and Six Rivers National Forest (0.07 ng/g ww; p = 0.001). While no current-use pesticides were detected in turtle plasma at any site, both current- and historic-use pesticides were found prominently in sediment and macroinvertebrates at the Sequoia National Park site, which is immediately downwind of Central Valley agriculture. SOC classes associated with urban and industrial pollution were found more often and at higher concentrations at Whiskeytown National Recreation Area. These findings demonstrate a range of SOC exposure in a turtle species with current and proposed conservation status and shed additional light on the fate of environmental contaminants in remote watersheds.

Mercury exposure associated with altered plasma thyroid hormones in the declining western pond turtle (Emys marmorata) from California mountain streams.

Mercury (Hg) is a global threat to wildlife health that can impair many physiological processes. Mercury has well-documented endocrine activity; however, little work on the effects of Hg on the thyroid hormones triiodothyronine (T3) and thyroxine (T4) in aquatic wildlife exists despite the fact that it is a sensitive endpoint of contaminant exposure. An emerging body of evidence points to the toxicological susceptibility of aquatic reptiles to Hg exposure. We examined the endocrine disrupting potential of Hg in the western pond turtle (Emys marmorata), a long-lived reptile that is in decline throughout California and the Pacific Northwest. We measured total Hg (THg) concentrations in red blood cells (RBCs) and plasma T3 and T4 of turtles from several locations in California that have been impacted by historic gold mining. Across all turtles from all sites, the geometric mean and standard error THg concentration was 0.805 ± 0.025 µg/g dry weight. Sampling region and mass were the strongest determinants of RBC THg. Relationships between RBC THg and T3 and T4 were consistent with Hg-induced disruption of T4 deiodination, a mechanism of toxicity that may cause excess T4 levels and depressed concentrations of biologically active T3.

Regional inhibition of cholinesterase in free-ranging western pond turtles (Emys marmorata) occupying California mountain streams.

The present study investigated the potential effects of cholinesterase (ChE)-inhibiting pesticides on western pond turtles (Emys marmorata) occupying streams in two regions of California, USA. The southern region was suspected of having increased exposure to atmospheric deposition of contaminants originating from Central Valley agriculture. The northern region represented reference ChE activities because this area was located outside of the prominent wind patterns that deposit pesticides into the southern region. Total ChE activity was measured in plasma from a total of 81 turtles from both regions. Cholinesterase activity of turtles was significantly depressed by 31% (p = 0.005) in the southern region after accounting for additional sources of variation in ChE activity. Male turtles had significantly increased ChE activity compared with females (p = 0.054). Cloaca temperature, length, mass, handling time, body condition, and lymph presence were not significant predictors of turtle ChE activity. In the southern region, 6.3% of the turtles were below the diagnostic threshold of two standard deviations less than the reference site mean ChE activity. Another diagnostic threshold determined that 75% of the turtles from the southern region had ChE activities depressed by 20% of the reference mean. The decrease in ChE activity in the southern region suggests sublethal effects of pesticide exposure, potentially altering neurotransmission, which can result in various deleterious behaviors.

Liver-specific overexpression of matrix metalloproteinase 9 (MMP-9) in transgenic mice accelerates development of hepatocellular carcinoma.

Matrix metalloproteinase-9 (MMP-9) plays a central role in tumor invasion and development of metastases. Expression of MMP-9 had been shown in human hepatocellular carcinomas (HCCs). However, it remained unclear whether MMP-9 could influence development of HCC. In order to address this issue, we generated transgenic mice overexpressing MMP-9 in the liver. In order to avoid embryonic lethality a Cre-lox system was utilized for conditional overexpression of MMP-9 under control of an albumin enhancer and promoter. Induction of MMP-9 overexpression in transgenic mice was achieved by i.v. injection of an adenovirus coding for the Cre recombinase. Initiation of liver carcinogenesis was achieved by injection of diethylnitrosamine (DEN) followed by Phenobarbital administration in drinking water. Transgene expression was induced at the age of 6 wk. Four and six months later mice were sacrificed and examined macroscopically and microscopically in a blinded manner. Alb/Cre/MMP-9-transgenic mice showed liver specific overexpression of MMP-9-mRNA and protein after induction. At the age of 6 months livers of transgenic mice showed 15.7 ± 11.6 tumors (mean ± SD) in contrast to wildtype mice with only 7.9 ± 11.0 tumors (P < 0.03). By histopathology examination of the livers HCCs were identified in 42% of the transgenic mouse livers but only 8% in wildtype animals. In summary, we established a novel MMP-9 transgenic mouse model, and report on a significantly increased susceptibility of MMP-9 transgenic mice to chemically induced carcinogenesis. This is the first in vivo proof that MMP-9 overexpression promotes liver tumor development.

The Observer XT: a tool for the integration and synchronization of multimodal signals.

The Observer was originally developed as a manual event recorder for the collection, management, analysis, and presentation of observational data in animals. Because of the flexibility of later versions, it became clear that The Observer was suitable for almost any study involving collection of observational data in both animals and humans. Furthermore, the most recent version of The Observer (The Observer XT) allows the integration and synchronization of multimodal signals from various sources, such as observational, video, tracking, and physiological data. This article describes how The Observer XT was used to integrate and synchronize video, observational, tracking, and physiological data from an experiment carried out in 2001 at the Wageningen Institute of Animal Sciences of Wageningen University and Research Centre. The integration and synchronization of these multimodal signals in The Observer XT allows the user to draw a more complete picture of the phenomena under study.

Transrenal nucleic acids: from proof of principle to clinical tests.

In spite of numerous publications on potential diagnostic application of circulating DNA and transrenal nucleic acid (Tr-NA) analysis, few, if any, tests based on this technology are available in clinical labs. This delay in test development and implementation is caused, at least in part, by the deficit in robust methods for isolation of short nucleic acid fragments from bodily fluids, as well as in techniques for analyzing these fragments. We have developed a new anion exchanger-based method for the isolation of cell-free nucleic acid fragments from large volumes of bodily fluids, and analyzed these fragments by PCR techniques specially designed to amplify "ultrashort" templates. The combination of these two techniques not only revealed the presence in urine of 10-150 bases or bp DNA and RNA fragments in addition to previously observed 150-200-bp DNA fragments and high molecular weight DNA, but also significantly increased the sensitivity of Tr-DNA detection. Additionally, we detected in urine a variety of miRNAs, including those excreted transrenally, thereby opening new diagnostic possibilities for Tr-NA analysis.

TGF-beta superfamily signaling is essential for tooth and hair morphogenesis and differentiation.

Members of the transforming growth factor beta (TGF-beta) superfamily of signaling molecules are involved in the regulation of many developmental processes that involve the interaction between mesenchymal and epithelial tissues. Smad7 is a potent inhibitor of many members of the TGF-beta family, notably TGF-beta and activin. In this study, we show that embryonic overexpression of Smad7 in stratified epithelia using a keratin 5 promoter, results in severe morphogenetic defects in skin and teeth and leads to embryonic and perinatal lethality. To further analyze the functions of Smad7 in epithelial tissues of adult mice, we used an expression system that allowed a controlled overexpression of Smad7 in terms of both space and time. Skin defects in adult mice overexpressing Smad7 were characterized by hyper-proliferation and missing expression of early markers of keratinocyte differentiation. Upon Smad7-mediated blockade of TGF-beta superfamily signaling, ameloblasts failed to produce an enamel layer in incisor teeth. In addition, TGF-beta blockade in adult mice altered the pattern of thymic T cell differentiation and the number of thymic T cells was significantly reduced. This study shows that TGF-beta superfamily signaling is essential for development of hair, tooth and T-cells as well as differentiation and proliferation control in adult tissues.

Liver fibrosis induced by hepatic overexpression of PDGF-B in transgenic mice.

BACKGROUND/AIMS: In hepatic fibrogenesis, stellate cells are activated leading to production and deposition of extracellular matrix. To clarify the role of PDGF-B in liver fibrogenesis, we overexpressed PDGF-B in the liver of transgenic mice. METHODS: Transgenic mice for the conditional overexpression of PDGF-B in the liver under control of an albumin promoter were generated utilising the Cre/loxP system. Constitutive PDGF-B expression was achieved after breeding with mice expressing Cre-recombinase under actin promoter control. Tamoxifen inducible expression was achieved after breeding with mice expressing Cre under transthyretin receptor promoter control. Levels of fibrosis were assessed and the expression of regulators of matrix remodelling was measured. RESULTS: PDGF-B expression caused hepatic stellate cell and myofibroblast activation marked by alpha-smooth muscle actin and PDGFR-beta expression. Liver fibrosis was verified macroscopically, histologically and by collagen I mRNA quantification in 4-6 week-old animals. MMP-2, MMP-9 and TIMP-1 were upregulated whereas TGF-beta expression was unchanged. CONCLUSIONS: We identified PDGF-B as a proliferative and profibrogenic stimulus and potential inducer of stellate cell transdifferentiation in vivo. PDGF-B overexpression causes liver fibrosis without significantly upregulating TGF-beta1, suggesting a TGF-beta-independent mechanism. The established model provides a tool for testing anti-PDGF-B therapeutic strategies in liver fibrosis in vivo.

Investigation of CC and CXC chemokine quaternary state mutants.

The chemokine family forms two different types of homodimer despite members sharing nearly identical folds. To study the formation of quaternary structure in this family, rational mutagenesis was employed on a representative member of each subfamily (MIP-1beta and IL-8). The variants were studied by analytical ultracentrifugation and NMR, and it was determined that formation of a folded monomer from a natural chemokine dimer is reasonably facile, while conversion between dimer types is not. Monomeric variants of MIP-1beta and IL-8 were randomly mutated and a lambda phage-based selection system was employed in a novel way to screen for dimerization. A total of 6,000,000 random mutants were screened, but no dimers were formed, suggesting again that the chemokine fold is robust and amenable to sequence variation, while the chemokine dimer is much more difficult to attain. This work represents a biophysical analysis of an array of chemokine quaternary state variants.

Hepatic over-expression of TGF-beta1 promotes LPS-induced inflammatory cytokine secretion by liver cells and endotoxemic shock.

Transforming growth factor-beta (TGF-beta) is an important suppressor of inflammation. However, TGF-beta has also been found to promote secretion of inflammatory cytokines, and transgenic mice, which constitutively express TGF-beta in liver, have been found to be more susceptible to endotoxemia. To approach this apparent paradox, we investigated the role of hepatic TGF-beta1 in endotoxemia by utilising inducible TGF-beta1-transgenic mice that express TGF-beta1 under control of the C-reactive protein promoter. In contrast to non-transgenic littermates, administration of lipopolysaccharide (LPS) induced strongly increased expression of TGF-beta and acute phase proteins in the TGF-beta1-transgenic mice. Hepatic TGF-beta1-expression in the transgenic mice started an inflammatory cytokine cascade, marked by increased and prolonged secretion of TNF-alpha and IL-6 by hepatocytes. The inflammatory response of the TGF-beta1-transgenic mice to LPS was associated with high rates of mortality due to endotoxemic shock, marked by systemic hypotension and hypothermia. Endotoxemic shock was primarily mediated by TNF-alpha and IL-6, since inhibitory antibody to TNF-alpha or, more effectively, to IL-6 could reduce mortality in these mice. In conclusion, while TGF-beta-signalling to immune cells may suppress inflammatory effector function, TGF-beta-signalling to liver cells seems to promote LPS-stimulated secretion of inflammatory cytokines and to predispose for lethal endotoxemic shock.

Reliability analysis of observational data: problems, solutions, and software implementation.

In the reliability analysis literature, little attention has been given to the various possible ways of creating a basis for the comparison required to compute observer agreement. One needs this comparison to turn a sequential list of behavioral records into a confusion matrix. It is shown that the way to do this depends on the research question one needs to answer. Four methods for creating a basis for comparison for the computation of observer agreement in observational data are presented. Guidelines are given for computing observer agreement in a way that fits one's goals. Finally, we discuss how these methods have been implemented in The Observer software. The Observer 4.1 supports all the methods that have been discussed. Most of these methods are not present in any other software package.