Desert Tortoise (Gopherus agassizii) Dietary Specialization Decreases across a Precipitation Gradient

We studied the plant resource use between and within populations of desert tortoise (Gopherus agassizii) across a precipitation gradient in the Sonoran Desert of Arizona. The carbon and nitrogen stable isotope values in animal tissues are a reflection of the carbon and nitrogen isotope values in diet, and consequently represent a powerful tool to study animal feeding ecology. We measured the δ¹³C and δ¹⁵N values in the growth rings on the shells of tortoises in different populations to characterize dietary specialization and track tortoise use of isotopically distinct C₄/CAM versus C₃ plant resources. Plants using C₃ photosynthesis are generally more nutritious than C₄ plants and these trait differences can have important growth and fitness consequences for consumers. We found that dietary specialization decreases in successively drier and less vegetated sites, and that broader population niche widths are accompanied by an increase in the dietary variability between individuals. Our results highlight how individual consumer plant resource use is bounded under a varying regime of precipitation and plant productivity, lending insight into how intra-individual dietary specialization varies over a spatial scale of environmental variability.     

Implications of Anthropogenic Landscape Change on Inter-Population Movements of the Desert Tortoise (Gopherus agassizii)

In the Sonoran Desert of North America, populations of the desert tortoise (Gopherus agassizii) occur in rocky foothills throughout southwestern Arizona and northwestern Mexico. Although tortoise populations appear to be isolated from each other by low desert valleys, individuals occasionally move long distances between populations. Increasingly, these movements are hindered by habitat fragmentation due to anthropogenic landscape changes. We used molecular techniques and radiotelemetry to examine movement patterns of desert tortoises in southern Arizona. We collected blood samples from 170 individuals in nine mountain ranges and analyzed variability in seven microsatellite loci to determine genetic differentiation among populations. Gene flow estimates between populations indicate that populations exchanged individuals historically at a rate greater than one migrant per generation, and positive correlation between genetic and geographic distance of population pairs suggests that the limiting factor for gene flow among populations is isolation by distance. Life history traits of the desert tortoise, a long-lived species with delayed sexual maturity, may severely constrain the ability of small populations to respond to disturbances that increase adult mortality. Historic gene flow estimates among populations suggests that recovery of declining populations may rely heavily on the immigration of new individuals from adjacent mountain ranges. Management strategies compatible with the evolutionary history of gene flow among disjunct populations will help ensure the long-term persistence of Sonoran desert tortoise populations.     

Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis

Reports in recent years indicate that the increasing emergence of resistance to drugs be using to TB treatment. The resistance to them severely affects to options for effective treatment. The emergence of multidrug-resistant tuberculosis has increased interest in understanding the mechanism of drug resistance in M. tuberculosis and the development of new therapeutics, diagnostics and vaccines. In this study, a label-free quantitative proteomics approach has been used to analyze proteome of multidrug-resistant and susceptible clinical isolates of M. tuberculosis and identify differences in protein abundance between the two groups. With this approach, we were able to identify a total of 1,583 proteins. The majority of identified proteins have predicted roles in lipid metabolism, intermediary metabolism, cell wall and cell processes. Comparative analysis revealed that 68 proteins identified by at least two peptides showed significant differences of at least twofolds in relative abundance between two groups. In all protein differences, the increase of some considering proteins such as NADH dehydrogenase, probable aldehyde dehydrogenase, cyclopropane mycolic acid synthase 3, probable arabinosyltransferase A, putative lipoprotein, uncharacterized oxidoreductase and six membrane proteins in resistant isolates might be involved in the drug resistance and to be potential diagnostic protein targets. The decrease in abundance of proteins related to secretion system and immunogenicity (ESAT-6-like proteins, ESX-1 secretion system associated proteins, O-antigen export system and MPT63) in the multidrug-resistant strains can be a defensive mechanism undertaken by the resistant cell.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0511-2) contains supplementary material, which is available to authorized users.     

Using motion-sensor camera technology to infer seasonal activity and thermal niche of the desert tortoise (Gopherus agassizii)

Understanding the relationships between environmental variables and wildlife activity is an important part of effective management. The desert tortoise (Gopherus agassizii), an imperiled species of arid environments in the southwest US, may have increasingly restricted windows for activity due to current warming trends. In summer 2013, we deployed 48 motion sensor cameras at the entrances of tortoise burrows to investigate the effects of temperature, sex, and day of the year on the activity of desert tortoises. Using generalized estimating equations, we found that the relative probability of activity was associated with temperature (linear and quadratic), sex, and day of the year. Sex effects showed that male tortoises are generally more active than female tortoises. Temperature had a quadratic effect, indicating that tortoise activity was heightened at a range of temperatures. In addition, we found significant support for interactions between sex and day of the year, and sex and temperature as predictors of the probability of activity. Using our models, we were able to estimate air temperatures and times (days and hours) that were associated with maximum activity during the study. Because tortoise activity is constrained by environmental conditions such as temperature, it is increasingly vital to conduct studies on how tortoises vary their activity throughout the Sonoran Desert to better understand the effects of a changing climate.     

Probing Diversity in the Plankton: Using Patterns in Tintinnids (Planktonic Marine Ciliates) to Identify Mechanisms

In diversity research, the use of survey data appears to have declined in favour of experimental or modeling approaches because direct relationships are difficult to demonstrate. Here we show that use of field data can yield information concerning the mechanisms governing diversity. First, we establish that tintinnids display a global latitudinal pattern of diversity similar to other pelagic organisms; species numbers appear to peak between 20° and 30° north or south. This common large scale spatial trend has been attributed to the gradient in water column structure across the global ocean. We then examine the generality of a relationship between planktonic diversity and water column structure by considering data from the Mediterranean Sea, in which water column structure changes seasonally. Among populations of foraminifera, tintinnids, and the dinoflagellates of the genus Ceratium, we compare data from trans-Mediterranean sampling conducted at different times and monthly changes in species richness at single sites. We find that water column structure alone appears to be a poor predictor of temporal changes in diversity. Lastly, we present an example of temporal changes in tintinnid diversity based on data from an oceanographic sampling station in the N. W. Mediterranean where resources, as chlorophyll, appear distinctly unrelated to changes in water column structure. We show that short-tem temporal changes in diversity (week to week shifts) can be related to changes in chlorophyll concentration. We conclude that in tintinnids diversity can be directly linked to characteristics of food resources.     

Estimation of Soil Erosion Dynamics in the Koshi Basin Using GIS and Remote Sensing to Assess Priority Areas for Conservation

High levels of water-induced erosion in the transboundary Himalayan river basins are contributing to substantial changes in basin hydrology and inundation. Basin-wide information on erosion dynamics is needed for conservation planning, but field-based studies are limited. This study used remote sensing (RS) data and a geographic information system (GIS) to estimate the spatial distribution of soil erosion across the entire Koshi basin, to identify changes between 1990 and 2010, and to develop a conservation priority map. The revised universal soil loss equation (RUSLE) was used in an ArcGIS environment with rainfall erosivity, soil erodibility, slope length and steepness, cover-management, and support practice factors as primary parameters. The estimated annual erosion from the basin was around 40 million tonnes (40 million tonnes in 1990 and 42 million tonnes in 2010). The results were within the range of reported levels derived from isolated plot measurements and model estimates. Erosion risk was divided into eight classes from very low to extremely high and mapped to show the spatial pattern of soil erosion risk in the basin in 1990 and 2010. The erosion risk class remained unchanged between 1990 and 2010 in close to 87% of the study area, but increased over 9.0% of the area and decreased over 3.8%, indicating an overall worsening of the situation. Areas with a high and increasing risk of erosion were identified as priority areas for conservation. The study provides the first assessment of erosion dynamics at the basin level and provides a basis for identifying conservation priorities across the Koshi basin. The model has a good potential for application in similar river basins in the Himalayan region.     

Using Participatory Risk Mapping (PRM) to Identify and Understand People's Perceptions of Crop Loss to Animals in Uganda

Considering how people perceive risks to their livelihoods from local wildlife is central to (i) understanding the impact of crop damage by animals on local people and (ii) recognising how this influences their interactions with, and attitudes towards, wildlife. Participatory risk mapping (PRM) is a simple, analytical tool that can be used to identify and classify risk within communities. Here we use it to explore local people''s perceptions of crop damage by wildlife and the animal species involved. Interviews (n = 93, n = 76) and seven focus groups were conducted in four villages around Budongo Forest Reserve, Uganda during 2004 and 2005. Farms (N = 129) were simultaneously monitored for crop loss. Farmers identified damage by wildlife as the most significant risk to their crops; risk maps highlighted its anomalous status compared to other anticipated challenges to agricultural production. PRM was further used to explore farmers'' perceptions of animal species causing crop damage and the results of this analysis compared with measured crop losses. Baboons (Papio anubis) were considered the most problematic species locally but measurements of loss indicate this perceived severity was disproportionately high. In contrast goats (Capra hircus) were considered only a moderate risk, yet risk of damage by this species was significant. Surprisingly, for wild pigs (Potamochoerus sp), perceptions of severity were not as high as damage incurred might have predicted, although perceived incidence was greater than recorded frequency of damage events. PRM can assist researchers and practitioners to identify and explore perceptions of the risk of crop damage by wildlife. As this study highlights, simply quantifying crop loss does not determine issues that are important to local people nor the complex relationships between perceived risk factors. Furthermore, as PRM is easily transferable it may contribute to the identification and development of standardised approaches of mitigation across sites of negative human-wildlife interaction.     

Using the Electronic Nose to Identify Airway Infection during COPD Exacerbations

Background

The electronic nose (e-nose) detects volatile organic compounds (VOCs) in exhaled air. We hypothesized that the exhaled VOCs print is different in stable vs. exacerbated patients with chronic obstructive pulmonary disease (COPD), particularly if the latter is associated with airway bacterial infection, and that the e-nose can distinguish them.

Methods

Smell-prints of the bacteria most commonly involved in exacerbations of COPD (ECOPD) were identified in vitro. Subsequently, we tested our hypothesis in 93 patients with ECOPD, 19 of them with pneumonia, 50 with stable COPD and 30 healthy controls in a cross-sectional case-controlled study. Secondly, ECOPD patients were re-studied after 2 months if clinically stable. Exhaled air was collected within a Tedlar bag and processed by a Cynarose 320 e-nose. Breath-prints were analyzed by Linear Discriminant Analysis (LDA) with “One Out” technique and Sensor logic Relations (SLR). Sputum samples were collected for culture.

Results

ECOPD with evidence of infection were significantly distinguishable from non-infected ECOPD (p = 0.018), with better accuracy when ECOPD was associated to pneumonia. The same patients with ECOPD were significantly distinguishable from stable COPD during follow-up (p = 0.018), unless the patient was colonized. Additionally, breath-prints from COPD patients were significantly distinguished from healthy controls. Various bacteria species were identified in culture but the e-nose was unable to identify accurately the bacteria smell-print in infected patients.

Conclusion

E-nose can identify ECOPD, especially if associated with airway bacterial infection or pneumonia.     

Defining TCE Plume Source Areas Using the Membrane Interface Probe (MIP)

A variety of traditional characterization methods, such as soil gas surveys, soil and groundwater sampling, and fixed laboratory analysis, is commonly used to define the magnitude and extent of soil and groundwater contamination in volatile organic compound source areas. One significant limitation of these methods is that they require multi-media sample collection to define the full unsaturated and saturated vertical profile in any given location. In addition, attaining higher resolution by increasing sample frequency increases costs substantially. A relatively new technology, the Membrane Interface Probe (MIP), was used to define trichloroethene plume source areas at F.E. Warren Air Force Base in Cheyenne, Wyoming, and at a confidential security products manufacturer in Tennessee. The MIP offered significant advantages over traditional drilling and direct-push methods and yielded data critical to a fuller understanding of subsurface conditions. The near-continuous MIP profile minimized the number of soil and groundwater samples required to fully delineate the extent of the plume-head source areas. In addition, the MIP is also able to collect data in the vadose and saturated zones, providing detailed vertical contaminant profiling information and geologic conditions based on soil conductivity that aided in the development of the site conceptual model. The MIP was not without its disadvantages; principal among these the relatively high detection limit (approximately 100 ppb in soil and groundwater), making the method useful for source characterization but limited for delineating lower levels of contamination. The data obtained from the MIP are considered screening-level data and need to be supplemented with analytical soil or groundwater data to fully support risk or remediation decisions. In summary, the vertical profiling obtained using the MIP aided in the interpretation of the complex relationship between the presence of gross contamination in soil and groundwater and the geologic conditions controlling contaminant distribution.     

Metabolomic Profiling to Identify Predictors of Response to Vitamin E for Non-Alcoholic Steatohepatitis (NASH)

Vitamin E was recently shown to improve hepatic histology in a randomized controlled trial of pioglitazone or vitamin E for nonalcoholic steatohepatitis (PIVENS). The current study utilized samples collected in the PIVENS trial to identify: (1) baseline metabolomic profiles that could identify who would respond to vitamin E treatment and (2) end of treatment metabolomic profiles reflective of histologic improvement. A comprehensive analysis of metabolomics profiles (n = 547) quantified by mass spectrometry was performed in vitamin E responders (n = 16), vitamin E non-responders (n = 15), and placebo responders (n = 15). At baseline, phenyl-propionic acid (Odds ratio: 29.4, p<0.01), indole-propionic acid levels (Odds ratio: 16.2, p<0.01) were directly associated with a subsequent histologic response to vitamin E treatment whereas γ-carboxyethylhydroxychroman (CEHC) levels were inversely related to histologic response. Adjusting for baseline values by analysis of covariance, the end of treatment levels of gamma-glutamyl leucine (Fold change: 0.82, p<0.02) and gamma-glutamyl valine (Fold change: 0.8, p<0.03) were significantly lower in vitamin E responders compared to non-responders. The levels of gamma-glutamyl transpeptidase were not significantly different across the two groups. Subjects receiving placebo who demonstrated a histologic improvement also demonstrated lower levels of gamma-glutamylated amino acids (leucine, valine and isoleucine) compared to vitamin E non-responders. These data provide exploratory proof that there are measurable differences in the metabolic profile of subjects who are likely (vs unlikely) to respond to vitamin E treatment for NASH and in those experiencing histologic improvement (vs no improvement) on treatment and support further studies to validate these biomarkers.     

Response of the Abundance of Key Soil Microbial Nitrogen-Cycling Genes to Multi-Factorial Global Changes

Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.     

Western blot can distinguish natural and acquired antibodies to Mycoplasma agassizii in the desert tortoise (Gopherus agassizii)

Mycoplasma agassizi has been identified as a cause of upper respiratory tract disease (URTD) in the threatened Mojave population of the desert tortoise (Gopherus agassizii), and anti-M. agassizii antibodies have been found by ELISA in as many as 15% of these animals across their geographic range. Here we report that a cohort of 16 egg-reared desert tortoises never exposed to M. agassizii had ELISA antibody titers to this organism that overlapped with titers obtained from some M. agassizii-infected tortoises. These natural antibodies were predominantly of the IgM class. Western blots of plasma from these non-infected tortoises produced a characteristic banding pattern against M. agassizii antigens. A group of 38 wild-caught desert tortoises was tested by ELISA, and although some of these tortoises had antibody titers significantly higher than the non-infected tortoises, there was considerable overlap at the lower titer levels. However, Western blot analysis revealed distinct banding patterns that could readily distinguish between the non-infected tortoises and tortoises with acquired antibodies, regardless of ELISA antibody titers. We conclude that desert tortoises have natural antibodies to M. agassizii that can compromise the determination of infection status by ELISA. However, the Western blot technique can distinguish between natural and acquired antibody patterns and can be used to confirm the diagnosis of M. agassizii infections in the desert tortoise.     

Ecological Modeling of the Spatial Distribution of Wild Waterbirds to Identify the Main Areas Where Avian Influenza Viruses are Circulating in the Inner Niger Delta,Mali

Predicting areas of disease emergence when no epidemiological data is available is essential for the implementation of efficient surveillance programs. The Inner Niger Delta (IND) in Mali is a major African wetland where >1 million Palearctic and African waterbirds congregate. Waterbirds are the main reservoir of Avian Influenza Viruses (AIV). Our objective was to model their spatial distribution in order to predict where these viruses would be more likely to circulate. We developed a generalized linear model (GLM) and a boosted regression trees (BRT) model based on total aerial bird counts taken in winter over 6 years. We used remotely sensed environmental variables with a high temporal resolution (10 days) to predict the spatial distribution of four waterbird groups. The predicted waterbird abundances were weighted with an epidemiological indicator based on the prevalence of low pathogenic AIV reported in the literature. The BRT model had the best predictive power and allowed prediction of the high variability of waterbird distribution. Years with low flood levels showed areas with a higher risk of circulation and had better spatial distribution predictions. Each year, the model identified a few areas with a higher risk of AIV circulation. This model can be applied every 10 days to evaluate the risk of AIV emergence in wild waterbirds. By taking into account the IND’s ecological variability, it allows better targeting of areas considered for surveillance. This could enhance the control of emerging diseases at a local and regional scale, especially when resources available for surveillance programs are scarce.     

An Antidote to the Imager's Fallacy,or How to Identify Brain Areas That Are in Limbo

Traditionally, fMRI data are analyzed using statistical parametric mapping approaches. Regardless of the precise thresholding procedure, these approaches ultimately divide the brain in regions that do or do not differ significantly across experimental conditions. This binary classification scheme fosters the so-called imager''s fallacy, where researchers prematurely conclude that region A is selectively involved in a certain cognitive task because activity in that region reaches statistical significance and activity in region B does not. For such a conclusion to be statistically valid, however, a test on the differences in activation across these two regions is required. Here we propose a simple GLM-based method that defines an “in-between” category of brain regions that are neither significantly active nor inactive, but rather “in limbo”. For regions that are in limbo, the activation pattern is inconclusive: it does not differ significantly from baseline, but neither does it differ significantly from regions that do show significant changes from baseline. This pattern indicates that measurement was insufficiently precise. By directly testing differences in activation, our procedure helps reduce the impact of the imager''s fallacy. The method is illustrated using concrete examples.     

网上实验室克隆与鉴定食管癌相关基因ECRG—4

利用生物信息学,探索网上克隆基因与鉴定基因的新方法。以因特网为平台,数据库为试验材料,各种软件为工具组成网上实验室,是人类基因组计划带来的实验技术革命。利用网上实验室以食管癌相关基因E－CRG－4的97bpEST为基础,成功克隆并鉴定了该基因。结果显示ECRG－4近似cDNA全长序列为772bp,其中含有一447bp的完整阅读框,编码148个氨基酸。氨基酸序列相似性分配表明ECRG－4与细胞膜上的免疫球蛋白超家族具有31％同源性。该基因定位于染色体2q141－14．3。组织分布表明ECRG-4须正常食管、膀胱组织中表达明显高于相应的癌组织。采用辐射杂交细胞系GeneBridge4RH嵌板作染色体定位进行初步验证,所得结果与网上克隆完全一致。研究提示,利用网上实验室克隆鉴定基因,是一种简便、精确的好方法。ECRG－4可能是一个在细胞癌变过程中具有非常重要意义的基因。     

Key to the genera of the subtribe Aphidina (Homoptera)

Abstract. A key is provided for the identification of the twenty-four genera of the world-wide subtribe Aphidina and for a few similar genera of uncertain taxonomic position.     

Using Species-Area Relationships to Inform Baseline Conservation Targets for the Deep North East Atlantic

Demands on the resources of the deep-sea have increased in recent years. Consequently, the need to create and implement a comprehensive network of Marine Protected Areas (MPAs) to help manage and protect these resources has become a global political priority. Efforts are currently underway to implement MPA networks in the deep North East Atlantic. To ensure these networks are effective, it is essential that baseline information be available to inform the conservation planning process. Using empirical data, we calculated conservation targets for sessile benthic invertebrates in the deep North East Atlantic for consideration during the planning process. We assessed Species-Area Relationships across two depth bands (200–1100 m and 1100–1800 m) and nine substrata. Conservation targets were predicted for each substratum within each depth band using z-values obtained from fitting a power model to the Species-Area Relationships of observed and estimated species richness (Chao1). Results suggest an MPA network incorporating 10% of the North East Atlantic’s deep-sea area would protect approximately 58% and 49% of sessile benthic species for the depth bands 200–1100 m and 1100–1800 m, respectively. Species richness was shown to vary with substratum type indicating that, along with depth, substratum information needs to be incorporated into the conservation planning process to ensure the most effective MPA network is implemented in the deep North East Atlantic.