Inference on diversity from forest inventories: a review

A number of international agreements and commitments emphasize the importance of appropriate monitoring protocols and assessments as prerequisites for sound conservation and management of the world’s forest ecosystems. Mandated periodic surveys, like forest inventories, provide a unique opportunity to identify and properly satisfy natural resource management information needs. Distinctively, there is an increasing need for detecting diversity by means of unambiguous diversity measures. Because all diversity measures are functions of tree species abundances, estimation of tree diversity indices and profiles is inevitably performed by estimating tree species abundances and then estimating indices and profiles as functions of the abundance estimates. This strategy can be readily implemented in the framework of current forest inventory approaches, where tree species abundances are routinely estimated by means of plots placed onto the surveyed area in accordance with probabilistic schemes. The purpose of this paper is to assess the effectiveness of this strategy by reviewing theoretical results from published case studies. Under uniform random sampling (URS), that is when plots are uniformly and independently located on the study region, consistency and asymptotic normality of diversity index estimators follow from standard limit theorems as the sampling effort increases. In addition, variance estimation and bias reduction are achieved using the jackknife method. Despite its theoretical simplicity, URS may lead to uneven coverage of the study region. In order to avoid unbalanced sampling, the use of tessellation stratified sampling (TSS) is suggested. TSS involves covering the study region by a polygonal grid and randomly selecting a plot in each polygon. Under TSS, the diversity index estimators are consistent, asymptotically normal and more precise than those achieved using URS. Variance estimation is possible and there is no need to reduce bias.     

Identifying conservation hotspots in non-breeding areas: a case study of Lake Sturgeon (<Emphasis Type="Italic">Acipenser fulvescens</Emphasis>) in the Great Lakes

Limited conservation resources necessitate the prioritization of management efforts and one of the mechanisms for prioritization is the identification of hotspots. For some species of conservation concern, hotspots have been delineated, often using individual abundance as the metric. However, areas that attract individuals from multiple breeding populations may be a higher priority for conservation. These areas may have more abundant resources or habitat quality, and multiple breeding populations simultaneously benefit from conservation actions in these areas. We identified non-spawning aggregations of Lake Sturgeon Acipenser fulvescens in lakes Huron and Erie of the Great Lakes. The spawning period in Lake Sturgeon only represents a brief portion of their life and conservation goals need to include non-spawning areas. Based on 12 microsatellite loci, we determined the population of origin of individuals in the aggregations and computed a modified population-level Simpson’s diversity index (pD). Using this criterion, two hotspots were identified. The North Channel of Lake Huron had the highest diversity of represented populations (pD = 3.14). The second identified hotspot was Saginaw Bay in Lake Huron (pD = 1.78). Both hotspots had evidence of long-distance movement into the area. Monitoring of aggregations should continue to assess temporal variability in hotspot delineation.     

Shrub-encroachment induced alterations in input chemistry and soil microbial community affect topsoil organic carbon in an Inner Mongolian grassland

Shrub encroachment frequently occurs in arid and semi-arid grasslands worldwide and affects the regional carbon balance. Many previous studies have revealed the effects of shrub encroachment on bulk carbon content of grasslands, but molecular evidence is surprisingly lacking. In this study, we examined the chemical composition of plant tissues and soil organic carbon (SOC), and soil microbial communities to identify the effects of shrub (Caragana microphylla) encroachment on SOC storage in the top layer (0–10 cm) along a gradient of natural shrub cover in the grasslands of Inner Mongolia. We found that SOC in the shrub patches was derived mainly from leaves, whereas SOC in the grassy matrix was composed of a mixture of fresh root- and leaf-derived compounds. Compared with pure grassland, the SOC decreased by 29% in the shrub-encroached grasslands (SEGs), and this decrease was enhanced by increasing shrub cover. We also found that free lipids and lignin-derived phenols increased while the ratios of ω-C₁₈/∑C₁₈ and suberin/cutin decreased with increasing shrub cover. In addition, the ratios of fungal to bacterial phospholipid fatty acids (PLFAs) and gram-negative to gram-positive bacterial PLFAs decreased with increasing shrub cover. These results indicate that the encroachment of nitrogen-rich legume shrubs can lead to carbon loss by altering the chemical composition of plant inputs as well as the soil microbial community in grassland ecosystems.     

Lost in the hybridisation vortex: high-elevation <Emphasis Type="Italic">Senecio hercynicus</Emphasis> (Compositae,Senecioneae) is genetically swamped by its congener <Emphasis Type="Italic">S. ovatus</Emphasis> in the Bavarian Forest National Park (SE Germany)

Hybridisation is an important evolutionary process. The investigation of hybridisation along elevational gradients, with their steep abiotic and biotic clines, provides insight into the adaptation and maintenance of species in adjacent habitats. The rare Senecio hercynicus and its spreading congener S. ovatus are vertically vicariant species that show hybridisation in their range overlaps. In the present study, we used AFLP fingerprinting of 689 individuals from 38 populations to analyse population structure and introgression patterns along four elevational transects (650–1350 m) in the Bavarian Forest National Park, Gemany. Subsequently, we searched for loci putatively under divergent selection that may maintain ‘pure’ species despite hybrid formation by identifying taxon-specific alleles. A maximum-likelihood based hybrid index shows that the overall genetic differentiation among all populations was very low with a vanishingly small number of pure parental individuals. Almost 75% of the investigated individuals were classified as backcrosses towards S. ovatus. The highest S. hercynicus ancestry was found in the uppermost populations of two transects. Further, we found seven taxon-specific alleles being under divergent selection that correlated with climatic variables and deviating from neutral introgression. According to our results, hybridisation of S. ovatus and S. hercynicus has reached an advanced state of genetic swamping and there seems to be no driving force that is strong enough to keep both species as different lineages. Rather, S. ovatus appears to benefit through putatively adaptive introgression.     

The difficult legacy of Turing’s wager

Neuron modeling may be said to have originated with the Hodgkin and Huxley action potential model in 1952 and Rall’s models of integrative activity of dendrites in 1964. Over the ensuing decades, these approaches have led to a massive development of increasingly accurate and complex data-based models of neurons and neuronal circuits. ModelDB was founded in 1996 to support this new field and enhance the scientific credibility and utility of computational neuroscience models by providing a convenient venue for sharing them. It has grown to include over 1100 published models covering more than 130 research topics. It is actively curated and developed to help researchers discover and understand models of interest. ModelDB also provides mechanisms to assist running models both locally and remotely, and has a graphical tool that enables users to explore the anatomical and biophysical properties that are represented in a model. Each of its capabilities is undergoing continued refinement and improvement in response to user experience. Large research groups (Allen Brain Institute, EU Human Brain Project, etc.) are emerging that collect data across multiple scales and integrate that data into many complex models, presenting new challenges of scale. We end by predicting a future for neuroscience increasingly fueled by new technology and high performance computation, and increasingly in need of comprehensive user-friendly databases such as ModelDB to provide the means to integrate the data for deeper insights into brain function in health and disease.     

Usefulness of 1,3 Beta-<Emphasis Type="SmallCaps">d</Emphasis>-Glucan Detection in non-HIV Immunocompromised Mechanical Ventilated Critically Ill Patients with ARDS and Suspected <Emphasis Type="Italic">Pneumocystis jirovecii</Emphasis> Pneumonia

Introduction

Pneumocystis jirovecii pneumonia (PCP) is a major cause of disease in immunocompromised individuals. Diagnosis is typically obtained by microscopy and/or PCR. For ambiguous PCR results, we evaluated the new biomarker 1,3-Beta-d-Glucan (BDG).

Methods

BDG serum levels were assessed and correlated to PCR results in immunosuppressed patients with ARDS.

Results

11 (22%) out of 50 patients had suspected PCP. APACHE II (26 vs. 24; p < 0.002), SOFA score (16 vs. 14; p < 0.010) and mortality rate (34 vs. 69% p < 0.004; 34 vs. 80% p < 0.003) were significantly altered in patients with positive (pPCR) and slightly positive (spPCR) PCJ PCR as compared to patients with no-PCP (nPCP). BDG levels were significantly lower in patients with nPCP (86; 30–315 pg/ml) than in patients with pPCR (589; 356–1000 pg/ml; p < 0.001) and spPCP (398; 297–516 pg/ml; p < 0.004) referring to the cutoff in this study for PCP of 275 pg/ml. An overall sensitivity (S) of 92% (95% CI 86–96%) and specificity (SP) of 84% (95% CI 79–85%) for PCP were found for the BDG Fungitell assay. In detail, S of 98% (95% CI 94–100%) and SP of 86% (95% CI 82–92%) for pPCP and S of 98% (95% CI 96–100%) and SP of 88% (95% CI 86–96%) for spPCO were found.

Conclusion

Serum BDG levels were strongly elevated in PCP, and the negative predictive value is high. BDG could be used as a preliminary test for patients with suspected PCP, especially in patients with slightly positive PCR results.

     

Silibinin ameliorates Aβ<Subscript>25-35</Subscript>-induced memory deficits in rats by modulating autophagy and attenuating neuroinflammation as well as oxidative stress

Alzheimer’s disease (AD) is a progressive, neurodegenerative disease. Accumulating evidence suggests that inflammatory response, oxidative stress and autophagy are involved in amyloid β (Aβ)-induced memory deficits. Silibinin (silybin), a flavonoid derived from the herb milk thistle, is well known for its hepatoprotective activities. In this study, we investigated the neuroprotective effect of silibinin on Aβ_25-35-injected rats. Results demonstrated that silibinin significantly attenuated Aβ_25-35-induced memory deficits in Morris water maze and novel object-recognition tests. Silibinin exerted anxiolytic effect in Aβ_25-35-injected rats as determined in elevated plus maze test. Silibinin attenuated the inflammatory responses, increased glutathione (GSH) levels and decreased malondialdehyde (MDA) levels, and upregulated autophagy levels in the Aβ_25-35-injected rats. In conclusion, silibinin is a potential candidate for AD treatment because of its anti-inflammatory, antioxidant and autophagy regulating activities.