Evaluating the performance of species richness estimators: sensitivity to sample grain size

1. Fifteen species richness estimators (three asymptotic based on species accumulation curves, 11 nonparametric, and one based in the species-area relationship) were compared by examining their performance in estimating the total species richness of epigean arthropods in the Azorean Laurisilva forests. Data obtained with standardized sampling of 78 transects in natural forest remnants of five islands were aggregated in seven different grains (i.e. ways of defining a single sample): islands, natural areas, transects, pairs of traps, traps, database records and individuals to assess the effect of using different sampling units on species richness estimations. 2. Estimated species richness scores depended both on the estimator considered and on the grain size used to aggregate data. However, several estimators (ACE, Chao 1, Jackknifel and 2 and Bootstrap) were precise in spite of grain variations. Weibull and several recent estimators [proposed by Rosenzweig et al. (Conservation Biology, 2003, 17, 864-874), and Ugland et al. (Journal of Animal Ecology, 2003, 72, 888-897)] performed poorly. 3. Estimations developed using the smaller grain sizes (pair of traps, traps, records and individuals) presented similar scores in a number of estimators (the above-mentioned plus ICE, Chao2, Michaelis-Menten, Negative Exponential and Clench). The estimations from those four sample sizes were also highly correlated. 4. Contrary to other studies, we conclude that most species richness estimators may be useful in biodiversity studies. Owing to their inherent formulas, several nonparametric and asymptotic estimators present insensitivity to differences in the way the samples are aggregated. Thus, they could be used to compare species richness scores obtained from different sampling strategies. Our results also point out that species richness estimations coming from small grain sizes can be directly compared and other estimators could give more precise results in those cases. We propose a decision framework based on our results and on the literature to assess which estimator should be used to compare species richness scores of different sites, depending on the grain size of the original data, and of the kind of data available (species occurrence or abundance data).     

Trypanosoma cruzi: Oxidative stress induces arginine kinase expression

Trypanosoma cruzi arginine kinase is a key enzyme in cell energy management and is also involved in pH and nutritional stress response mechanisms. T. cruzi epimastigotes treated with hydrogen peroxide presented a time-dependent increase in arginine kinase expression, up to 10-fold, when compared with untreated parasites. Among other oxidative stress-generating compounds tested, only nifurtimox produced more than 2-fold increase in arginine kinase expression. Moreover, parasites overexpressing arginine kinase showed significantly increased survival capability during hydrogen peroxide exposure. These findings suggest the participation of arginine kinase in oxidative stress response systems.     

A new method for the automated age-at-death evaluation by tooth-cementum annulation (TCA)

A valid age at death estimation is required in historical and also forensic anthropology. Tooth cementum annulation (TCA) is a method for age at death estimation of adult individuals. The method is based on light microscope images taken from tooth-root cross sections. The age is then estimated by manually counting the cementum incremental lines and adding this to the chronological age at the assumed point of tooth eruption. Manual line counting, however, is time consuming, potentially subjective and the number of individual counts is insufficient for statistical evaluations. Software developed for the automated evaluation of TCA images, that uses Fourier analysis and algorithms for image analysis and pattern recognition is presented here. It involves "line-by-line" scanning and the counting of gray scale peaks within a selected region-of-interest (ROI). Each scanning process of a particular ROI yields up to 400 counts that are subsequently statistically evaluated. This simple and time saving program seeks to substitute manual counting and supply consistent and reproducible results as well as reduce the demand of human error by eliminating unavoidable factors such as subjectivity and fatigue.     

Degradation of biomolecules in bones: effects of the biological forensics as an example of the stability of isotope ratios in collagen

Modern bone samples were experimentally degraded by incubation into water at increased temperature and examined in terms of their collagen content, the stable C and N isotopic ratios, and the molar C/N ratio. The same analyses were carried out with archaeological human bone of varying age (300 up to 8000 years). The experimentally degraded samples exhibited changes of the collagen's integrity, which influence the stable isotope ratios. In the case of the archaeological material, a correlation between stable delta13C- and delta15N-values and collagen content could be demonstrated. The molar C:N ratio was no suitable criterion for the assessment of the state of preservation of extractable collagen.     

The fusogenic state of mayaro virus induced by low pH and by hydrostatic pressure

Mayaro virus is an enveloped virus that belongs to the Alphavirus genus. To gain insight into the mechanism involved in Mayaro virus membrane fusion, we used hydrostatic pressure and low pH to isolate a fusion-active state of Mayaro glycoproteins. In response to pressure, E1 glycoprotein undergoes structural changes resulting in the formation of a stable conformation. This state was characterized and correlated to that induced by low pH as measured by intrinsic fluorescence, 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid, dipotassium salt fluorescence, fluorescence resonance energy transfer, electron microscopy, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In parallel, we used a neutralization assay to show that Mayaro virus in the fusogenic state retained most of the original immunogenic properties and could elicit high titers of neutralizing antibodies.     

Pollen-mediated gene flow in maize in real situations of coexistence

We present the first study on cross-fertilization between Bt and conventional maize in real situations of coexistence in two regions in which Bt and conventional maize were cultivated. A map was designed and the different crops were identified, as were the sowing and flowering dates, in Bt and conventional maize fields. These data were used to choose the non-transgenic fields for sampling and analysis by the real-time quantification system-polymerase chain reaction (RTQ-PCR) technique. In general, the rate of cross-fertilization was higher in the borders and, in most of the fields, decreased towards the centre of the field. Nine fields had values of genetically modified organism DNA to total DNA of much lower than 0.9%, whereas in three the rate was higher. Some differences were found when comparing our results with those of common field trials. In real conditions of coexistence and in cropping areas with smaller fields, the main factors that determined cross-pollination were the synchronicity of flowering and the distances between the donor and receptor fields. By establishing an index based on these two variables, the rate of the adventitious presence of genetically modified maize could be predicted, as well as the influence of other factors. By applying this index, and in the case of a fully synchronous flowering time, a security distance between transgenic and conventional fields of about 20 m should be sufficient to maintain the adventitious presence of genetically modified organisms as a result of pollen flow below the 0.9% threshold in the total yield of the field.     

Ultraviolet Radiation on Innate Immunity and Growth of Broad-Snouted Caiman (Caiman latirostris): Implications for Facilities Design

Sunlight is a key environmental factor in almost all ecosystems, and it is necessary for many physiological functions. Many vertebrates require ultraviolet (UV) radiation to perform different physiological processes. Artificial light is used to supplement UV in captive animals, through appropriate photoperiods and UV wavelengths. Previous studies reported that repeated exposure to artificial UV radiation may cause damage to the immune system. Taking into account the importance of UV effects and the serum complement system, the relationship between them was investigated. The study lasted 90 days and was carried out in plastic chambers. Ninety six broad‐snouted caiman (C. latirostris) were assigned to four treatment groups with two replicates each: total darkness (TD), 8 hr per day (8 hr) and 16 hr per day (16 hr) of artificial UV/visible light exposure, and normal photoperiod of natural light (NP). Snout–vent length was measured to determine animal growth. Hemolytic assays were performed to evaluate the effects of artificial UV/visible light, TD, and NP on the serum complement system. Results showed that animals grew more in the NP group. The capacity of C. latirostris serum to hemolyze sheep red blood cells was higher in the NP group than when they are maintained in constant light–dark cycles (8 and 16 hr) or in TD. These data demonstrate that artificial UV should be considered as a potential hazard for captive crocodilians if it is not properly managed, and this should be taken into account in the general design of facilities for reptilian husbandry. Zoo Biol 31:523‐533, 2012. © 2011 Wiley Periodicals, Inc.     

Rhodopsin 5- and Rhodopsin 6-mediated clock synchronization in Drosophila melanogaster is independent of retinal phospholipase C-β signaling

Circadian clocks of most organisms are synchronized with the 24-hour solar day by the changes of light and dark. In Drosophila, both the visual photoreceptors in the compound eyes as well as the blue-light photoreceptor Cryptochrome expressed within the brain clock neurons contribute to this clock synchronization. A specialized photoreceptive structure located between the retina and the optic lobes, the Hofbauer-Buchner (H-B) eyelet, projects to the clock neurons in the brain and also participates in light synchronization. The compound eye photoreceptors and the H-B eyelet contain Rhodopsin photopigments, which activate the canonical invertebrate phototransduction cascade after being excited by light. We show here that 2 of the photopigments present in these photoreceptors, Rhodopsin 5 (Rh5) and Rhodopsin 6 (Rh6), contribute to light synchronization in a mutant (norpA(P41) ) that disrupts canonical phototransduction due to the absence of Phospholipase C-β (PLC-β). We reveal that norpA(P41) is a true loss-of-function allele, resulting in a truncated PLC-β protein that lacks the catalytic domain. Light reception mediated by Rh5 and Rh6 must therefore utilize either a different (nonretinal) PLC-β enzyme or alternative signaling mechanisms, at least in terms of clock-relevant photoreception. This novel signaling mode may distinguish Rhodopsin-mediated irradiance detection from image-forming vision in Drosophila.     

Genetic control of duration of pre-anthesis phases in wheat (Triticum aestivum L.) and relationships to leaf appearance, tillering, and dry matter accumulation

The duration of pre-anthesis developmental phases is of interest in breeding for improved adaptation and yield potential in temperate cereals. Yet despite numerous studies on the genetic control of anthesis (flowering) time and floral initiation, little is known about the genetic control of other pre-anthesis phases. Furthermore, little is known about the effect that changes in the duration of pre-anthesis phases could have on traits related to leaf appearance and tillering, or dry matter accumulation before terminal spikelet initiation (TS). The genetic control of the leaf and spikelet initiation phase (LS; from sowing to TS), the stem elongation phase (SE; from TS to anthesis), and, within the latter, from TS to flag leaf appearance and from then to anthesis, was studied in two doubled-haploid, mapping bread wheat populations, Cranbrook × Halberd and CD87 × Katepwa, in two field experiments (ACT and NSW, Australia). The lengths of phases were estimated from measurements of both TS and the onset of stem elongation. Dry weight per plant before TS, rate of leaf appearance, tillering rate, maximum number of tillers and number of leaves, and dry weight per plant at TS were also estimated in the Cranbrook × Halberd population. More genomic regions were identified for the length of the different pre-anthesis phases than for total time to anthesis. Although overall genetic correlations between LS and SE were significant and positive, independent genetic variability between LS and SE, and several quantitative trait loci (QTLs) with different effects on both phases were found in the two populations. Several of these QTLs (which did not seem to coincide with reported major genes) could be of interest for breeding purposes since they were only significant for either LS or SE. There was no relationship between LS and the rate of leaf appearance. LS was strongly and positively correlated with dry weight at TS but only slightly negatively correlated with early vigour (dry weight before TS). Despite significant genetic correlations between LS and some tillering traits, shortening LS so as to lengthen SE without modifying total time to anthesis would not necessarily reduce tillering capacity, as QTLs for tillering traits did not coincide with those QTLs significant only for LS or SE. Therefore, the study of different pre-anthesis phases is relevant for a better understanding of genetic factors regulating developmental time and may offer new tools for fine-tuning it in breeding for both adaptability and yield potential.