Neoperla spio (Plecoptera): a species complex?

Abstract. Almost thirty Neoperla species have been described from Africa, but have subsequently been grouped together as one very variable species, Nspio (Newman), only one author publicly disagreeing. In this study new techniques have been used to test the hypothesis that only a single species of African perlid exists. Samples were collected from an area where three morphologically dissimilar forms were sympatric on a temporal and spatial basis. These are here considered to belong to three species of Neoperla as a result of differences in chorionic features of the egg (elucidated by the scanning electron microscope). Multivariate analysis and electrophoretic data support the conclusion that Nspio is a species complex. Sexes of the three species were associated on the basis of mating experiments, and ecological data pertaining to mating.     

Population genetics of haplodiploid insects

Genic variation of seven species of Hymenoptera is described, using electrophoretic techniques. The heterozygosities range from 0.033 to 0.084. An average heterozygosity is calculated for 23 species of haplodiploid insects, and this value is significantly different from the same value for 18 Drosophila species or for 24 diploid insect species (including Drosophila). The niche width-genetic variation hypothesis is rejected as an explanation. A comparison of selection models and neutral models shows that both hypotheses are capable of explaining the data.     

Laparoscopic techniques for biomedical research.

The techniques used for laparoscopic observation of reproductive systems in 23 species are described. The application of various techniques to biomedical research is examined, and the methods used for laparoscopic follicular aspiration and injection, as well as the techniques for uterine flushing collection from swine and nonhuman primates, and oviductal deposition of test solutions are described.     

Estimating species trees using multiple-allele DNA sequence data

Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multiple-allele, multilocus sequence data, building on a recently proposed method for estimating species trees from single allele multilocus data. A two-step Markov Chain Monte Carlo (MCMC) algorithm is adopted to estimate the posterior distribution of the species tree. The model is applied to estimate the posterior distribution of species trees for two multiple-allele datasets--yeast (Saccharomyces) and birds (Manacus-manakins). The estimates of the species trees using our method are consistent with those inferred from other methods and genetic markers, but in contrast to other species tree methods, it provides credible regions for the species tree. The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics.     

Revision of the superfamily Acrotheloidea (Brachiopoda,class Linguliformea,order Lingulida) from the Lower and Middle Cambrian of the Siberian Platform

This paper continues our revision of Yu.L. Pelman’s collection of the superfamily Acrotheloidea (phosphatic brachiopods) and of our own material from the Early–Middle Cambrian of the Siberian Platform. The following representatives of the superfamily Acrotheloidea (order Lingulida, class Linguliformea) are restudied and revised based on new techniques: the genus Botsfordia (family Botsfordiidae Schindewolf, 1955) and the genera Acrothele, Eothele, and Orbithele (family Acrothelidae), which are widespread on the Siberian Platform. Only one out of the three Acrothele species described by Pelman is recognized as a valid species, and one new species of this genus that comprises some part of the brachiopods that Pelman figured and placed in another taxon is described. All these species are described using data on shell microsculpture and microstructure. In addition, the genera Eothele and Orbithele are described for the first time from the Siberian Platform.     

Corrigendum to Streicker et al. (2013) Differential sources of host species heterogeneity influence the transmission and control of multi‐host parasites

In a recent article, we described a conceptual and analytical model to identify the key host species for parasite transmission in multi‐host communities and used data from 11 gastro‐intestinal parasites infecting up to five small mammal host species as an illustrative example of how the framework could be applied. A limitation of these empirical data was uncertainty in the identification of parasite species using egg/oocyst morphology, which could overestimate parasite sharing between host species. Here, we show that the key results of the original analysis, namely that (1) parasites naturally infect multiple host species, but typically rely on a small subset of infected host species for long‐term maintenance, (2) that different mechanisms underlie how particular host species dominate transmission and (3) that these different mechanisms influence the predicted efficiency of disease control measures, are robust to analysis of a smaller subset of host–parasite combinations that we have greatest confidence in identifying. We further comment briefly on the need for accurate parasite identification, ideally using molecular techniques to quantify cross‐species transmission and differentiate covert host specificity from true host generalism.     

Microbial community analysis in incompletely or destructively sampled systems

Analyses of microbial community dynamics are often constrained by the destructive, indirect, and incomplete nature of most sampling techniques. These methodological constraints compel assumptions that are rarely verified about the relationships among separate communities. We evaluated the consequences for community analysis of the common assumption that separate microbial communities are described by the same species abundance distribution. Sample data were generated from simulated communities in which the species abundance distributions were the same or were different. Samples from communities that had the same number of species or were described by the same species abundance distribution sometimes had significantly different numbers of species. Samples from simulated communities that had different species number-species abundance distribution combinations sometimes contained indistinguishable numbers of species. When sampling from independent communities described by unknown distributions (e.g., microbial communities on plant surfaces), the simulations showed that standardization of sample size (number of individuals or colony-forming units) does not guarantee samples of equal proportions of the total species in a community. Sample sizes that are logistically feasible for many microbial systems will provide only limited information for differentiating species numbers or species abundance distributions among separate communities over time. For ecologists studying destructively or incompletely sampled communities this seriously influences both the sample designs that are reasonable and the questions that can be addressed in such systems. Send offprint requests to: L. Kinkel.     

Leishmania (Viannia) lainsoni (Kinetoplastida: Trypanosomatidae), a divergent Leishmania of the Viannia subgenus--a mini review

Leishmania (Viannia) lainsoni is the Leishmania species that presents the most distinct biological (morphology, growth in axenic culture medium), biochemical (enzymatic electrophoresis profile), and molecular biology characteristics, when compared to other species of the Viannia subgenus. Development of promastigote forms of this parasite attached to the wall of the pyloric and hind gut regions of sand fly vectors is a solid characteristic that allows its positioning in the Viannia subgenus. However, taxonomic data from biochemical and molecular techniques on this Leishmania species are still not conclusive. It is evident the difficulty in taxonomically positioning this borderline Leishmania species. In this review we present the data accumulated since L. (Viannia) lainsoni has been described and we discuss its position in the Viannia subgenus.     

LIVEWEIGHTS AND BODY MEASUREMENTS OF SERENGETI GAME ANIMALS

More than 300 game animals shot in the Grumeti Controlled Area, Tanzania during research into game utilisation were weighed and measured. The results are presented and compared with other available data. Considerable variation is apparent between animals of the same species from different areas.
The techniques of linear measurement are fully described in an attempt to standardise measurements for comparative purposes.     

<Emphasis Type="Italic">Candida dubliniensis</Emphasis>: Epidemiology and Phenotypic Methods for Identification

Candida dubliniensis is an emerging pathogen first described in 1995, which shares many phenotypic features with Candida albicans and therefore may be misidentified in microbial laboratories. Despite various phenotypic techniques described in the literature to differentiate the two species, the correct identification of C. dubliniensis remains problematic due to phenotypic similarities between these species. Thus, as the differences between both are best characterized at genetic levels, several molecular methods have been proposed to provide a specific and rapid identification of this species. Epidemiological studies have shown that C. dubliniensis is prevalent throughout the world and it is primarily associated with oral carriage and oropharyngeal infections in patients infected with human immunodeficiency virus (HIV). However, data acquired from its isolation from other healthy and immunocompromised patients are variable, and there is still no real consensus on the epidemiological relevance of this species. In this article, we review the various phenotypic methods used in the identification of C. dubliniensis and the epidemiological impact of this new species.     

Soil Sampling and Isolation of Entomopathogenic Nematodes (Steinernematidae,Heterorhabditidae)

Entomopathogenic nematodes (a.k.a. EPN) represent a group of soil-inhabiting nematodes that parasitize a wide range of insects. These nematodes belong to two families: Steinernematidae and Heterorhabditidae. Until now, more than 70 species have been described in the Steinernematidae and there are about 20 species in the Heterorhabditidae. The nematodes have a mutualistic partnership with Enterobacteriaceae bacteria and together they act as a potent insecticidal complex that kills a wide range of insect species.Herein, we focus on the most common techniques considered for collecting EPN from soil. The second part of this presentation focuses on the insect-baiting technique, a widely used approach for the isolation of EPN from soil samples, and the modified White trap technique which is used for the recovery of these nematodes from infected insects. These methods and techniques are key steps for the successful establishment of EPN cultures in the laboratory and also form the basis for other bioassays that consider these nematodes as model organisms for research in other biological disciplines. The techniques shown in this presentation correspond to those performed and/or designed by members of S. P. Stock laboratory as well as those described by various authors.     

分子生物学技术在腐霉菌分类上的应用研究

腐霉是一类世界性分布菌物,它可腐生、寄生或兼性寄生,又可陆生、水生或者水陆两栖生。目前世界各地被描述的腐霉种达250个,超过80种是植物重要的病原菌。腐霉主要引起各种植物根腐和幼苗猝倒,对农作物造成较大的损失。通过对近年来发展起来的腐霉分子生物学分类技术,诸如核糖体DNA(rDNA)转录内间隔区(ITS)的直接测序方法、分子杂交技术、PCR及改良PCR技术、基于线粒体DNA(mtDNA)的分析方法等进行了简述,为更快捷、准确的病原腐霉的鉴定及诊断技术的开发打下基础。     

Nesting Material and Nest Building Technique in Two Species of Broadbill (<Emphasis Type="Italic">Cymbirhynchus macrorhynchos</Emphasis> and <Emphasis Type="Italic">Corydon sumatranus</Emphasis>, Passeriformes,Eurylaimidae) from Southern Vietnam

Despite the relatively small number of species, the biology of most representatives of Suboscines of the Old World, particularly that of broadbills, (Eurylaimidae) remains poorly studied. The nest-building behavior of two species from the monospecific genera of broadbills Corydon sumatranus (Dusky Broadbill) and Cymbirhynchus macrorhynchos (Black-and-red Broadbill) has been described. A detailed study of nest structures has allowed us to determine the materials used in the construction, as well as to study in detail the techniques of its application at different stages of construction. Some unique techniques of nest-building were described. The connection between the properties of the building materials, design features, and construction techniques was characterized. The study of nests in the described species provides a key to understanding the construction of nests in other species of broadbills and in bird species building similar domed pendent nests.     

Techniques to obtain uniformly growing young roots for the study of salt effects

Summary Two techniques are described for set ups to provide seedlings with regularly growing roots which may be used as biological test material for externally applied substances. The techniques were tried out with different plant species, and a model trial with wheat only is described.     

Global analysis of fluorescence lifetime imaging microscopy data

Global analysis techniques are described for frequency domain fluorescence lifetime imaging microscopy (FLIM) data. These algorithms exploit the prior knowledge that only a limited number of fluorescent molecule species whose lifetimes do not vary spatially are present in the sample. Two approaches to implementing the lifetime invariance constraint are described. In the lifetime invariant fit method, each image in the lifetime image sequence is spatially averaged to obtain an improved signal-to-noise ratio. The lifetime estimations from these averaged data are used to recover the fractional contribution to the steady-state fluorescence on a pixel-by-pixel basis for each species. The second, superior, approach uses a global analysis technique that simultaneously fits the fractional contributions in all pixels and the spatially invariant lifetimes. In frequency domain FLIM the maximum number of lifetimes that can be fit with the global analysis method is twice the number of lifetimes that can be fit with conventional approaches. As a result, it is possible to discern two lifetimes with a single-frequency FLIM setup. The algorithms were tested on simulated data and then applied to separate the cellular distributions of coexpressed green fluorescent proteins in living cells.     

Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data

MOTIVATION: Analysis of high-throughput proteomic/genomic data, in particular, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) data and microarray data, has led to a multitude of techniques aimed at identifying potential biomarkers. Most of the statistical techniques for comparing two groups are based on qualitative measures such as P-value. A quantitative way such as interval estimation for the contrasts of two groups is more appealing. RESULTS: We have devised a simultaneous confidence bands method capable of detecting potential biomarkers, while controlling for overall confidence coverage level, in high-dimensional datasets that discriminate two treatment groups using a permutation scheme. For example, for the SELDI-TOF MS data, we deal with the entire spectrum simultaneously and construct (1 - alpha) confidence bands for the mean differences between groups. Furthermore, peaks were identified based on the maximal differences between the groups as determined by the confidence bands. The analysis method herein described gives both qualitative (P-value) and quantitative data (magnitude of difference). The Clinical Proteomics Programs Databank's ovarian cancer dataset and data from in-house samples containing known spiked-in proteins were analyzed. We were able to identify potential biomarkers similar to those described in previous analysis of the ovarian cancer data, however, while these markers are highly significant between cancer and normal groups, our analysis indicated the absolute difference between the two groups was minimal. In addition, we found additional markers than those previously described with greater differences in average intensities. The proposed confidence bands method successfully detected the spiked-in peaks, as well as, secondary peaks generated by adducts and double-charged species. We also illustrate our method utilizing paired gene expression data from a prostate cancer microarray experiment by constructing confidence bands for the fold changes between cancer and normal samples. AVAILABILITY: R-package, 'seie.zip' (license: GNU GPL), is publiclly available at http://research2.dfci.harvard.edu/dfci/MS_spike-in_data/