A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups

A major part of the barcoding of life problem is assigning newly sequenced or sampled individuals to existing groups that are preidentified externally (by a taxonomist, for example). This problem involves evaluating the statistical evidence towards associating a sequence from a new individual with one group or another. The main concern of our current research is to perform this task in a fast and accurate manner. To accomplish this we have developed a model-based, decision-theoretic framework based on the coalescent theory. Under this framework, we utilized both distance and the posterior probability of a group, given the sequences from members of this group and the sequence from a newly sampled individual to assign this new individual. We believe that this approach makes efficient use of the available information in the data. Our preliminary results indicated that this approach is more accurate than using a simple measure of distance for assignment.     

Spumochlamys iliensis n.g. n. sp. (Testacealobosia, Microchlamyiidae) from Central Asia, with notes on the diversity of Microchlamys-like testate amoebae

Spumochlamys iliensis n. g., n. sp. was isolated from a mineral pond in an arid, semi-desert region in Kazakhstan (Central Asia). This amoeba is covered with a plate-shaped, flexible organic spongious test. The thin membranous margin of this test extends ventrally to surround a flexible ventral aperture. In its morphological features and behaviour this amoeba is very similar to Microchlamys patella (Claparède and Lachmann, 1859) Cockerell, 1911, but differs from this species and from M. sylvatica Golemansky, Skarlato and Todorov, 1987 in the lack of an additional membrane separating the cell body from the test, a feature that can only be detected using electron microscopy. The presence of this membrane is considered to be a principal characteristic of the genus Microchlamys and family Microchlamyiidae; however, this conclusion was reached from the study of only two species. The data presented show a higher diversity of Microchlamys-like testate amoebae; we therefore suggest that the described species should be included in the family Microchlamyiidae with emendation of its diagnosis, but that a separate genus within this family should be established to accommodate it.     

The 245 kb amplified chromosome of Leishmania (V.) braziliensis contains a biopterin transporter gene

Leishmania (V.) braziliensis M2903 presents a small linear and stable 245 kb chromosome originating from a genomic amplification. Similar amplifications present in other species of Leishmania contain a gene coding for a biopterin transporter. Since Leishmania is auxotrophic for this metabolite, this amplification could result from the need to better capture biotpterin from growth media under specific circumstances. In this paper we show that this gene is also present in L. (V.) braziliensis small chromosome, which shares sequences with other genomic amplifications already described.     

Diversity of Phytases in the Rumen

Examples of a new class of phytase related to protein tyrosine phosphatases (PTP) were recently isolated from several anaerobic bacteria from the rumen of cattle. In this study, the diversity of PTP-like phytase gene sequences in the rumen was surveyed by using the polymerase chain reaction (PCR). Two sets of degenerate primers were used to amplify sequences from rumen fluid total community DNA and genomic DNA from nine bacterial isolates. Four novel PTP-like phytase sequences were retrieved from rumen fluid, whereas all nine of the anaerobic bacterial isolates investigated in this work contained PTP-like phytase sequences. One isolate, Selenomonas lacticifex, contained two distinct PTP-like phytase sequences, suggesting that multiple phytate hydrolyzing enzymes are present in this bacterium. The degenerate primer and PCR conditions described here, as well as novel sequences obtained in this study, will provide a valuable resource for future studies on this new class of phytase. The observed diversity of microbial phytases in the rumen may account for the ability of ruminants to derive a significant proportion of their phosphorus requirements from phytate.     

Isolation of Actinobacillus suis from a Canada goose (Branta canadensis)

Blindness from conjunctivitis caused by Actinobacillus suis was found in a Canada goose (Branta canadensis) from a wildlife refuge in Kentucky. Lesions were not observed elsewhere and other body organs were grossly normal. Actinobacillus spp. in birds is rare and this is apparently the first report of conjunctivitis resulting from this infection in waterfowl.     

EPR characterization of an oxygen-evolving photosystem II preparation from the transformable cyanobacterium Synechocystis 6803.

The transformable cyanobacterium Synechocystis 6803 has a photosynthetic apparatus that is similar to that of plants. Because of the ease with which this organism can be genetically manipulated and isotopically labeled, Synechocystis has been used extensively in recent studies of electron transfer in the water-splitting complex, photosystem II. Here, we present the first EPR characterization of a highly active oxygen-evolving preparation from this organism. This preparation shows oxygen-evolution activities in the range from 2400-2600 mumol of O2/(mg of chlorophyll.h). We show that this preparation is stable enough for room temperature EPR studies. We then use this assay to show that the lineshapes of the D+ and Z+ tyrosine radicals are identical in this preparation, as has been observed in photosystem II complexes from a wide variety of photosynthetic species. We also present the first multiline EPR spectrum that has been observed from the Synechocystis manganese cluster.     

Plant signaling endosomes and endosome trafficking

A discovery of a possibility for signal transduction from endosomes differing quantitatively and qualitatively from signaling from the plasma membrane became a reliably proved fact for animal and yeast receptors but was unaddressed by plant researches for a long time. In this lecture, I describe briefly recent progress in this research area and also the involvement of the actin cytoskeleton in endosome transport from the plasma membrane to acceptor compartments.     

Blood parasites of some birds from northeastern Mexico

A total of 196 birds of 31 species from 15 families from northeastern Mexico was examined for blood parasites; 25 birds (12.8%) of 11 species harbored 1 or more species of hematozoans. Species of Haemoproteus accounted for half of the total infections encountered. Leucocytozoon simondi was found in 2 Mexico ducks (Anas diazi) and this represents the first record of the transmission of this parasite in Mexico. The results of this survey were compared with those obtained nearly 50 yr ago from a survey of birds from the same general area; prevalence in both samples was similar, despite the change to a more agricultural environment over this period.     

A probabilistic meta-predictor for the MHC class II binding peptides

Several computational methods for the prediction of major histocompatibility complex (MHC) class II binding peptides embodying different strengths and weaknesses have been developed. To provide reliable prediction, it is important to design a system that enables the integration of outcomes from various predictors. The construction of a meta-predictor of this type based on a probabilistic approach is introduced in this paper. The design permits the easy incorporation of results obtained from any number of individual predictors. It is demonstrated that this integrated method outperforms six state-of-the-art individual predictors based on computational studies using MHC class II peptides from 13 HLA alleles and three mouse MHC alleles obtained from the Immune Epitope Database and Analysis Resource. It is concluded that this integrative approach provides a clearly enhanced reliability of prediction. Moreover, this computational framework can be directly extended to MHC class I binding predictions.     

Recent intron gain in elongation factor-1alpha of colletid bees (Hymenoptera: Colletidae)

We discovered the presence of a unique spliceosomal intron in the F1 copy of elongation factor-1alpha (EF-1alpha) restricted to the bee family Colletidae (Hymenoptera: Apoidae). The intron ranges in size from 101 to 1044 bp and shows no positional sliding. Our data also demonstrate the complete absence of this intron from exemplars representing all other bee families, as well as from close hymenopteran relatives. A review of the literature finds that this intron is likewise absent from all other arthropods for which data are available. This provides unambiguous evidence for a relatively recent intron insertion event in the colletid common ancestor and, at least in this specific instance, lends support to the introns-late hypothesis. The comparative distribution of this novel intron also supports the monophyly of Colletidae and the exclusion of the Stenotritidae from this family, providing an example of the potential of some introns to act as robust markers of shared descent.     

T4-Induced Activity Required for Specific Cleavage of a Bacteriophage Protein In Vitro

We have examined the acid-soluble products formed during incubation of labeled substrate protein from T4-infected cells with unlabeled phage-infected cell extracts. If the substrate protein is prepared from cells infected with a T4 mutant blocked in cleavage of phage head precursor proteins, the products formed in vitro include a peptide indistinguishable by several criteria from one of the T4 internal peptides. Denatured as well as undenatured protein can serve as the substrate for the formation of this peptide. As expected, this peptide is not formed if protein from either uninfected cells or cells infected with wild-type T4 is used as substrate. The formation of this peptide in vitro is dependent on a factor present in extracts of phage-infected cells but absent from extracts of uninfected cells.     

Evidence for a novel cryoprotective protein from freeze-tolerant larvae of the goldenrod gall fly Eurosta solidaginis

Third-instar larvae of the goldenrod gall fly Eurosta solidaginis (Diptera: Tephritidae) from populations in northern North America transition from freeze-susceptible to freeze-tolerant just prior to the onset of winter. While studies have documented the accumulation of carbohydrate cryoprotectants during this transition, protein cryoprotectants common to other freeze-tolerant species have not been reported in the gall fly. Using larvae collected from a population in Madison County, NY, which changes from freeze-susceptible to freeze-tolerant in early October, we assayed for the presence of factors that could preserve the catalytic activity of the cold-labile enzyme, rabbit muscle lactate dehydrogenase. Freezing this enzyme with a heat-stable, hydrophilic fraction derived from homogenates of both freeze-tolerant larvae and those in the process of becoming freeze-tolerant preserved between 70% and 80% of this enzyme's activity. Neither a comparable solution of bovine serum albumin nor the naturally-occurring carbohydrates (glycerol, sorbitol, or trehalose) conferred this level of cryoprotection. The putative cryoprotective protein from gall fly larvae did not bind to a weak anion exchanger, implying that its character may be cationic.     

A Hausa Man Makes a Decision: A Contribution to the Anthropological Perspective on Decision-Making

In anthropology, decision-making has mainly been studied from two perspectives: rationalist and ethnographic. These approaches lack a theoretical basis which would integrate their findings in a coherent manner. Taking inspiration from Tugendhat and Berthoz, this article argues that a way out of this impasse is to conceptualise decision-making as an action. At the same time, this conceptualisation allows us to establish a continuum of decision-making processes from simple through complex to fundamental, and to understand these processes as malleable across milieux, societies and cultures. This article also goes beyond this by discussing the decision-making process that led a Hausa villager from Niger to decide not to migrate. This discussion shows that the anthropological literature has largely overlooked a type of decision that could be called a ‘maturing decision’. It also sheds light on the role of emotions in decision-making and on the constitutive role of emic ideas about decision-making in these processes.     

记陕西镇安早更新世的两种爪兽化石

2001年8月,本文作者在地处秦岭腹地的陕西镇安黄家湾一河流相沉积层中采集到大量的哺乳类化石。化石埋藏集中,种类丰富,均为大型哺乳类,不见啮齿类等小型哺乳动物及其他脊椎动物。从埋藏情况看,应属原生层位化石。本文记述了动物群中的2种爪兽类化石。爪兽是奇蹄目中一个较为特殊的类群,我国以前发现的爪兽绝大多数都是在第三纪早期或中期的地层中找到的(胡长康,1959;周明镇,1962;张玉萍,1976;邱占祥等,1998),这次在镇安黄家湾发现的2种爪兽对了解我国爪兽化石的地理及时代分布有一定的价值。     

Assembly of a Marine Viral Metagenome after Physical Fractionation

Metagenomic analyses of marine viruses generate an overview of viral genes present in a sample, but the percentage of the resulting sequence fragments that can be reassembled is low and the phenotype of the virus from which a given sequence derives is usually unknown. In this study, we employed physical fractionation to characterize the morphological and genomic traits of a subset of uncultivated viruses from a natural marine assemblage. Viruses from Kāne‘ohe Bay, Hawai‘i were fractionated by equilibrium buoyant density centrifugation in a cesium chloride (CsCl) gradient, and one fraction from the CsCl gradient was then further fractionated by strong anion-exchange chromatography. One of the fractions resulting from this two-dimensional separation appeared to be dominated by only a few virus types based on genome sizes and morphology. Sequences generated from a shotgun clone library of the viruses in this fraction were assembled into significantly more numerous contigs than have been generated with previous metagenomic investigations of whole DNA viral assemblages with comparable sequencing effort. Analysis of the longer contigs (up to 6.5 kb) assembled from our metagenome allowed us to assess gene arrangement in this subset of marine viruses. Our results demonstrate the potential for physical fractionation to facilitate sequence assembly from viral metagenomes and permit linking of morphological and genomic data for uncultivated viruses.     

Development of genetic techniques for the psychrotrophic fish pathogen Flavobacterium psychrophilum

Flavobacterium psychrophilum, a member of the Cytophaga-Flavobacterium-Bacteroides group, is an important pathogen of salmonid fish. Previous attempts to develop genetic techniques for this fastidious, psychrotrophic bacterium have met with failure. Here we describe the development of techniques for the genetic manipulation of F. psychrophilum and the identification of plasmids, selectable markers, a reporter system, and a transposon that function in several isolates of this fish pathogen. The antibiotic resistance genes ermF, cfxA, and tetQ function in F. psychrophilum. Cloning vectors based on the F. psychrophilum cryptic plasmid pCP1 which carried these selectable markers were introduced by conjugation from E. coli, resulting in antibiotic-resistant colonies of F. psychrophilum. Conjugative transfer of DNA into F. psychrophilum was strain dependent. Efficient transfer was observed for two of the seven strains tested (THC02-90 and THC04-90). E. coli lacZY functioned in F. psychrophilum when expressed from a pCP1 promoter, allowing its development as a reporter for studies of gene expression. Plasmids isolated from F. psychrophilum were efficiently introduced into F. psychrophilum by electroporation, but plasmids isolated from E. coli were not suitable for transfer by this route, suggesting the presence of a restriction barrier. DNA isolated from F. psychrophilum was resistant to digestion by Sau3AI and BamHI, indicating that a Sau3AI-like restriction modification system may constitute part of this barrier. Tn4351 was introduced into F. psychrophilum from E. coli and transposed with apparent randomness, resulting in erythromycin-resistant colonies. The techniques developed in this study allow for genetic manipulation and analysis of this important fish pathogen.     

Reference standards for flow cytometry and application in comparative studies of nuclear DNA content

Nuclear DNA mass in cells from a reference species can be used to obtain high-resolution estimates of DNA mass from a target species. In our study of DNA mass in cells from 45 selected species, representing each of the major vertebrate classes, we have obtained values of from 1.5 to 110.0 pg of DNA. Because values in or near this range would be expected in the study of nuclear DNA mass in vertebrates and other organisms, the species in this report can provide a useful catalogue of references for comparative studies of DNA.     

Endemism,palaeoendemism and migration: the case for the ‘European endemic’, Mallomonas intermedia

The Synurophyceae is a well-supported clade of ecologically important heterokont algae found largely in freshwater planktonic habitats worldwide, whose members have cell coverings consisting of species-specific siliceous scales overlapped in a highly organized manner. Many synurophytes have been described as endemic and are found only in specific regions of the world. A thriving population of the European endemic, Mallomonas intermedia, was discovered in a remote desert pond situated in the Virgin Valley, Nevada, USA and in a stratigraphic sequence from the middle Eocene fossil locality known as Horsefly in British Columbia, Canada. Both North American finds were closely compared with populations from Europe, confirming the identifications. Before these discoveries, this species was recorded from numerous waterbodies exclusively in Europe, but was lacking from hundreds of sites examined from other continents. Its presence in western North America during the warm middle Eocene confirms that historically this species had a significantly wider distribution and may be best classified as a palaeoendemic. Additional species uncovered from a second fossil locality that are closely related to M. intermedia further support the presence of this lineage in North America during the Eocene. The living population in northern Nevada presents an enigma. Does this remote desert population represent a remnant population that has gone undetected until now, or is it a recent arrival from an unknown region by an unknown vector?     

A molecular basis for familial hypertrophic cardiomyopathy: a beta cardiac myosin heavy chain gene missense mutation

A point mutation in exon 13 of the beta cardiac myosin heavy chain (MHC) gene is present in all individuals affected with familial hypertrophic cardiomyopathy (FHC) from a large kindred. This missense mutation converts a highly conserved arginine residue (Arg-403) to a glutamine. Affected individuals from an unrelated family lack this missense mutation, but instead have an alpha/beta cardiac MHC hybrid gene. Identification of two unique mutations within cardiac MHC genes in all individuals with FHC from two unrelated families demonstrates that defects in the cardiac MHC genes can cause this disease. The pathology resulting from a missense mutation at residue 403 further suggests that a critical function of myosin is disrupted by this mutation.