Binocular fusion in Panum’s limiting case of stereopsis obeys the uniqueness constraint

In the information processing procedure of stereo vision, the uniqueness constraint has been used as one of the constraints to solve the “correspondence problem”. While the uniqueness constraint is valid in most cases, whether it is still valid in some particular stimulus configuration (such as Panum’s limiting case) has been a problem of widespread debate for a long time. To investigate the problem, we adopted the Panum’s limiting case as its basic stimulus configuration, and delved into the phenomenon of binocular fusion from two distinct aspects: visual direction and orientation disparity. The results show that in Panum’s limiting case binocular fusion does not comply with the rules governing regular binocular fusion as far as visual direction and orientation disparity are concerned. This indicates that double fusion does not happen in Panum’s limiting case and that the uniqueness constraint is still valid.     

Binocular fusion in Panum’s limiting case of stereopsis obeys the uniqueness constraint

In the information processing procedure of stereo vision, the uniqueness constraint has been used as one of the constraints to solve the “correspondence problem”. While the uniqueness constraint is valid in most cases, whether it is still valid in some particular stimulus configuration (such as Panum’s limiting case) has been a problem of widespread debate for a long time. To investigate the problem, we adopted the Panum’s limiting case as its basic stimulus configuration, and delved into the phenomenon of binocular fusion from two distinct aspects: visual direction and orientation disparity. The results show that in Panum’s limiting case binocular fusion does not comply with the rules governing regular binocular fusion as far as visual direction and orientation disparity are concerned. This indicates that double fusion does not happen in Panum’s limiting case and that the uniqueness constraint is still valid.     

Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota

The evolutionary origin of “orphan” genes, genes that lack sequence similarity to any known gene, remains a mystery. One suggestion has been that most orphan genes evolve rapidly so that similarity to other genes cannot be traced after a certain evolutionary distance. This can be tested by examining the divergence rates of genes with different degrees of lineage specificity. Here the lineage specificity (LS) of a gene describes the phylogenetic distribution of that gene’s orthologues in related species. Highly lineage-specific genes will be distributed in fewer species in a phylogeny. In this study, we have used the complete genomes of seven ascomycotan fungi and two animals to define several levels of LS, such as Eukaryotes-core, Ascomycota-core, Euascomycetes-specific, Hemiascomycetes-specific, Aspergillus-specific, and Saccharomyces-specific. We compare the rates of gene evolution in groups of higher LS to those in groups with lower LS. Molecular evolutionary analyses indicate an increase in nonsynonymous nucleotide substitution rates in genes with higher LS. Several analyses suggest that LS is correlated with the evolutionary rate of the gene. This correlation is stronger than those of a number of other factors that have been proposed as predictors of a gene’s evolutionary rate, including the expression level of genes, gene essentiality or dispensability, and the number of protein-protein interactions. The accelerated evolutionary rates of genes with higher LS may reflect the influence of selection and adaptive divergence during the emergence of orphan genes. These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Martin Kreitman]     

Mycetoma caused by Fusarium solani with osteolytic lesions on the hand: case report

Eumycetoma is a mycotic disease caused by saprophytic soil fungi that are usually inoculated through minor injuries. A case of mycetoma in a Brazilian farmer aged71 years is reported. This patient presented erythema and edema on the dorsal surface of the left hand with multiple crusted and cicatricial lesions. No macroscopic grains were observed. The histopathological findings showed grains consisted of numerous hyphae which stained well with Gomori-Grocott method. This material obtained by cutaneous biopsy was submitted to culture on Sabouraud’s medium and the colonies were identified as Fusarium solani. The radiological studies revealed bone osteolytic lesions and the ultrasound showed pseudocysts and fistulae at the site of this infection. The patient was treated with oral ketoconazole with a good clinical response. This revised version was published online in June 2006 with corrections to the Cover Date.     

Reciprocal interactions between Scots pine and soil food web structure in the presence and absence of ectomycorrhiza

Mycorrhizal plants are commonly believed to direct much more of their photosynthates into the soil than non-mycorrhizal plants. As the growth of most organisms of the detrital food web is limited by energy, the flow of C through mycorrhizal plants into the below-ground milieu is widely assumed to nourish a variety of decomposer organisms in soils. In the current experiment, I explored whether some representatives of soil mesofauna, either fungivores or microbi-detritivores, derive benefit from the presence of ectomycorrhizal (EM) fungi growing on the roots of Scots pine (Pinus sylvestris). I also investigated whether the role of soil mesofauna in affecting pine growth depends on the presence of EM fungi in the pine rhizosphere. The study was established in microcosms with a mixture of raw humus and sand. The soil was defaunated, reinoculated with 10 species of soil bacteria and 11 species of saprophytic soil fungi, and pine seedlings, either infected or non-infected with four taxa of EM fungi, were planted in the microcosms. Five treatments with different food web configurations were established: (1) saprophytic microbes alone, (2) as (1) but with the omnivorous enchytraeid species Cognettia sphagnetorum present, (3) as (1) but with Collembola (Hypogastrura assimilis), (4) as (1) but with four species of oribatid mites (Acari) involved, and (5) as 1) but with C. sphagnetorum, H. assimilis and the Acari. The microcosms were incubated in a climate chamber with varying temperature and illumination regimes for two growing periods for the pine. After 60 weeks, pine biomass production was significantly greater in the mycorrhizal systems, the total biomass being 1.43 times higher in the presence than absence of EM fungi. Similarly, almost ten times more fungal biomass was detected on pine roots growing in the mycorrhizal than in the non-mycorrhizal systems. The presence of EM fungi was also associated with significantly lowered pH and percent organic matter of the soil. Despite the clearly larger biomass of both the pines and the fungi on the pine roots, neither the numbers nor biomasses of the mesofauna differed significantly between the EM and non-EM systems. The presence of Collembola and C. sphagnetorum had a positive influence on pine growth, particularly in the absence of EM fungi, whereas oribatid mites had no effects on pine growth. The complexity of the mesofaunal community was not related to the biomass production of the pines in a straightforward manner; for example, the complex systems with each faunal group present did not produce more pine biomass than the simple systems where C. sphagnetorum existed alone. The results of this experiment suggest that the short-term role of EM fungi in fuelling the detrital food web is less significant than generally considered, but that their role as active decomposers and/or stimulators of the activity of saprophytic microbes can be more important than is often believed. Received: 22 December 1999 / Accepted: 14 April 2000     

A differential equation model for functional mapping of a virus-cell dynamic system

The dynamic pattern of viral load in a patient’s body critically depends on the host’s genes. For this reason, the identification of those genes responsible for virus dynamics, although difficult, is of fundamental importance to design an optimal drug therapy based on patients’ genetic makeup. Here, we present a differential equation (DE) model for characterizing specific genes or quantitative trait loci (QTLs) that affect viral load trajectories within the framework of a dynamic system. The model is formulated with the principle of functional mapping, originally derived to map dynamic QTLs, and implemented with a Markov chain process. The DE-integrated model enhances the mathematical robustness of functional mapping, its quantitative prediction about the temporal pattern of genetic expression, and therefore its practical utilization and effectiveness for gene discovery in clinical settings. The model was used to analyze simulated data for viral dynamics, aimed to investigate its statistical properties and validate its usefulness. With an increasing availability of genetic polymorphic data, the model will have great implications for probing the molecular genetic mechanism of virus dynamics and disease progression.     

INDeGenIUS,a new method for high-throughput identification of specialized functional islands in completely sequenced organisms

Genomic islands (GIs) are regions in the genome which are believed to have been acquired via horizontal gene transfer events and are thus likely to be compositionally distinct from the rest of the genome. Majority of the genes located in a GI encode a particular function. Depending on the genes they encode, GIs can be classified into various categories, such as ‘metabolic islands’, ‘symbiotic islands’, ‘resistance islands’, ‘pathogenicity islands’, etc. The computational process for GI detection is known and many algorithms for the same are available. We present a new method termed as Improved N-mer based Detection of Genomic Islands Using Sequence-clustering (INDeGenIUS) for the identification of GIs. This method was applied to 400 completely sequenced species belonging to proteobacteria. Based on the genes encoded in the identified GIs, the GIs were grouped into 6 categories: metabolic islands, symbiotic islands, resistance islands, secretion islands, pathogenicity islands and motility islands. Several new islands of interest which had previously been missed out by earlier algorithms were picked up as GIs by INDeGenIUS. The present algorithm has potential application in the identification of functionally relevant GIs in the large number of genomes that are being sequenced. Investigation of the predicted GIs in pathogens may lead to identification of potential drug/vaccine candidates.     

Post-Haeckelian comparative biology — Adolf Naef’s idealistic morphology

Summary The present study describes the conceptual framework of Adolf Naef’s idealistic morphology as presented at the onset of the 20^th century. According to Naef, Haeckel’s and Gegenbaur’s approaches towards a phylogenetic biology were insufficient. He made it clear that Haeckel’s ideas were based on typological morphology. Thus, Haeckel’s views on comparative biology pointed back to pre-Darwinian concepts. Naef’s consequence was not to work out his own evolutionary morphology but to systematize the earlier typological concept. Consequently, he separated comparative morphology from phylogenetic studies. This idea was adopted by Hennig and was even imported into modern cladism.     

Ectomycorrhizal colonization slows root decomposition: the post-mortem fungal legacy

The amount of carbon plants allocate to mycorrhizal symbionts exceeds that emitted by human activity annually. Senescent ectomycorrhizal roots represent a large input of carbon into soils, but their fate remains unknown. Here, we present the surprising result that, despite much higher nitrogen concentrations, roots colonized by ectomycorrhizal (EM) fungi lost only one-third as much carbon as non-mycorrhizal roots after 2 years of decomposition in a piñon pine ( Pinus edulis ) woodland. Experimentally excluding live mycorrhizal hyphae from litter, we found that live mycorrhizal hyphae may alter nitrogen dynamics, but the afterlife (litter-mediated) effects of EM fungi outweigh the influences of live fungi on root decomposition. Our findings indicate that a shift in plant allocation to mycorrhizal fungi could promote carbon accumulation in soil by this pathway. Furthermore, EM litters could directly contribute to the process of stable soil organic matter formation, a mechanism that has eluded soil scientists.     

The Coevolution of Genes and Genetic Codes: Crick’s Frozen Accident Revisited

The standard genetic code is the nearly universal system for the translation of genes into proteins. The code exhibits two salient structural characteristics: it possesses a distinct organization that makes it extremely robust to errors in replication and translation, and it is highly redundant. The origin of these properties has intrigued researchers since the code was first discovered. One suggestion, which is the subject of this review, is that the code’s organization is the outcome of the coevolution of genes and genetic codes. In 1968, Francis Crick explored the possible implications of coevolution at different stages of code evolution. Although he argues that coevolution was likely to influence the evolution of the code, he concludes that it falls short of explaining the organization of the code we see today. The recent application of mathematical modeling to study the effects of errors on the course of coevolution, suggests a different conclusion. It shows that coevolution readily generates genetic codes that are highly redundant and similar in their error-correcting organization to the standard code. We review this recent work and suggest that further affirmation of the role of coevolution can be attained by investigating the extent to which the outcome of coevolution is robust to other influences that were present during the evolution of the code. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Martin Kreitman]     

Further advances in orchid mycorrhizal research

Orchid mycorrhizas are mutualistic interactions between fungi and members of the Orchidaceae, the world’s largest plant family. The majority of the world’s orchids are photosynthetic, a small number of species are myco-heterotrophic throughout their lifetime, and recent research indicates a third mode (mixotrophy) whereby green orchids supplement their photosynthetically fixed carbon with carbon derived from their mycorrhizal fungus. Molecular identification studies of orchid-associated fungi indicate a wide range of fungi might be orchid mycobionts, show common fungal taxa across the globe and support the view that some orchids have specific fungal interactions. Confirmation of mycorrhizal status requires isolation of the fungi and restoration of functional mycorrhizas. New methods may now be used to store orchid-associated fungi and store and germinate seed, leading to more efficient culture of orchid species. However, many orchid mycorrhizas must be synthesised before conservation of these associations can be attempted in the field. Further gene expression studies of orchid mycorrhizas are needed to better understand the establishment and maintenance of the interaction. These data will add to efforts to conserve this diverse and valuable association.     

Characterization of the carbohydrase productions of an ectomycorrhizal fungus, Tricholoma matsutake

To evaluate the potential of the production of the ectomycorrhizal fungus Tricholoma matsutake to produce carbohydrases, (1) the distribution of carbohydrase activities among the different strains (18 strains) was investigated and (2) the abilities of T. matsutake and saprophytic fungi to produce β-glucosidase were compared. The results showed that the carbohydrase productions patterns of T. matsutake still resemble one another. Moreover, this fungus exhibited markedly higher β-glucosidase than did the saprophytic mushrooms. Tricholoma matsutake showed weak production of α-amylase and α-glucosidase in a static cultur filtrate. On the other hand, glucoamylase activity was not observed. Surprisingly, we discovered that β-glucosidase demonstrated strong activity. This finding suggests that this fungus has saprotrophic abilities. The carbohydrase production systems in T. matsutake were characterized from our experimental results. Also, we point out some weak points in the carbohydrase production systems of T. matsutake.     

A gene’s eye view of Darwinian populations

Biologists and philosophers differ on whether selection should be analyzed at the level of the gene or of the individual. In Peter Godfrey-Smith’s book, Darwinian Populations and Natural Selection, he argues that individuals can be good members of Darwinian populations, whereas genes rarely can. I take issue with parts of this view, and suggest that Godfrey-Smith’s scheme for thinking about Darwinian populations is also applicable to populations of genes.     

Regulation of the external mycoflora of the giant Madagascar hissing-cockroach,gromphadorhina portentosa, by its mite associate,gromphadorholaelaps schaeferi, and its implications on human health

The giant Madagascar hissing-cockroach,Gromphadorhina portentosa, and its mite associate,Gromphadorholaelaps schaeferi, constitute an intimate commensalistic symbiosis. While the mite’s very survival is dependent by feeding on cockroach saliva and associated organic debris, the degree that the cockroach benefits from this association is unclear. We investigated the mite’s potential role at regulating surface fungi on the exoskeletons of this insect. Numbers of fungal isolates that resulted were compared between captive-bred cockroaches with and without mites. The mycoflora of both groups consisted of common molds (Alternaria sp.,Aspergillus sp.,Cladosporium sp.,Geotrichum sp.,Mucor sp.,Penicillium sp.,Rhizopus sp.,Trichoderma sp.). The presence of mites reduced the number of isolates by 1/2 in mature females, 1/3 in males, and 1/4 in sixth (final) instar nymphs. Fungus levels continued to drop when mite-free cockroaches were artificially supplemented with mites. A direct correlation was detected between mites and the reduction in the quantity of surface molds up to 20 mites per cockroach. The addition of more mites above 20 per cockroach, even 4x more, had a minimal, but still reducing, effect. Mites regulated all types of fungi, not just a select few taxa. We propose that mites reduce the mycoflora not because they consume fungi, but because mites and molds compete for the same resources in an ecological niche, saliva and organic debris that accumulate in between cockroach’s legs. Cockroaches reared in captivity do not apparently benefit by the removal of surface molds by mites, lending support for a commensalistic symbiosis. This cockroach species has been linked to severe allergic reactions in children, in part, because it harbors antagonistic molds. GivenG. schaeferi’s regulatory role at suppressing fungi, these mites could conceivably impose a small indirect, albeit beneficial role to humans by reducing the amount of fungal inoculum (conidia) that might otherwise be inhaled.     

Mutant Bacteriophages,Frank Macfarlane Burnet,and the Changing Nature of “Genespeak” in the 1930s

In 1936, Frank Macfarlane Burnet published a paper entitled “Induced lysogenicity and the mutation of bacteriophage within lysogenic bacteria,” in which he demonstrated that the introduction of a specific bacteriophage into a bacterial strain consistently and repeatedly imparted a specific property – namely the resistance to a different phage – to the bacterial strain that was originally susceptible to lysis by that second phage. Burnet’s explanation for this change was that the first phage was causing a mutation in the bacterium which rendered it and its successive generations of offspring resistant to lysogenicity. At the time, this idea was a novel one that needed compelling evidence to be accepted. While it is difficult for us today to conceive of mutations and genes outside the context of DNA as the physico-chemical basis of genes, in the mid 1930s, when this paper was published, DNA’s role as the carrier of hereditary information had not yet been discovered and genes and mutations were yet to acquire physical and chemical forms. Also, during that time genes were considered to exist only in organisms capable of sexual modes of replication and the status of bacteria and viruses as organisms capable of containing genes and manifesting mutations was still in question. Burnet’s paper counts among those pieces of work that helped dispel the notion that genes, inheritance and mutations were tied to an organism’s sexual status. In this paper, I analyze the implications of Burnet’s paper for the understanding of various concepts – such as “mutation,” and “gene,” – at the time it was published, and how those understandings shaped the development of the meanings of these terms and our modern conceptions thereof.     

Evidence for mutualist limitation: the impacts of conspecific density on the mycorrhizal inoculum potential of woodland soils

The ability of seedlings to establish can depend on the availability of appropriate mycorrhizal fungal inoculum. The possibility that mycorrhizal mutualists limit the distribution of seedlings may depend on the prevalence of the plant hosts that form the same type of mycorrhizal association as the target seedling species and thus provide inoculum. We tested this hypothesis by measuring ectomycorrhizal (EM) fine root distribution and conducting an EM inoculum potential bioassay along a gradient of EM host density in a pinyon–juniper woodland where pinyon is the only EM fungal host while juniper and other plant species are hosts for arbuscular mycorrhizal (AM) fungi. We found that pinyon fine roots were significantly less abundant than juniper roots both in areas dominated aboveground by juniper and in areas where pinyon and juniper were co-dominant. Pinyon seedlings establishing in pinyon–juniper zones are thus more likely to encounter AM than EM fungi. Our bioassay confirmed this result. Pinyon seedlings were six times less likely to be colonized by EM fungi when grown in soil from juniper-dominated zones than in soil from either pinyon–juniper or pinyon zones. Levels of EM colonization were also reduced in seedlings grown in juniper-zone soil. Preliminary analyses indicate that EM community composition varied among sites. These results are important because recent droughts have caused massive mortality of mature pinyons resulting in a shift towards juniper-dominated stands. Lack of EM inoculum in these stands could reduce the ability of pinyon seedlings to re-colonize sites of high pinyon mortality, leading to long-term vegetation shifts.     

Why aren’t we all hutterites?

In this paper I explore the psychology of ritual performance and present a simple graphical model that clarifies several issues in William Irons’s theory of religion as a “hard-to-fake” sign of commitment. Irons posits that religious behaviors or rituals serve as costly signals of an individual’s commitment to a religious group. Increased commitment among members of a religious group may facilitate intra-group cooperation, which is argued to be the primary adaptive benefit of religion. Here I propose a proximate explanation for how individuals are able to pay the short-term costs of ritual performance to achieve the long-term fitness benefits offered by religious groups. The model addresses three significant problems raised by Irons’s theory. First, the model explains why potential free-riders do not join religious groups even when there are significant net benefits that members of religious groups can achieve. Second, the model clarifies how costly a ritual must be to achieve stability and prevent potential free-riders from joining the religious group. Third, the model suggests why religious groups may require adherents to perform private rituals that are not observed by others. Several hypotheses generated from the model are also discussed. Richard Sosis is an assistant professor of anthropology at the University of Connecticut. His research interests include the evolution of cooperation, utopian societies, and the behavioral ecology of religion. In collaboration with Bradley Ruffle (Ben Gurion University) he is currently investigating the impact of privatization and religiosity on intra-group trust within Israeli Kibbutzim.     

Ontogenetic allometry of the bluemouth, <Emphasis Type="Italic">Helicolenus dactylopterus dactylopterus</Emphasis> (Teleostei: Scorpaenidae), in the Northeast Atlantic and Mediterranean based on geometric morphometrics

Since the emergence of the ‘microbial loop’ concept, heterotrophic flagellates have received particular attention as grazers in aquatic ecosystems. These microbes have historically been regarded incorrectly as a homogeneous group of bacterivorous protists in aquatic systems. More recently, environmental rDNA surveys of small heterotrophic flagellates in the pelagic zone of freshwater ecosystems have provided new insights. (i) The dominant phyla found by molecular studies differed significantly from those known from morphological studies with the light microscope, (ii) the retrieved phylotypes generally belong to well-established eukaryotic clades, but there is a very large diversity within these clades and (iii) a substantial part of the retrieved sequences cannot be assigned to bacterivorous but can be assigned instead to parasitic and saprophytic organisms, such as zoosporic true fungi (chytrids), fungus-like organisms (stramenopiles), or virulent alveolate parasites (Perkinsozoa and Amoebophrya sp.). All these microorganisms are able to produce small zoospores to assure dispersal in water during their life-cycles. Based on the existing literature on true fungi and fungus-like organisms, and on the more recently published eukaryotic rDNA environmental studies and morphological observations, we conclude that previously overlooked microbial diversity and related ecological potentials require intensive investigation (i) for an improved understanding of the roles of heterotrophic flagellates in pelagic ecosystems and (ii) to properly integrate the concept of ‘the microbial loop’ into modern pelagic microbial ecology.