Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)

The 2010 International Conference on Bioinformatics, InCoB2010, which is the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet) has agreed to publish conference papers in compliance with the proposed Minimum Information about a Bioinformatics investigation (MIABi), proposed in June 2009. Authors of the conference supplements in BMC Bioinformatics, BMC Genomics and Immunome Research have consented to cooperate in this process, which will include the procedures described herein, where appropriate, to ensure data and software persistence and perpetuity, database and resource re-instantiability and reproducibility of results, author and contributor identity disambiguation and MIABi-compliance. Wherever possible, datasets and databases will be submitted to depositories with standardized terminologies. As standards are evolving, this process is intended as a prelude to the 100 BioDatabases (BioDB100) initiative whereby APBioNet collaborators will contribute exemplar databases to demonstrate the feasibility of standards-compliance and participate in refining the process for peer-review of such publications and validation of scientific claims and standards compliance. This testbed represents another step in advancing standards-based processes in the bioinformatics community which is essential to the growing interoperability of biological data, information, knowledge and computational resources.     

Roche Susceptibility Test (RST) medium,a defined formulation for susceptibility testing: I. Nutrient interaction and optimization studies

Roche Susceptibility Test (RST) Medium represents the most completely optimized and convenient fully defined medium described. It requires no post-autoclaving supplementation with vitamins, supports good growth of all common aerobic and anaerobic pathogens and may be used as a broth or agar gel on which the swarming of Proteus spp. is virtually eliminated. The broth as a superior buffering capacity to most complex media and an osmolality and pH close to those of human serum. RST is highly satisfactory for the susceptibility testing of commonly used antibiotics and meets the requirements of the National Committe for Clinical Laboratory Standards of the U.S.A. in almost every respect.     

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).     

Cryptic diversity within the Moroccan endemic day geckos Quedenfeldtia (Squamata: Gekkonidae): a multidisciplinary approach using genetic,morphological and ecological data

Quedenfeldtia (Boettger, 1883) is a genus of diurnal geckos, endemic to the Atlas Mountains in Morocco, with two species being recognized: Quedenfeldtia moerens and Quedenfeldtia trachyblepharus. Quedenfeldtia moerens is found across a wide variety of habitats, from sea level to 3000 m a.s.l., whereas Q. trachyblepharus occupies exclusively high mountain regions reaching up to 4000 m a.s.l. This differentiation, offers an interesting model for study biogeographical patterns and evolutionary scenarios in a North African endemic. Analysis of two mitochondrial (12S rRNA and ND4) and four nuclear (ACM4, MC1R, PDC, and Rag1) DNA markers revealed high genetic variation, consistent with other recent phylogeographical studies, and with the two currently described species. However, within each species, a subdivision into two groups with geographical consistence was found. Multivariate morphological analyses confirmed the existence of two main phenotypes, whereas ecological niche modelling identified various environmental variables associated with the distribution of each species, and helped to predict occurrences outside the confirmed ranges. The results obtained in the present study indicate the possible existence of additional ‘cryptic’ species within this genus, a condition found in many North African reptiles, and particularly common in geckos. In general, North African montane fauna appears to reflect the occurrence of diverse palaeoendemics, as seen in Central Africa Mountain systems, rather than the pattern of recent postglacial recolonization observed in Europe. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Input data needed for a risk model for the entry,establishment and spread of a pathogen (Phomopsis vaccinii) of blueberries and cranberries in the EU

International trade in live plant materials has increased worldwide over the last four decades. This has led to a dramatic increase in the introduction, establishment and spread of non‐native plant pathogens. Regulatory authorities need advice on measures that may mitigate these adverse consequences of trade. Risk models may be used to underpin such advice. In this review, we give a systematic overview of the data needed for a quantitative risk model for Phomopsis vaccinii, which causes stem and fruit infections on Vaccinium species, and sometimes death, potentially also on native wild Vaccinium species in the EU. P. vaccinii is a quarantine organism worldwide, except for North America, where it is endemic. Despite extensive knowledge of the aetiology of the diseases caused by this pathogen and its taxonomy, quantitative data on transportation and detection of infected plants for planting and berries are scarce, and quantitative assessment of the future introduction, establishment and spread of P. vaccinii is difficult. Estimation of the potential impact of this pathogen in production fields and wild Vaccinium stands is even more difficult. P. vaccinii is not unique in this respect, and this review indicates the need for more and better quantitative data for assessment of the risks posed by newly introduced plant pathogens in areas where they are not endemic.     

Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree

It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRNA, 16S rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2.2kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira-Hasegawa tests, with the (P. platyrhinos+P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcalliixP. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: (1) Tapaja, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; (2) Anota, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); (3) Doliosaurus, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and (4) Brevicauda, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus).     

Large net cage for captive breeding and behavioural studies of damselfly Lestes sponsa (Hansemann, 1823) (Odonata: Lestidae): submerged oviposition as a model behaviour

Odonata have a strong potential as model organisms for testing ecological and evolutionary hypotheses because of their short life history, relative ease and cost-effectiveness of care. Unfortunately, very few studies have examined how to create a semi-natural environment for odonates, limiting the biological validity of laboratory manipulation. To better study odonate life cycle and behaviour under controlled conditions, we designed a large net cage that imitated the natural terrestrial as well as aquatic habitat of the damselfly Lestes sponsa (Hansemann, 1823). This species is thought to be capable of submerged oviposition, an unusual behaviour in odonates. We compared multiple variables across natural conditions and the net cage. We demonstrated that between-year variability under natural conditions was generally greater than variability between natural and artificial environments. Overall, semi-natural conditions did not substantially change the L. sponsa life cycle (including the unique behaviour of submerged oviposition), suggesting that results from the net cage are likely generalisable to the field.     

Common ringtail possum (Pseudocheirus peregrinus) as a management model for the Pseudocheiridae: Reproductive scope,behavior, and biomedical values on a browse-free diet

The purposes of this study were to determine 1) the life history characteristics of a captive colony of the arboreal folivore Pseudocheirus peregrinus maintained on a browse free diet under enhanced laboratory conditions, 2) the direction and magnitude of life history differences from wild population values, and 3) the feasibility of developing captive colonies of this and related species for conservation and research programs. Rates of reproduction, growth, and development; demographic trends; behavioral patterns pertinent to exhibition; and management and medical techniques are reported. Fecundity was 67% greater than that of wild populations and there was an approximate four-fold increase in the rate of offspring survival to sexual maturity. These trends were due largely to reduced post-pouch emergence mortality and the decay of reproductive seasonality. The results indicate that a properly designed “artificial” diet can support significantly enhanced reproduction in a trophic specialist. Other demographic, developmental, and behavioral measures found to be consistent with those reported from wild populations indicate that there was no significant life history distortion caused by the management regime. Empirical data are presented showing that the common ringtail is nocturnal, has low rates of activity, and has specific space and substrate preferences. These results suggest ways in which the animals' physical environment can be manipulated to improve exhibition. We conclude that the reproductive rates of other ringtail possum species might also be enhanced under comparable management conditions.     

Morphological changes of skeletal muscle, tendon and periosteum in the senescence-accelerated mouse (SAMP6): a murine model for senile osteoporosis

SAMP6, a substrain of senescence-accelerated mouse, was developed as an animal model for senile osteoporosis. Previously we observed age-related changes of the bone in SAMP6. In the present study, we investigated the morphology of the skeletal muscle, tendon and periosteum in SAMP6 and age-matched normal mouse SAMR1. We did not find any significant differences between SAMR1 and SAMP6 at 1 and 2 months of age. As compared with SAMR1, the cross-sectional area of type I and type II muscle fibers of the soleus muscle were significantly low in SAMP6 at 8 months of age. The projections in the interface of the muscle-tendon junctions were significantly decreased in SAMP6 at 8 months of age. The number of fibroblasts and the diameter of the tendon collagen fibers in Achilles fiber were significantly reduced in SAMP6 at 8 months of age. The diameter of Sharpey's fiber reduced in SAMP6 at 5 and 8 months of age. Some chondrocytes in the insertions of Achilles tendon and some osteogenic cells in the periosteum showed degenerative changes in SAMP6 at 5 and 8 months of age. The pronounced degenerative changes were detected in the skeletal muscle, muscle-tendon junction, tendon, tendon-bone interface and periosteum in SAMP6 with age. These findings indicated the atrophy of skeletal muscle, degeneration of tendon and periosteum in SAMP6, which may be involved in the bone loss for senile osteoporosis.     

Developing a land evaluation model for faba bean cultivation using geographic information system and multi-criteria analysis (A case study: Gonbad-Kavous region,Iran)

This study was carried out to assess the land suitability for rainfed faba bean (Vicia faba L.) cultivation in Gonbad-Kavous region (Golestan province, north of Iran) using geographic information system (GIS) and analytical hierarchy process (AHP), the most common methods for evaluation of land use suitability. Several parameters were considered in this study, including the annual average, minimum and maximum temperatures, annual precipitation, slope, elevation, and some soil properties such as organic matter, pH, EC, texture, phosphorus, potassium, calcium, iron, and zinc. The environmental parameters and the classification system used in the this work are inspired by the United Nations Food and Agriculture Organization (FAO) method dedicated to land suitability. In determining the weights of parameters, expert opinions were consulted and the final land suitability map was generated in five classes. As evidenced by the results, it was estimated that 23.48% of the study area (48,354.5 ha) is highly suitable for faba bean cropping, while 25.38% (52,237.37 ha) is moderately suitable and 25.03% (51,522.85 ha) is marginally suitable. In addition, our results indicated that just 26.11% of total agricultural lands are non-suitable for crop production. The currently non-suitable (49,778.80 ha) and permanently non-suitable (3997.09 ha) classes are located in the north and northwest parts of Gonbad-Kavous township. Soil salinity, low organic matter, low precipitation, high Ca content, and deficiency of P and Fe contents were found to be key limiting factors in this area.     

Rearing the pale grass blue Zizeeria maha (Lepidoptera,Lycaenidae): Toward the establishment of a lycaenid model system for butterfly physiology and genetics

Although some nymphalid butterflies have been intensively used to study mechanisms of the colour pattern formation on butterfly wings, lycaenid butterflies are equally attractive, having easily identifiable distinct spot patterns and highly diverse colour patterns among species. To establish a lycaenid model system for physiological and genetic experiments, we here describe a series of methods for rearing the Japanese pale grass blue Zizeeria maha (Kollar) (Lepidoptera, Lycaenidae) in a small laboratory space with an artificial diet for generations. Adult individuals readily mated and oviposited in a small cage with sufficient light, flowers, and host plants. Eggs were harvested in the cage, and larvae were successfully reared to normal adults with an artificial diet made from fresh leaves (AD‐F), although they were smaller than those reared with a natural diet. Feeding an artificial diet made from dried leaves (AD‐D) frequently produced adult individuals with aberrant wing colour patterns. Using our rearing methods, it is now possible to rear this species in a laboratory and to establish specific strains for physiological and genetic experiments on the wing colour pattern development, diversity, and evolution.     

Compilation of morphological and molecular data,a necessity for taxonomy: The case of Hormogaster abbatissae sp. n. (Annelida,Clitellata, Hormogastridae)

Conflict among data sources can be frequent in evolutionary biology, especially in cases where one character set poses limitations to resolution. Earthworm taxonomy, for example, remains a challenge because of the limited number of morphological characters taxonomically valuable. An explanation to this may be morphological convergence due to adaptation to a homogeneous habitat, resulting in high degrees of homoplasy. This sometimes impedes clear morphological diagnosis of species. Combination of morphology with molecular techniques has recently aided taxonomy in many groups difficult to delimit morphologically. Here we apply an integrative approach by combining morphological and molecular data, including also some ecological features, to describe a new earthworm species in the family Hormogastridae, Hormogaster abbatissae sp. n., collected in Sant Joan de les Abadesses (Girona, Spain). Its anatomical and morphological characters are discussed in relation to the most similar Hormogastridae species, which are not the closest species in a phylogenetic analysis of molecular data. Species delimitation using the GMYC method and genetic divergences with the closest species are also considered. The information supplied by the morphological and molecular sources is contradictory, and thus we discuss issues with species delimitation in other similar situations. Decisions should be based on a profound knowledge of the morphology of the studied group but results from molecular analyses should also be considered.     

Brief communication: Reaction to fire by savanna chimpanzees (Pan troglodytes verus) at Fongoli,Senegal: Conceptualization of “fire behavior” and the case for a chimpanzee model

The use and control of fire are uniquely human traits thought to have come about fairly late in the evolution of our lineage, and they are hypothesized to correlate with an increase in intellectual complexity. Given the relatively sophisticated cognitive abilities yet small brain size of living apes compared to humans and even early hominins, observations of wild chimpanzees' reactions to naturally occurring fire can help inform hypotheses about the likely responses of early hominins to fire. We use data on the behavior of savanna chimpanzees (Pan troglodytes verus) at Fongoli, Senegal during two encounters with wildfires to illuminate the similarities between great apes and humans regarding their reaction to fire. Chimpanzees' close relatedness to our lineage makes them phylogenetically relevant to the study of hominid evolution, and the open, hot and dry environment at Fongoli, similar to the savanna mosaic thought to characterize much of hominid evolution, makes these apes ecologically important as a living primate model as well. Chimpanzees at Fongoli calmly monitor wildfires and change their behavior in anticipation of the fire's movement. The ability to conceptualize the “behavior” of fire may be a synapomorphic trait characterizing the human‐chimpanzee clade. If the cognitive underpinnings of fire conceptualization are a primitive hominid trait, hypotheses concerning the origins of the control and use of fire may need revision. We argue that our findings exemplify the importance of using living chimpanzees as models for better understanding human evolution despite recently published suggestions to the contrary. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.