ISMB 2003 Bio-ontologies SIG and Sixth Annual Bio-ontologies Meeting Report

The Annual Bio-Ontologies meeting (http://www.cs.man.ac.uk/ stevens/meeting03/) has now been running for 6 consecutive years, as a special interest group (SIG) of the much larger ISMB conference. It met in Brisbane, Australia, this summer, the first time it was held outside North America or Europe. The bio-ontologies meeting is 1 day long and normally has around 100 attendees. This year there were many fewer, no doubt a result of the distance, global politics and SARS. The meeting consisted of a series of 30 min talks with no formal peer review or publication. Talks ranged in style from fairly formal and complete pieces of work, through works in progress, to the very informal and discursive. Each year's meeting has a theme and this year it was 'ontologies, and text processing'. There is a tendency for those submitting talks to ignore the theme completely, but this year's theme obviously struck a chord, as half the programme was about ontologies and text analysis (http://www.cs.man.ac.uk/ stevensr/meeting03/programme.html). Despite the smaller size of the meeting, the programme was particularly strong this year, meaning that the tension between allowing time for the many excellent talks, discussion and questions from the floor was particular keenly felt. A happy problem to have!     

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010

This report summarizes the proceedings of the first day of the Metagenomics, Metadata and MetaAnalysis (M3) workshop held at the Intelligent Systems for Molecular Biology 2010 conference. The second day, which was dedicated to the inaugural meeting of the BioSharing initiative is presented in a separate report. The Genomic Standards Consortium (GSC) hosted the first day of this Special Interest Group (SIG) at ISMB to continue exploring the bottlenecks and emerging solutions for obtaining biological insights through large-scale comparative analysis of metagenomic datasets. The M3 SIG included invited and selected talks and a panel discussion at the end of the day involving the plenary speakers. Further information about the GSC and its range of activities can be found at http://gensc.org. Information about the newly established BioSharing effort can be found at http://biosharing.org/.     

Meeting Report: BioSharing at ISMB 2010

This report summarizes the proceedings of the one day BioSharing meeting held at the Intelligent Systems for Molecular Biology (ISMB) 2010 conference in Boston, MA, USA This inaugural BioSharing event was hosted by the Genomic Standards Consortium as part of its M3 & BioSharing special interest group (SIG) workshop. The BioSharing event included invited talks from a range of community leaders and a panel discussion at the end of the day. The panel session led to the formal agreement among community leaders to join together to promote cross-community knowledge exchange and collaborations. A key focus of the newly formed Biosharing community will be linking up resources to promote real-world data sharing (virtuous cycle of data) and supporting compliance with data policies through the creation of a one-stop-portal of information. Further information about the newly established BioSharing effort can be found at http://biosharing.org.     

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009

This report summarizes the proceedings of the "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group (SIG) meeting held at the Intelligent Systems for Molecular Biology 2009 conference. The Genomic Standards Consortium (GSC) hosted this meeting to explore the bottlenecks and emerging solutions for obtaining biological insights through large-scale comparative analysis of metagenomic datasets. The M3 SIG included 16 talks, half of which were selected from submitted abstracts, a poster session and a panel discussion involving members of the GSC Board. This report summarizes this one-day SIG, attempts to identify shared themes and recapitulates community recommendations for the future of this field. The GSC will also host an M3 workshop at the Pacific Symposium on Biocomputing (PSB) in January 2010. Further information about the GSC and its range of activities can be found at http://gensc.org/.     

Modelling the heart: insights,failures and progress

Mathematical models of the heart have developed over a period of about 40 years. Cell types in all regions of the heart have been modelled and they are now being incorporated into anatomically detailed models of the whole organ. This combination is leading to the creation of the first 'virtual organ,' which is being used in drug discovery and testing, and in simulating the action of devices, such as cardiac defibrillators. Simulation is a necessary tool of analysis in attempting to understand biological complexity. We often learn as much from the failures as from the successes of mathematical models. It is the iterative interaction between experiment and simulation that is important. Examples are given where this process has been instrumental in some of the major advances in the field.     

Microbes at their best: first Mol Micro Meeting Würzburg

Founded on ground-breaking discoveries such as the operon model by Jacob and Monod more than 50 years ago, molecular microbiology is now one of the most vibrant disciplines of the life sciences. The first Mol Micro Meeting Würzburg ('M3W') hosted more than 160 scientists from 14 countries to exchange their latest ideas in this field of research. Divided into the four main sessions Gene Regulation, Pathogenesis, Microbial Cell Biology and Signalling, the conference provided insight into current advances and future goals and challenges.     

Early predictors of life-history events: the link between first feeding date, dominance and seaward migration in Atlantic salmon, Salmo salar L.

Previous studies have suggested that the earliest fry to emerge from a salmonid redd may have an advantage in the subsequent competition for feeding sites, partly through a 'prior residence' effect. Here we examined whether there was any relationship between the relative date of first feeding and subsequent dominance status and growth in a sibling group of Atlantic salmon, Salmo salar L., fry. Earlier-feeding fry were dominant over their later-feeding siblings (controlling for prior residence), despite not being any larger. However, these early fish soon established and then maintained a size advantage. This led to an increased probability of early-feeding fish migrating to sea at age 1 year (rather than 2 or more). Thus a difference of less than 1 week in the relative timing of first feeding can translate into a year's difference in the timing of migration.     

描述和比较鱼类生长的快慢不宜使用生长指标(lgl_(t 1)-lgl_t)/0.4343)×l_t

生长率(l_(t 1)-(l_t))/l_t与生长指标((lgl_(t 1)-lgl_t)/0.4343)×l_t具有如下截然相反的数学特性：一个世代在t龄年初的平均体长l_t的年生长量l_(t 1)-l_t如果取常数值,则随着l_t增大,生长率单调减小表示生长减慢;但生长指标单调增大。由此可以看出,生长率符合而生长指标违背它们所要描述和比较的生长快慢固有的生物学概念。因此,有必要建议世界各国的鱼类生态学界停止使用生长指标。     

(2'-5') oligoadenylate synthetase in chicken embryo erythrocytes and immature red blood cells

The appearance and induction of (2'-5')oligoadenylate synthetase (2-5A synthetase) in chicken embryo erythrocytes during development, and the activity and molecular size of this enzyme in immature red blood cells from anemic chickens were studied. Enzyme activity first appeared in the embryos on the 15th day of incubation, a marked increase being seen 1 or 2 days after hatching. In erythrocytes from early embryos without 2-5A synthetase activity, chicken interferon (5 IU/ml at most) induced the production of a large amount of the enzyme. In immature red blood cells from anemic chickens, only a small amount of 2-5A synthetase was detected in the nuclear fraction. The cytoplasmic fraction contained the smaller enzyme (about 45 kilodaltons), but the larger enzyme (85-120 kilodaltons) was scarcely detected in either fraction. The larger enzyme may be synthesized during the maturation of red blood cells.     

Metal-induced toxicity, carcinogenesis, mechanisms and cellular responses

A wide variety of metals have been reported to act as mutagenic and carcinogenic agents in both human and animal studies. The underlying mechanisms are being extensively investigated. Recently, a new sub-discipline of molecular carcinogenesis has surfaced and new techniques and instruments are being developed which allow exploration of the complex biological relationships and signaling pathways involved in response to metal exposure at the molecular level. The 2nd Conference on Molecular Mechanisms of Metal Toxicity and Carcinogenesis was held at NIOSH in Morgantown, West Virginia, Sept. 8-11, 2002. One hundred thirty scientist from sixteen countries presented their novel findings and investigations of metal-induced carcinogenesis. The conference focused on state-of-the-art research and developments in metal toxicity and carcinogenesis. Emphasis was placed on delineating molecular mechanisms involved in free radical effects, cellular uptake, signaling pathways/interaction, dose response, biomarkers, and resistance mechanisms. This article reviews some of the novel information presented at the conference and discusses future avenues of research in this field.     

Molecular structure of the core-modified siRNA duplexes containing diastereomeric pair of [C6'(R)-OH]- versus [C6'(S)-OH]-carba-LNAs suggests a model for RNAi action

Molecular structures of native and a pair of modified small interfering RNA-RNA duplexes containing carbocyclic [6?'-(R)-OH/7?'-(S)-methyl]- and [6?'-(S)-OH/7?'-(S)-methyl]-carba-LNA-thymine nucleotides, which are two diastereomeric analogs of the native T nucleotide, incorporated at position 13 in the antisense (AS) strand of siRNA, have been simulated using molecular mechanics/dynamics techniques. The main aim of the project has been to find a plausible structural explanation of why modification of siRNA at T(13) position by the [6?'(R)-O-(p-Toluoyl)-7?'(S)-methyl]-carba-LNA-Thymine [IC(50) of 3.32 ± 0.17 nM] is ca 24 times more active as an RNA silencing agent against the target HIV-1 TAR RNA than the [6?'(S)-O-(p-Toluoyl)-7?'(S)-methyl]-counterpart [IC(50) of 79.8 ± 17 nM] [1]. The simulations reveal that introduction of both C6?'(R)-OH and C6?'(S)-OH stereoisomers does not lead even to local perturbation of the siRNA-RNA duplex structures compared to the native, and the only significant difference between 6?'(S)- and 6?'(R)-diastereomers found is the exposure of the 6?'-OH group of the 6?'(R)-diastereoisomer toward the edge of the duplex while the 6?'-hydroxyl group of the 6?'(S)-diastereoisomer is somewhat buried in the minor groove of the duplex. This rules out a hypothesis about any possible local distortion by the nature of chemical modification of the siRNA-target the RNA duplex, which might have influenced the formation of the effective RNA silencing complex (RISC) and puts some weight on the hypothesis about the 6?'-hydroxy group being directly involved with most probably Ago protein, since it is known from exhaustive X-ray studies [2, 3] that the core residues are indeed involved with hydrogen bonding with the internucleotidyl phosphates. Further systematic investigation is in progress to map the position-dependent functional and nonfunctional interactions of the modified [6?'(R or S)-O-(p-Toluoyl)-7?'(S)-methyl]-carba-LNA-T with the Ago2 protein of the RISC.     

Evolution and current status of ecological phytochemistry

Phytochemical studies have experienced a great deal of change during the last century, not only regarding the number of compounds described, but also in the concept of phytochemistry itself. This change has mainly been related to two key points: the methodologies used in phytochemical studies and the questions regarding 'why secondary metabolites appeared in plants and in other living organisms?' and 'what is their role?'. This transformation in the field has led to new questions concerning such different subjects as evolution, paleobotany, biochemistry, plant physiology and ethnography. However, the main issue is to clarify the role that secondary metabolites play in the plant (and other organisms) and whether the resources invested in their production (C and N allocation, genes encoding their biogenetic pathways, specific enzymes, energy-rich molecules such as ATP and NADPH) have or lack a reasonable reward in terms of advantages for survival. Consequently, in this review the main emphasis will be placed on two subjects related to the evolution of phytochemical studies. The first aim is to describe briefly the influence that the development of the methodologies needed for compound isolation and structure elucidation have had on the field of phytochemistry. The second area to be covered concerns the new theories addressing the role of secondary metabolites from an ecological point of view: co-evolution of plants and their potential enemies (phytophagous insects, microbes, herbivores and other plants), chemical plant defence, adaptative strategies of phytophagues to plant toxins (among them sequestration will be briefly mentioned), and models and theories for carbon and nitrogen allocation. Some final remarks are made to summarize our opinion about the immediate future of phytochemical ecology and phytochemical studies.     

The ontology of organisms: Mechanistic modules or patterned processes?

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles.     

Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL

   

The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a well-defined semantic basis for the Knowledge Representation language being used. In this article, we will first describe why this community is so insistent. Second, we will illustrate this by examining the semantics of the Web Ontology Language and the semantics placed on the Directed Acyclic Graph as used by the Gene Ontology. Finally we will reconcile the two representations, including the broader Open Biomedical Ontologies format. The ability to exchange between the two representations means that we can capitalise on the features of both languages. Such utility can only arise by the understanding of the semantics of the languages being used. By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community.     

Frequency Dependence of Signal Power and Spatial Reach of the Local Field Potential

Despite its century-old use, the interpretation of local field potentials (LFPs), the low-frequency part of electrical signals recorded in the brain, is still debated. In cortex the LFP appears to mainly stem from transmembrane neuronal currents following synaptic input, and obvious questions regarding the ‘locality’ of the LFP are: What is the size of the signal-generating region, i.e., the spatial reach, around a recording contact? How far does the LFP signal extend outside a synaptically activated neuronal population? And how do the answers depend on the temporal frequency of the LFP signal? Experimental inquiries have given conflicting results, and we here pursue a modeling approach based on a well-established biophysical forward-modeling scheme incorporating detailed reconstructed neuronal morphologies in precise calculations of population LFPs including thousands of neurons. The two key factors determining the frequency dependence of LFP are the spatial decay of the single-neuron LFP contribution and the conversion of synaptic input correlations into correlations between single-neuron LFP contributions. Both factors are seen to give low-pass filtering of the LFP signal power. For uncorrelated input only the first factor is relevant, and here a modest reduction (<50%) in the spatial reach is observed for higher frequencies (>100 Hz) compared to the near-DC () value of about . Much larger frequency-dependent effects are seen when populations of pyramidal neurons receive correlated and spatially asymmetric inputs: the low-frequency () LFP power can here be an order of magnitude or more larger than at 60 Hz. Moreover, the low-frequency LFP components have larger spatial reach and extend further outside the active population than high-frequency components. Further, the spatial LFP profiles for such populations typically span the full vertical extent of the dendrites of neurons in the population. Our numerical findings are backed up by an intuitive simplified model for the generation of population LFP.