Genome-scale models of bacterial metabolism: reconstruction and applications

Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities.     

Increased Gene Targeting in Ku70 and Xrcc4 Transiently Deficient Human Somatic Cells

The insertion of foreign DNA at a specific genomic locus directed by homologous DNA sequences, or gene targeting, is an inefficient process in mammalian somatic cells. Given the key role of non-homologous end joining (NHEJ) pathway in DNA double-strand break (DSB) repair in mammalian cells, we investigated the effects of decreasing NHEJ protein levels on gene targeting. Here we demonstrate that the transient knockdown of integral NHEJ proteins, Ku70 and Xrcc4, by RNAi in human HCT116 cells has a remarkable effect on gene targeting/random insertions ratios. A timely transfection of an HPRT-based targeting vector after RNAi treatment led to a 70% reduction in random integration events and a 33-fold increase in gene targeting at the HPRT locus. These findings bolster the role of NHEJ proteins in foreign DNA integration in vivo, and demonstrate that their transient depletion by RNAi is a viable approach to increase the frequency of gene targeting events. Understanding how foreign DNA integrates into a cell’s genome is important to advance strategies for biotechnology and genetic medicine.     

Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis

The traditional approach to bioinformatics analyses relies onindependent task-specific services and applications, using differentinput and output formats, often idiosyncratic, and frequentlynot designed to inter-operate. In general, such analyses wereperformed by experts who manually verified the results obtainedat each step in the process. Today, the amount of bioinformaticsinformation continuously being produced means that handlingthe various applications used to study this information presentsa major data management and analysis challenge to researchers.It is now impossible to manually analyse all this informationand new approaches are needed that are capable of processingthe large-scale heterogeneous data in order to extract the pertinentinformation. We review the recent use of integrated expert systemsaimed at providing more efficient knowledge extraction for bioinformaticsresearch. A general methodology for building knowledge-basedexpert systems is described, focusing on the unstructured informationmanagement architecture, UIMA, which provides facilities forboth data and process management. A case study involving a multiplealignment expert system prototype called AlexSys is also presented.      

Spatial organization of transmembrane receptor signalling

The spatial organization of transmembrane receptors is a critical step in signal transduction and receptor trafficking in cells. Transmembrane receptors engage in lateral homotypic and heterotypic cis‐interactions as well as intercellular trans‐interactions that result in the formation of signalling foci for the initiation of different signalling networks. Several aspects of ligand‐induced receptor clustering and association with signalling proteins are also influenced by the lipid composition of membranes. Thus, lipid microdomains have a function in tuning the activity of many transmembrane receptors by positively or negatively affecting receptor clustering and signal transduction. We review the current knowledge about the functions of clustering of transmembrane receptors and lipid–protein interactions important for the spatial organization of signalling at the membrane.     

BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon

A better understanding of the genotype–phenotype correlation of Atlantic salmon is of key importance for a whole range of production, life history and conservation biology issues attached to this species. High-density linkage maps integrated with physical maps and covering the complete genome are needed to identify economically important genes and to study the genome architecture. Linkage maps of moderate density and a physical bacterial artificial chromosome (BAC) fingerprint map for the Atlantic salmon have already been generated. Here, we describe a strategy to combine the linkage mapping with the physical integration of newly identified single nucleotide polymorphisms (SNPs). We resequenced 284 BAC-ends by PCR in 14 individuals and detected 180 putative SNPs. After successful validation of 152 sequence variations, genotyping and genetic mapping were performed in eight salmon families comprising 376 individuals. Among these, 110 SNPs were positioned on a previously constructed linkage map containing SNPs derived from expressed sequence tag (EST) sequences. Tracing the SNP markers back to the BACs enabled the integration of the genetic and physical maps by assigning 73 BAC contigs to Atlantic salmon linkage groups.     

重组腺相关病毒载体的整合性研究进展

重组腺相关病毒(rAAV)载体是一种具有高靶向性和良好安全性的病毒载体,在基因治疗中得到了较为广泛的应用。目前全球范围内已有70余项以rAAV为基因药物的临床研究已经完成或正在进行中。与野生型AAV(wtAAV)定点整合不同,不表达Rep蛋白的rAAV载体与宿主染色体发生的是随机整合,而这给临床应用带来了可能的潜在的安全隐患。该文在综述wtAAV和rAAV整合机理的基础上对rAAV的因随机整合而可能导致的致癌性及其他后果进行探讨,并总结了相应应对策略,特别是目前利用Rep蛋白所开展的定点整合研究。     

Characterization of T-DNA Insertion Mutants and RNAi Silenced Plants of Arabidopsis thaliana UV-damaged DNA Binding Protein 2 (AtUV-DDB2)

The human UV-damaged DNA binding protein (UV-DDB), a heterodimeric protein composed of 127 kDa (UV-DDB1) and 48 kDa (UV-DDB2) subunits, has been shown to be involved in DNA repair. To elucidate the in vivo function of plant UV-DDB2, we have analyzed T-DNA insertion mutants of the Arabidopsis thaliana UV-DDB2 subunit (atuv-ddb2 mutants) and AtUV-DDB2 RNAi silenced plants (atuv-ddb2 silenced plants). atuv-ddb2 mutants and atuv-ddb2 silenced plants were both viable, suggesting that AtUV-DDB2 is not essential for survival. Interestingly, both plant types showed a dwarf phenotype, implying impaired growth of the meristem. To the best of our knowledge, this is the first occasion that a dwarf phenotype has been found to be associated with a UV-DDB2 mutation in either plants or animals. The mutants also demonstrated increased sensitivity to UV irradiation, methyl methanesulfonate and hydrogen peroxide treatment, indicating that AtUV-DDB2 is also involved in DNA repair. Our results lead us to suggest that not only does AtUV-DDB2 function in DNA repair, it also has a direct or indirect influence on cell proliferation in the plant meristem. Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries.     

The night-time temporal window of locomotor activity in the Namib Desert long-distance wandering spider, Leucorchestris arenicola

Even though being active exclusively after sunset, the male Leucorchestris arenicola spiders are able to return to their point of departure by following bee-line routes of up to several hundreds of meters in length. While performing this kind of long-distance path integration they must rely on external cues to adjust for navigational errors. Many external cues which could be used by the spiders change dramatically or disappear altogether in the transition period from day to night. Hence, it is therefore imperative to know exactly when after sunset the spiders navigate in order to find out how they do it. To explore this question, we monitored their locomotor activity with data loggers equipped with infrared beam sensors. Our results show that the male spiders are most active in the period between the end and the beginning of the astronomical twilight period. Moreover, they prefer the moonless, i.e. darkest times at night. Hence, we conclude that the males are truly—and extremely—nocturnal. We further show that they are able to navigate under the very dim light conditions prevailing on moonless nights, and thus do not have to rely on the moon or on moon-related patterns of polarised light as potential compass cues.     

Desert ants: is active locomotion a prerequisite for path integration?

Desert ants Cataglyphis fortis have been shown to be able to employ two mechanisms of distance estimation: exploiting both optic flow and proprioceptive information. This study aims at understanding possible interactions between the two possibly redundant mechanisms of distance estimation. We ask whether in Cataglyphis the obviously minor contribution of optic flow would increase or even take over completely if the ants were deprived of reliable proprioceptive information. In various experimental paradigms ants were subjected to passive horizontal displacements during which they perceived optic flow, but were prohibited from active locomotion. The results show that in desert ants active locomotion is essential for providing the ants’ odometer and hence its path integrator with the necessary information.     

Micro- and macroevolutionary decoupling of cichlid jaws: a test of Liem's key innovation hypothesis

The extent to which elements of functional systems can change independently (modularity) likely influences the diversification of lineages. Major innovations in organismal design, like the pharyngeal jaw in cichlid fishes, may be key to a group's success when they relax constraints on diversification by increasing phenotypic modularity. In cichlid fishes, pharyngeal jaw modifications that enhanced the ability to breakdown prey may have freed their oral jaws from serving their ancestral dual role as a site of both prey capture and prey processing. This functional decoupling that allowed the oral jaws to become devoted solely to prey capture has been hypothesized to have permitted the two sets of cichlid jaws to evolve independently. We tested the hypothesis that oral and pharyngeal jaw mechanics are evolutionarily decoupled both within and among Neotropical Heroine cichlids. In the trophically polymorphic species Herichthys minckleyi, molariforms that exhibit enlarged molarlike pharyngeal jaw teeth were found to have approximately 400% greater lower jaw mass compared to H. minckleyi with the alternative papilliform pharyngeal morphology. However, oral jaw gape, lower jaw velocity ratios, anterior jaw linkage mechanics, and jaw protrusion did not differ between the morphotypes. In 40 other Heroine species, there was a weak correlation between oral jaw mechanics and pharyngeal jaw mass when phylogenetic history was ignored. Yet, after expansion of the cytochrome b phylogeny for Heroines, change in oral jaw mechanics was found to be independent of evolutionary change in pharyngeal jaw mass based on independent contrasts. Evolutionary decoupling of oral and pharyngeal jaw mechanics has likely played a critical role in the unparalleled trophic diversification of cichlid fishes.