Ribosome hibernation factor promotes Staphylococcal survival and differentially represses translation

In opportunistic Gram-positive Staphylococcus aureus, a small protein called hibernation-promoting factor (HPF_Sa) is sufficient to dimerize 2.5-MDa 70S ribosomes into a translationally inactive 100S complex. Although the 100S dimer is observed in only the stationary phase in Gram-negative gammaproteobacteria, it is ubiquitous throughout all growth phases in S. aureus. The biological significance of the 100S ribosome is poorly understood. Here, we reveal an important role of HPF_Sa in preserving ribosome integrity and poising cells for translational restart, a process that has significant clinical implications for relapsed staphylococcal infections. We found that the hpf null strain is severely impaired in long-term viability concomitant with a dramatic loss of intact ribosomes. Genome-wide ribosome profiling shows that eliminating HPF_Sa drastically increased ribosome occupancy at the 5′ end of specific mRNAs under nutrient-limited conditions, suggesting that HPF_Sa may suppress translation initiation. The protective function of HPF_Sa on ribosomes resides at the N-terminal conserved basic residues and the extended C-terminal segment, which are critical for dimerization and ribosome binding, respectively. These data provide significant insight into the functional consequences of 100S ribosome loss for protein synthesis and stress adaptation.     

Two-level parallelization of Ehrenfest force calculations in ab initio molecular dynamics simulation

A two-level parallel code for Ehrenfest force calculations in ab initio molecular dynamics simulations was developed for a shared memory multiprocessor cluster. Coarse-grain parallelism was implemented by atomic decomposition and a fine-grained parallelism was exploited to perform matrix multiplications. This two-level parallelism efficiently enhances the speed of computations.     

Network modeling and analysis of lumbar muscle surface EMG signals during flexion–extension in individuals with and without low back pain

In this paper, we propose modeling the activity coordination network between lumbar muscles using surface electromyography (sEMG) signals and performing the network analysis to compare the lumbar muscle coordination patterns between patients with low back pain (LBP) and healthy control subjects. Ten healthy subjects and eleven LBP patients were asked to perform flexion–extension task, and the sEMG signals were recorded. Both the subject-level and the group-level PC_fdr algorithms are applied to learn the sEMG coordination networks with the error-rate being controlled. The network features are further characterized in terms of network symmetry, global efficiency, clustering coefficient and graph modules. The results indicate that the networks representing the normal group are much closer to the order networks and clearly exhibit globally symmetric patterns between the left and right sEMG channels. While the coordination activities between sEMG channels for the patient group are more likely to cluster locally and the group network shows the loss of global symmetric patterns. As a complementary tool to the physical and anatomical analysis, the proposed network analysis approach allows the visualization of the muscle coordination activities and the extraction of more informative features from the sEMG data for low back pain studies.     

ANDY: a general, fault-tolerant tool for database searching on computer clusters

SUMMARY: ANDY (seArch coordination aND analYsis) is a set of Perl programs and modules for distributing large biological database searches, and in general any sequence of commands, across the nodes of a Linux computer cluster. ANDY is compatible with several commonly used distributed resource management (DRM) systems, and it can be easily extended to new DRMs. A distinctive feature of ANDY is the choice of either dedicated or fair-use operation: ANDY is almost as efficient as single-purpose tools that require a dedicated cluster, but it runs on a general-purpose cluster along with any other jobs scheduled by a DRM. Other features include communication through named pipes for performance, flexible customizable routines for error-checking and summarizing results, and multiple fault-tolerance mechanisms. Availability: ANDY is freely available and can be obtained from http://compbio.berkeley.edu/proj/andy. SUPPLEMENTARY INFORMATION: Supplemental data, figures, and a more detailed overview of the software are found at http://compbio.berkeley.edu/proj/andy.     

The [4Fe–4S]-cluster coordination of [FeFe]-hydrogenase maturation protein HydF as revealed by EPR and HYSCORE spectroscopies

[FeFe] hydrogenases are key enzymes for bio(photo)production of molecular hydrogen, and several efforts are underway to understand how their complex active site is assembled. This site contains a [4Fe–4S]-2Fe cluster and three conserved maturation proteins are required for its biosynthesis. Among them, HydF has a double task of scaffold, in which the dinuclear iron precursor is chemically modified by the two other maturases, and carrier to transfer this unit to a hydrogenase containing a preformed [4Fe–4S]-cluster. This dual role is associated with the capability of HydF to bind and dissociate an iron–sulfur center, due to the presence of the conserved FeS-cluster binding sequence CxHx_46–53HCxxC. The recently solved three-dimensional structure of HydF from Thermotoga neapolitana described the domain containing the three cysteines which are supposed to bind the FeS cluster, and identified the position of two conserved histidines which could provide the fourth iron ligand. The functional role of two of these cysteines in the activation of [FeFe]-hydrogenases has been confirmed by site-specific mutagenesis. On the other hand, the contribution of the three cysteines to the FeS cluster coordination sphere is still to be demonstrated. Furthermore, the potential role of the two histidines in [FeFe]-hydrogenase maturation has never been addressed, and their involvement as fourth ligand for the cluster coordination is controversial. In this work we combined site-specific mutagenesis with EPR (electron paramagnetic resonance) and HYSCORE (hyperfine sublevel correlation spectroscopy) to assign a role to these conserved residues, in both cluster coordination and hydrogenase maturation/activation, in HydF proteins from different microorganisms.     

Modular analysis of the probabilistic genetic interaction network

MOTIVATION: Epistatic Miniarray Profiles (EMAP) has enabled the mapping of large-scale genetic interaction networks; however, the quantitative information gained from EMAP cannot be fully exploited since the data are usually interpreted as a discrete network based on an arbitrary hard threshold. To address such limitations, we adopted a mixture modeling procedure to construct a probabilistic genetic interaction network and then implemented a Bayesian approach to identify densely interacting modules in the probabilistic network. RESULTS: Mixture modeling has been demonstrated as an effective soft-threshold technique of EMAP measures. The Bayesian approach was applied to an EMAP dataset studying the early secretory pathway in Saccharomyces cerevisiae. Twenty-seven modules were identified, and 14 of those were enriched by gold standard functional gene sets. We also conducted a detailed comparison with state-of-the-art algorithms, hierarchical cluster and Markov clustering. The experimental results show that the Bayesian approach outperforms others in efficiently recovering biologically significant modules.     

Unusual Biosynthesis and Structure of Locillomycins from Bacillus subtilis 916

Three families of Bacillus cyclic lipopeptides—surfactins, iturins, and fengycins—have well-recognized potential uses in biotechnology and biopharmaceutical applications. This study outlines the isolation and characterization of locillomycins, a novel family of cyclic lipopeptides produced by Bacillus subtilis 916. Elucidation of the locillomycin structure revealed several molecular features not observed in other Bacillus lipopeptides, including a unique nonapeptide sequence and macrocyclization. Locillomycins are active against bacteria and viruses. Biochemical analysis and gene deletion studies have supported the assignment of a 38-kb gene cluster as the locillomycin biosynthetic gene cluster. Interestingly, this gene cluster encodes 4 proteins (LocA, LocB, LocC, and LocD) that form a hexamodular nonribosomal peptide synthetase to biosynthesize cyclic nonapeptides. Genome analysis and the chemical structures of the end products indicated that the biosynthetic pathway exhibits two distinct features: (i) a nonlinear hexamodular assembly line, with three modules in the middle utilized twice and the first and last two modules used only once and (ii) several domains that are skipped or optionally selected.     

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license.     

A Cluster Operating System Supporting Parallel Computing

The single factor limiting the harnessing of the enormous computing power of clusters for parallel computing is the lack of appropriate software. Present cluster operating systems are not built to support parallel computing – they do not provide services to manage parallelism. The cluster operating environments that are used to assist the execution of parallel applications do not provide support for both Message Passing (MP) or Distributed Shared Memory (DSM) paradigms. They are only offered as separate components implemented at the user level as library and independent servers. Due to poor operating systems users must deal with computers of a cluster rather than to see this cluster as a single powerful computer. A Single System Image of the cluster is not offered to users. There is a need for an operating system for clusters. We claim and demonstrate that it is possible to develop a cluster operating system that is able to efficiently manage parallelism, support Message Passing and DSM and offer the Single System Image. In order to substantiate the claim the first version of a cluster operating system, called GENESIS, that manages parallelism and offers the Single System Image has been developed.     

An introduction to the European Terrestrial Ecosystem Modelling Activity

The objective of the European Terrestrial Ecosystem Modelling Activity (ETEMA) was to address some of the major challenges in developing generalized models to examine responses of natural and seminatural ecosystems to environmental change at the regional to European scale. The approach described herein was to break down the totality of ecosystem functioning into its key components, each with its characteristic spatial and temporal scales. A conceptual framework was developed describing the configuration of these components as modules within a generalized simulation model. The framework describes the key inputs, outputs and state variables, their spatial and temporal contexts, and information flows between modules. The ‘backbone’ of the model is a system of nested timing loops corresponding to the disparate time scales at which different ecosystem processes occur. The framework is a theoretical construct into which ecosystem models at levels of complexity ranging from the very general to the highly detailed can be mapped, and thus provides a guide for development of models for novel, particularly regional‐scale, applications. A number of subsystem studies of the major components of ecosystem functioning, i.e. modules of the conceptual framework, are briefly introduced herein. The general aim of the subsystem studies was to identify the key alternative formulations (as opposed to minor variants) and test these against observational data. The various subsystem studies concern planetary boundary layer–ecosystem interactions, ecosystem CO₂ and H₂O fluxes, vegetation physiology and phenology, biogeography and vegetation dynamics, detritus and SOM dynamics, soil moisture and human and natural disturbances and, as individual papers, they complete this special ETEMA issue.     

Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments

The antiproliferative response to anticancer treatment is the result of concurrent responses in all cell cycle phases, extending over several cell generations, whose complexity is not captured by current methods. In the proposed experimental/computational approach, the contemporary use of time-lapse live cell microscopy and flow cytometric data supported the computer rendering of the proliferative process through the cell cycle and subsequent generations during/after treatment. The effects of treatments were modelled with modules describing the functional activity of the main pathways causing arrest, repair and cell death in each phase. A framework modelling environment was created, enabling us to apply different types of modules in each phase and test models at the complexity level justified by the available data. We challenged the method with time-course measures taken in parallel with flow cytometry and time-lapse live cell microscopy in X-ray-treated human ovarian cancer cells, spanning a wide range of doses. The most suitable model of the treatment, including the dose-response of each effect, was progressively built, combining modules with a rational strategy and fitting simultaneously all data of different doses and platforms. The final model gave for the first time the complete rendering in silico of the cycling process following X-ray exposure, providing separate and quantitative measures of the dose-dependence of G₁, S and G₂M checkpoint activities in subsequent generations, reconciling known effects of ionizing radiations and new insights in a unique scenario.     

Imagene: an integrated computer environment for sequence annotation and analysis

MOTIVATION: To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS: This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub- tasks are graphically displayed to the user and may be further re- started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT: imagene home page: http://wwwabi.snv.jussieu.fr/imagene      

Geometric distortions on a three-coordinated T1 Cu site model as a potential strategy to modulate redox potential. A theoretical study

A model of the three-coordinated T1 Cu site from Trametes versicolor was considered to evaluate the effect on redox potential of geometrical distortions in the copper coordination sphere. Systematic modifications of geometrical parameters (distances and angles) of the coordination sphere of the T1 Cu site were carried out within a density functional theory (DFT) framework, to evaluate their effects on electron affinity directly related to redox potential. The most promising result in terms of redox potential increment was distortion of the dihedral angle C_{methylthiolate}–S–Cu–N_ImA (ω), which can be rationalized as a decrease in the overlap of imidazole orbitals in the redox-active molecular orbital (β-LUMO). This overlap is minimized when ω achieves the value of 10°, therefore, this conformation might have the highest redox potential. From the molecular orbital viewpoint, a parallelism was found between the effect caused by the presence of a fourth ligand and the distorted three-coordination, which could be extrapolated to spectroscopic properties. It was also found that solvation effects on the redox potentials during geometrical distortions produce a very similar tendency, independently of the polarity of the solvent.     

Arsenic trioxide induces human pulmonary fibroblast cell death via the regulation of Bcl-2 family and caspase-8

Arsenic trioxide (ATO; As₂O₃) can induce apoptotic cell death in various cancer cells including lung cancer cells. However, little is known about the toxicological effects of ATO on normal primary lung cells. In this study, we investigated the cellular effects of ATO on human pulmonary fibroblast (HPF) cells in relation to cell growth inhibition and death. ATO inhibited HPF cell growth with an IC₅₀ of approximately 30–40 μM at 24 h and induced cell death accompanied by the loss of mitochondrial membrane potential (MMP; ΔΨ_m). Thus, HPF cells were considered to be very resistant to ATO insults. ATO increased the expression of p53 protein and decreased that of Bcl-2 protein. This agent activated caspase-8 but not caspase-3 in HPF cells. Z-VAD (a pan-caspase inhibitor; 15 μM) did not significantly decrease cell growth inhibition, death and MMP (ΔΨ_m) loss by ATO. Moreover, administration of Bax or casase-8 siRNA attenuated HPF cell death by ATO whereas p53 or caspase-3 siRNAs did not affect cell death. In conclusion, HPF cells were resistant to ATO and higher doses of ATO induced the growth inhibition and death in HPF cells via the regulation of Bcl-2 family and caspase-8.     

Chimpanzees are more skilful in competitive than in cooperative cognitive tasks

In a series of four experiments, chimpanzees, Pan troglodytes, were given two cognitive tasks, an object choice task and a discrimination task (based on location), each in the context of either cooperation or competition. In both tasks chimpanzees performed more skilfully when competing than when cooperating, with some evidence that competition with conspecifics was especially facilitatory in the discrimination location task. This is the first study to demonstrate a facilitative cognitive effect for competition in a single experimental paradigm. We suggest that chimpanzee cognitive evolution is best understood in its socioecological context.     

Relatedness and the evolution of mechanisms to divide labor in microorganisms

Division of labor occurs when cooperating individuals specialize to perform different tasks. In bacteria and other microorganisms, some species divide labor by random specialization, where an individual''s role is determined by random fluctuations in biochemical reactions within the cell. Other species divide labor by coordinating across individuals to determine which cells will perform which task, using mechanisms such as between‐cell signaling. However, previous theory, examining the evolution of mechanisms to divide labor between reproductives and sterile helpers, has only considered clonal populations, where there is no potential for conflict between individuals. We used a mixture of analytical and simulation models to examine nonclonal populations and found that: (a) intermediate levels of coordination can be favored, between the extreme of no coordination (random) and full coordination; (b) as relatedness decreases, coordinated division of labor is less likely to be favored. Our results can help explain why coordinated division of labor is relatively rare in bacteria, where groups may frequently be nonclonal.     

A Biomathematical Model of Human Erythropoiesis under Erythropoietin and Chemotherapy Administration

Anaemia is a common haematologic side effect of dose-dense multi-cycle cytotoxic polychemotherapy requiring erythrocyte transfusions or erythropoietin (EPO) administration. To simulate the effectiveness of different EPO application schedules, we performed both modelling of erythropoiesis under chemotherapy and pharmacokinetic and dynamic modelling of EPO applications in the framework of a single comprehensive biomathematical model. For this purpose, a cell kinetic model of bone marrow erythropoiesis was developed that is based on a set of differential compartment equations describing proliferation and maturation of erythropoietic cell stages. The system is regulated by several feedback loops comprising those mediated by EPO. We added a model of EPO absorption after injection at different sites and a pharmacokinetic model of EPO derivatives to account for the effects of external EPO applications. Chemotherapy is modelled by a transient depletion of bone marrow cell stages. Unknown model parameters were determined by fitting the predictions of the model to data sets of circulating erythrocytes, haemoglobin, haematocrit, percentage of reticulocytes or EPO serum concentrations derived from the literature or cooperating clinical study groups. Parameter fittings resulted in a good agreement of model and data. Depending on site of injection and derivative (Alfa, Beta, Delta, Darbepoetin), nine groups of EPO applications were distinguished differing in either absorption kinetics or pharmacokinetics. Finally, eight different chemotherapy protocols were modelled. The model was validated on the basis of scenarios not used for parameter fitting. Simulations were performed to analyze the impact of EPO applications on the risk of anaemia during chemotherapy. We conclude that we established a model of erythropoiesis under chemotherapy that explains a large set of time series data under EPO and chemotherapy applications. It allows predictions regarding yet untested EPO schedules. Prospective clinical studies are needed to validate model predictions and to explore the feasibility and effectiveness of the proposed schedules.     

Growth Medium and Phosphorus Supply Affect Cluster Root Formation and Citrate Exudation by Lupinus albus Grown in a Sand/Solution Split-Root System

We examined cluster root formation and root exudation by white lupin (Lupinus albus L. cv. Kiev Mutant) in response to growth medium and phosphorus supply in a sand/solution split-root system. The split-root system consisted of a nutrient solution compartment and a siliceous sand compartment. Phosphorus was applied at 1 (low-P plants) or 50 (high-P plants) μM as KH₂PO₄ to the solution compartment and at 10, 50 or 250 mg P kg⁻¹ as hydroxyapatite (Ca-P) to the sand compartment. In contrast to the high-P plants, P concentration and P uptake in the low-P plants increased with increasing P supply to the sand compartment. The NaHCO₃-extractable P was lower in the rhizosphere of the low-P plants than the high-P ones. The proton extrusion rate by the solution-grown roots of the low-P plants was higher than that of the high-P plants at the early growth stage. For the low-P plants, the proportion of dry root biomass allocated to cluster roots was higher in the solution compartment than that in the sand compartment. The citrate exudation increased in the sand compartment and decreased in the solution compartment with time, showing a lack of synchronization in citrate exudation by two root halves grown in different media. The cluster root proportion and citrate exudation in both compartments decreased with increasing shoot P concentration. An additional experiment with no P added to either root compartment showed that the proportion of cluster roots was about 9% lower in the sand than solution compartments. The results suggest that cluster root formation and citrate exudation can be significantly affected by the root growth medium in addition to being regulated by shoot P status. More P can be exploited from sparingly available Ca-P by the low-P plants than the high-P ones due to greater citrate exudation under P deficiency.     

Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy

We have developed a global strategy based on the Bayesian network framework to prioritize the functional modules mediating genetic perturbations and their phenotypic effects among a set of overlapping candidate modules. We take lethality in Saccharomyces cerevisiae and human cancer as two examples to show the effectiveness of this approach. We discovered that lethality is more conserved at the module level than at the gene level and we identified several potentially 'new' cancer-related biological processes.