The non-photosynthetic, pathogenic green alga Helicosporidium sp. has retained a modified, functional plastid genome

A fragment of the Helicosporidium sp. (Chlorophyta: Trebouxiophyceae) plastid genome has been sequenced. The genome architecture was compared to that of both a non-photosynthetic relative (Prototheca wickerhamii) and a photosynthetic relative (Chlorella vulgaris). Comparative genomic analysis indicated that Helicosporidium and Prototheca are closely related genera. The analyses also revealed that the Helicosporidium sp. plastid genome has been rearranged. In particular, two ribosomal protein-encoding genes (rpl19 and rps23) appeared to have been transposed, or lost from the Helicosporidium sp. plastid genome. RT-PCR reactions demonstrated that the retained plastid genes were transcribed, suggesting that, despite rearrangement(s), the Helicosporidium sp. plastid genome has remained functional. The modified plastid genome architecture is a novel apomorphy that indicates that the Helicosporidia are highly derived green algae, more so than Prototheca spp. As such, they represent a promising model to study organellar genome reorganizations in parasitic protists

Control Across Scales by Positive and Negative Feedback

Feedback is a key element of regulation, as it shapes the sensitivity of a process to its environment. Positive feedback upregulates, and negative feedback downregulates. Many regulatory processes involve a mixture of both, whether in nature or in engineering. This article revisits the mixed-feedback paradigm, with the aim of investigating control across scales. We propose that mixed feedback regulates excitability and that excitability plays a central role in multiscale neuronal signaling. We analyze this role in a multiscale network architecture inspired by neurophysiology. The nodal behavior defines a mesoscale that connects actuation at the microscale to regulation at the macroscale. We show that mixed-feedback nodal control provides regulatory principles at the network scale, with a nodal resolution. In this sense, the mixed-feedback paradigm is a control principle across scales. </jats:p

Switchable slow cellular conductances determine robustness and tunability of network states.

Neuronal information processing is regulated by fast and localized fluctuations of brain states. Brain states reliably switch between distinct spatiotemporal signatures at a network scale even though they are composed of heterogeneous and variable rhythms at a cellular scale. We investigated the mechanisms of this network control in a conductance-based population model that reliably switches between active and oscillatory mean-fields. Robust control of the mean-field properties relies critically on a switchable negative intrinsic conductance at the cellular level. This conductance endows circuits with a shared cellular positive feedback that can switch population rhythms on and off at a cellular resolution. The switch is largely independent from other intrinsic neuronal properties, network size and synaptic connectivity. It is therefore compatible with the temporal variability and spatial heterogeneity induced by slower regulatory functions such as neuromodulation, synaptic plasticity and homeostasis. Strikingly, the required cellular mechanism is available in all cell types that possess T-type calcium channels but unavailable in computational models that neglect the slow kinetics of their activation

Neuronal behaviors: A control perspective

The purpose of this tutorial is to introduce and analyze models of neurons from a control perspective and to show how recently developed analytical tools help to address important biological questions. A first objective is to review the basic modeling principles of neurophysiology in which neurons are modeled as equivalent nonlinear electrical circuits that capture their excitable properties. The specific architecture of the models is key to the tractability of their analysis: in spite of their high-dimensional and nonlinear nature, the model properties can be understood in terms of few canonical positive and negative feedback motifs localized in distinct timescales. We use this insight to shed light on a key problem in experimental neurophysiology, the challenge of understanding the sensitivity of neuronal behaviors to underlying parameters in empirically-derived models. Finally, we show how sensitivity analysis of neuronal excitability relates to robustness and regulation of neuronal behaviors.This paper presents research results of the Belgian Network DYSCO (Dynamical Systems, Control, and Optimization), funded by the Interuniversity Attraction Poles Programme, initiated by the Belgian State, Science Policy Office. G.D. is a Marie-Curie COFUND postdoctoral fellow at the University of Liege. Co-funded by the European Union. J.D. is supported by the F.R.S.-FNRS (Belgian Fund for Scientific Research. The scientific responsibility rests with its authors.This is the author accepted manuscript. The final version is available from IEEE via http://dx.doi.org/10.1109/CDC.2015.740249

Analyse préliminaire de la situation et des perspectives de la culture du haricot de Lima (Phaseolus lunatus L.) sur la Côte péruvienne (Vallées d'Ica, Pisco et Casma)

Preliminary analysis of the situation and prospects of the Lima bean crop (Phaseolus lunatus L.) in the Peruvian Coast (Valleys of Ica, Pisco and Casma). The Lima bean, Phaseolus lunatus L., is a crop of regional importance on the Peruvian Coast. Within the framework of a collaborative project between the ""faculté universitaire des Sciences agronomiques'"" in Gembloux and the ""Universidad Nacional Agraria La Molina"" in Lima, we carried out a diagnosis of this speculation in the Ica, Pisco and Casma valleys in order to define the constraints which limit crop yields and to suggest improvements within the reach of the smallholders. To achieve these objectives we carried out a formal survey, centred on the Lima bean crop and smallholder relations with the agro-socio-economical environment, and an informal survey, centred on the studied farm systems. To complete these data we met some key informants belonging to all the sectors in contact with agriculture. This study allowed us to identify five undersystems in the farm systems of the Peruvian Coastal Valleys. These undersystems are: cotton, commercial food crops, self-subsistence food crops, livestock and fruit trees. The Lima bean usually belongs to the commercial food crops undersystem. There are two types of constraints. External constraints affect all the components of the farm system and are mainly: end of State support to agriculture, liberalization of trade and unavailability of credit. Internal constraints directly affect the Lima bean crop. Low income leads to a deficiency in pest control and adequate crop management. The Lima bean is also in competition with other components of the system such as cotton and common bean

Comparison of plastid 16S rDNA (rrn16) genes from Helicosporidium spp.: evidence supporting the reclassification of Helicosporidia as green algae (Chlorophyta)

The Helicosporidia are invertebrate pathogens that have recently been identified as non-photosynthetic green algae (Chlorophyta). In order to confirm the algal nature of the genus Helicosporidium, the presence of a retained chloroplast genome in Helicosporidia cells was investigated. Fragments homologous to plastid 16S rRNA (rrn16) genes were amplified successfully from cellular DNA extracted from two different Helicosporidium isolates. The fragment sequences are 1269 and 1266 bp long, are very AT-rich (60.7 %) and are similar to homologous genes sequenced from non-photosynthetic green algae. Maximum-parsimony, maximum-likelihood and neighbour-joining methods were used to infer phylogenetic trees from an rrn16 sequence alignment. All trees depicted the Helicosporidia as sister taxa to the non-photosynthetic, pathogenic alga Prototheca zopfii. Moreover, the trees identified Helicosporidium spp. as members of a clade that included the heterotrophic species Prototheca spp. and the mesotrophic species Chlorella protothecoides. The clade is always strongly supported by bootstrap values, suggesting that all these organisms share a most recent common ancestor. Phylogenetic analyses inferred from plastid 16S rRNA genes confirmed that the Helicosporidia are non-photosynthetic green algae, close relatives of the genus Prototheca (Chlorophyta, Trebouxiophyceae). Such phylogenetic affinities suggest that Helicosporidium spp. are likely to possess Prototheca-like organelles and organelle genomes

Sequence analysis of a non-classified, non-occluded DNA virus that causes salivary gland hypertrophy of Musca domestica, MdSGHV

AbstractThe genome of the virus that causes salivary gland hypertrophy in Musca domestica (MdSGHV) was sequenced. This non-classified, enveloped, double stranded, circular DNA virus had a 124,279bp genome. The G + C content was 43.5% with 108 putative methionine-initiated open reading frames (ORFs). Thirty ORFs had homology to database proteins: eleven to proteins coded by both baculoviruses and nudiviruses (p74, pif-1, pif-2, pif-3, odv-e66, rr1, rr2, iap, dUTPase, MMP, and Ac81-like), seven to nudiviruses (mcp, dhfr, ts, tk and three unknown proteins), one to baculovirus (Ac150-like), one to herpesvirus (dna pol), and ten to cellular proteins. Mass spectrum analysis of the viral particles' protein components identified 29 structural ORFs, with only p74 and odv-e66 previously characterized as baculovirus structural proteins. Although most of the homology observed was to nudiviruses, phylogenetic analysis showed that MdSGHV was not closely related to them or to the baculoviruses

Phylogenetic analysis identifies the invertebrate pathogen Helicosporidium sp. as a green alga (Chlorophyta)

Historically, the invertebrate pathogens of the genus Helicosporidium were considered to be either protozoa or fungi, but the taxonomic position of this group has not been considered since 1931. Recently, a Helicosporidium sp., isolated from the blackfly Simulium jonesi Stone & Snoddy (Diptera: Simuliidae), has been amplified in the heterologous host Helicoverpa zea. Genomic DNA has been extracted from gradient-purified cysts. The 185, 28S and 5.8S regions of the Helicosporidium rDNA, as well as partial sequences of the actin and beta-tubulin genes, were amplified by PCR and sequenced. Comparative analysis of these nucleotide sequences was performed using neighbour-joining and maximum-parsimony methods. All inferred phylogenetic trees placed Helicosporidium sp. among the green algae (Chlorophyta), and this association was supported by bootstrap and parsimony jackknife values. Phylogenetic analysis focused on the green algae depicted Helicosporidium sp. as a close relative of Prototheca wickerhamii and Prototheca zopfii (Chlorophyta, Trebouxiophyceae), two achlorophylous, pathogenic green algae. On the basis of this phylogenetic analysis, Helicosporidium sp. is clearly neither a protist nor a fungus, but appears to be the first described algal invertebrate pathogen. These conclusions lead us to propose the transfer of the genus Helicosporidium to Chlorophyta, Trebouxiophyceae

Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes

<p>Abstract</p> <p>Background</p> <p>Termite lignocellulose digestion is achieved through a collaboration of host plus prokaryotic and eukaryotic symbionts. In the present work, we took a combined host and symbiont metatranscriptomic approach for investigating the digestive contributions of host and symbiont in the lower termite <it>Reticulitermes flavipes</it>. Our approach consisted of parallel high-throughput sequencing from (i) a host gut cDNA library and (ii) a hindgut symbiont cDNA library. Subsequently, we undertook functional analyses of newly identified phenoloxidases with potential importance as pretreatment enzymes in industrial lignocellulose processing.</p> <p>Results</p> <p>Over 10,000 expressed sequence tags (ESTs) were sequenced from the 2 libraries that aligned into 6,555 putative transcripts, including 171 putative lignocellulase genes. Sequence analyses provided insights in two areas. First, a non-overlapping complement of host and symbiont (prokaryotic plus protist) glycohydrolase gene families known to participate in cellulose, hemicellulose, alpha carbohydrate, and chitin degradation were identified. Of these, cellulases are contributed by host plus symbiont genomes, whereas hemicellulases are contributed exclusively by symbiont genomes. Second, a diverse complement of previously unknown genes that encode proteins with homology to lignase, antioxidant, and detoxification enzymes were identified exclusively from the host library (laccase, catalase, peroxidase, superoxide dismutase, carboxylesterase, cytochrome P450). Subsequently, functional analyses of phenoloxidase activity provided results that were strongly consistent with patterns of laccase gene expression. In particular, phenoloxidase activity and laccase gene expression are mostly restricted to symbiont-free foregut plus salivary gland tissues, and phenoloxidase activity is inducible by lignin feeding.</p> <p>Conclusion</p> <p>To our knowledge, this is the first time that a dual host-symbiont transcriptome sequencing effort has been conducted in a single termite species. This sequence database represents an important new genomic resource for use in further studies of collaborative host-symbiont termite digestion, as well as development of coevolved host and symbiont-derived biocatalysts for use in industrial biomass-to-bioethanol applications. Additionally, this study demonstrates that: (i) phenoloxidase activities are prominent in the <it>R. flavipes </it>gut and are not symbiont derived, (ii) expands the known number of host and symbiont glycosyl hydrolase families in <it>Reticulitermes</it>, and (iii) supports previous models of lignin degradation and host-symbiont collaboration in cellulose/hemicellulose digestion in the termite gut. All sequences in this paper are available publicly with the accession numbers <ext-link ext-link-id="FL634956" ext-link-type="gen">FL634956</ext-link>-<ext-link ext-link-id="FL640828" ext-link-type="gen">FL640828</ext-link> (Termite Gut library) and <ext-link ext-link-id="FL641015" ext-link-type="gen">FL641015</ext-link>-<ext-link ext-link-id="FL645753" ext-link-type="gen">FL645753</ext-link> (Symbiont library).</p