Protein domains and architectural innovation in plant-associated Proteobacteria.

Journal ArticleResearch Support, Non-U.S. Gov'tCopyright © 2005 Studholme et al; licensee BioMed Central Ltd.BACKGROUND: Evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. The functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. We clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by Pfam (release 16.0). This revealed that, although there was a correlation between phylogeny and domain content, other factors also have an influence. This observation motivated an investigation of the relationship between an organism's lifestyle and the complement of domains and domain architectures found within its proteome. RESULTS: We took a census of all protein domains and domain combinations (architectures) encoded in the completely-sequenced proteobacterial genomes. Nine protein domain families were identified that are found in phylogenetically disparate plant-associated bacteria but are absent from non-plant-associated bacteria. Most of these are known to play a role in the plant-associated lifestyle, but they also included domain of unknown function DUF1427, which is found in plant symbionts and pathogens of the alpha-, beta- and gamma-Proteobacteria, but not known in any other organism. Further, several domains were identified as being restricted to phytobacteria and Eukaryotes. One example is the RolB/RolC glucosidase family, which is found only in Agrobacterium species and in plants. We identified the 0.5% of Pfam protein domain families that were most significantly over-represented in the plant-associated Proteobacteria with respect to the background frequencies in the whole set of available proteobacterial proteomes. These included guanylate cyclase, domains implicated in aromatic catabolism, cellulase and several domains of unknown function. We identified 459 unique domain architectures found in phylogenetically diverse plant pathogens and symbionts that were absent from non-pathogenic and non-symbiotic relatives. The vast majority of these were restricted to a single species or several closely related species and so their distributions could be better explained by phylogeny than by lifestyle. However, several architectures were found in two or more very distantly related phytobacteria but absent from non-plant-associated bacteria. Many of the proteins with these unique architectures are predicted to be secreted. In Pseudomonas syringae pathovar tomato, those genes encoding genes with novel domain architectures tended to have atypical GC contents and were adjacent to insertion sequence elements and phage-like sequences, suggesting acquisition by horizontal transfer. CONCLUSIONS: By identifying domains and architectures unique to plant pathogens and symbionts, we highlighted candidate proteins for involvement in plant-associated bacterial lifestyles. Given that characterisation of novel gene products in vivo and in vitro is time-consuming and expensive, this computational approach may be useful for reducing experimental search space. Furthermore we discuss the biological significance of novel proteins highlighted by this study in the context of plant-associated lifestyles.Gatsby Charitable Foundatio

Spray-Drying Cellulose Nanofibrils: Effect of Drying Process Parameters on Particle Morphology and Size Distribution

Spray-drying was chosen as an appropriately scalable manufacturing method to dry cellulose nanofibril (CNF) suspensions. Spray-drying of two different types of CNF suspensions—nanofibrillated cellulose (NFC) and cellulose nanocrystals (CNC)—was carried out using a laboratory-scale spray dryer. Effects of three spray-drying process parameters on particle morphology and particle size distribution were evaluated: 1) gas flow rate; 2) liquid feed rate; and 3) suspension solids concentration. Particle morphology was characterized by scanning electron microscopy (SEM) and a morphology analyzer. SEM showed that spray-drying of NFC formed fibrous particles and fibrous agglomerates, whereas spray-drying CNCs produced spherical and mushroom cap (or donut)-shaped particles. Particle morphology formation mechanisms are proposed for spray-drying nanocellulose suspensions. The effect of the three spray-drying process parameters on particle size distribution depended on the drying nature of the materials. The three parameters interacted to significantly affect particle size of CNC suspensions, whereas they did not interact to affect particle size of NFC suspensions. For the CNC suspension, a higher gas flow rate produced smaller particle sizes. The gas flow rate did not affect particle size for NFC suspensions. The effect of liquid feed rate and solids concentration on CNF particle size was negligible in this study. The smallest mean circle equivalent diameters produced in this study were 3.95 μm for NFC and 3.64 μm for CNC

Two in one: cryptic species discovered in biological control agent populations using molecular data and crossbreeding experiments

There are many examples of cryptic species that have been identified through DNA-barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution

The rise of the citizen author: Writing within social media

The concept of the citizen author is defined and explored within the publishing industry. In order to understand what positions the citizen author currently, and potentially could, hold it begins with a historical view of their rise, including concepts of their eighteenth century antecedents. But the focus of this research is on their growth alongside that of social media platforms. This allows for drawing out relationships between genre fiction, publishers, and the citizen author, which provides a more full understanding of the power dynamics involved when publishers, social media, and the citizen authors mix in the current industry climate.N/

Neutron scattering sum rules, symmetric exchanges, and helicoidal magnetism in MnSb2O6

MnSb2O6 is based on the noncentrosymmetric P321 space group with magnetic Mn2+ (S=5/2, L≈0) spins ordering below TN=12K in a cycloidal structure. The spin rotation plane was found to be tilted away from the c axis [Kinoshita, Phys. Rev. Lett. 117, 047201 (2016)10.1103/PhysRevLett.117.047201] resulting as a helicoidal ground state, which we refer as the tilted structure. In our previous diffraction study [Chan, Phys. Rev. B 106, 064403 (2022)10.1103/PhysRevB.106.064403] we found no evidence that this tilted structure is favored over the pure cycloidal order (referred as the untilted structure). The ground-state magnetic structure, expected to be built and originate from seven nearest-neighbor Heisenberg exchange constants, has been shown to be coupled to the underlying crystallographic chirality with polar domain switching being reported. We apply neutron spectroscopy to extract these symmetric exchange constants. Given the high complexity of the magnetic exchange network, crystallographic structure and complications fitting many parameter linear spin-wave models, we take advantage of multiplexed neutron instrumentation to use the first moment sum rule of neutron scattering to estimate these symmetric exchange constants. The first moment of neutron scattering provides a way of deriving the Heisenberg exchange constant between two neighboring spins if the relative angle and distance of the two ordered spins is known. We show that the first moment sum rule combined with the known magnetic ordering wavevector fixes six of the seven exchange constants. The remaining exchange constant is not determined by this analysis because of the equal spatial bond distances present for different chiral exchange interactions. However, we find this parameter is fixed by the magnon dispersion near the magnetic zone boundary, which is not sensitive to the tilting of the global magnetic structure. We then use these parameters to calculate the low-energy spin-waves in the Néel state to reproduce the neutron response without strong antisymmetric coupling. Using Green's response functions, the stability of long-wavelength excitations in the context of our proposed untilted magnetic structures is then discussed. The results show the presence of strong symmetric exchange constants for the chiral exchange pathways and illustrate an underlying coupling between crystallographic and magnetic "chirality"through predominantly symmetric exchange. We further argue that the excitations can be consistently modelled in terms of an untilted magnetic structure in the presence of symmetric-only exchange constants

Common Risk Variants in AHI1 Are Associated With Childhood Steroid Sensitive Nephrotic Syndrome

Introduction: Steroid-sensitive nephrotic syndrome (SSNS) is the most common form of kidney disease in children worldwide. Genome-wide association studies (GWAS) have demonstrated the association of SSNS with genetic variation at HLA-DQ/DR and have identified several non-HLA loci that aid in further understanding of disease pathophysiology. We sought to identify additional genetic loci associated with SSNS in children of Sri Lankan and European ancestry. Methods: We conducted a GWAS in a cohort of Sri Lankan individuals comprising 420 pediatric patients with SSNS and 2339 genetic ancestry matched controls obtained from the UK Biobank. We then performed a transethnic meta-analysis with a previously reported European cohort of 422 pediatric patients and 5642 controls. Results: Our GWAS confirmed the previously reported association of SSNS with HLA-DR/DQ (rs9271602, P = 1.12 × 10−27, odds ratio [OR] = 2.75). Transethnic meta-analysis replicated these findings and identified a novel association at AHI1 (rs2746432, P = 2.79 × 10−8, OR = 1.37), which was also replicated in an independent South Asian cohort. AHI1 is implicated in ciliary protein transport and immune dysregulation, with rare variation in this gene contributing to Joubert syndrome type 3. Conclusions: Common variation in AHI1 confers risk of the development of SSNS in both Sri Lankan and European populations. The association with common variation in AHI1 further supports the role of immune dysregulation in the pathogenesis of SSNS and demonstrates that variation across the allele frequency spectrum in a gene can contribute to disparate monogenic and polygenic diseases

A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments

The volatile compound dimethylsulphide (DMS) is important in climate regulation, the sulphur cycle and signalling to higher organisms. Microbial catabolism of the marine osmolyte dimethylsulphoniopropionate (DMSP) is thought to be the major biological process generating DMS. Here we report the discovery and characterisation of the first gene for DMSP-independent DMS production in any bacterium. This gene, mddA, encodes a methyltransferase that methylates methanethiol (MeSH) and generates DMS. MddA functions in many taxonomically diverse bacteria including sediment-dwelling pseudomonads, nitrogen-fixing bradyrhizobia and cyanobacteria, and mycobacteria, including the pathogen Mycobacterium tuberculosis. The mddA gene is present in metagenomes from varied environments, being particularly abundant in soil environments, where it is predicted to occur in up to 76% of bacteria. This novel pathway may significantly contribute to global DMS emissions, especially in terrestrial environments, and could represent a shift from the notion that DMSP is the only significant precursor of DMS

Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere

Background and aims: To form nitrogen-fixing nodules on pea roots, Rhizobium leguminosarum biovar viciae must be competitive in the rhizosphere. Our aim was to identify genes important for rhizosphere fitness. Methods: Signature-tagged mutants were screened using microarrays to identify mutants reduced for growth in pea rhizospheres. Candidate mutants were assessed relative to controls for growth in minimal medium, growth in pea rhizospheres and for infection of peas in mixed inoculants. Mutated genes were identified by DNA sequencing and confirmed by transduction. Results: Of 5508 signature-tagged mutants, microarrays implicated 50 as having decreased rhizosphere fitness. Growth tests identified six mutants with rhizosphere-specific phenotypes. The mutation in one of the genes (araE) was in an arabinose catabolism operon and blocked growth on arabinose. The mutation in another gene (pcaM), encoding a predicted solute binding protein for protocatechuate and hydroxybenzoate uptake, decreased growth on protocatechuate. Both mutants were decreased for nodule infection competitiveness with mixed inoculants, but nodulated peas normally when inoculated alone. Other mutants with similar phenotypes had mutations predicted to affect secondary metabolism. Conclusions: Catabolism of arabinose and protocatechuate in the pea rhizosphere is important for competitiveness of R.l. viciae. Other genes predicted to be involved in secondary metabolism are also important

Baubles, Bangles, and Biotypes: A Critical Review of the use and Abuse of the Biotype Concept

Pest species of insects are notoriously prone to escape the weapons deployed in management efforts against them. This is particularly true in herbivorous insects. When a previously successful tactic fails the insect population has apparently adapted to it and is often considered to be a new or distinct entity, and given the non-formal category ‘biotype’. The entities falling under the umbrella term ‘biotype’ are not consistent either within or between biotypes, and their underlying genetic composition and origins, while generally unknown, are likely heterogeneous within and variable between biotypes. In some cases race or species may be more appropriate referents. Some examples of applications of the concept in the context of host plant resistance are discussed. It is argued here that the term ‘biotype’ and its applications are overly simplistic, confused, have not proved useful in current pest management, and lack predictive power for future management

Intensive group training protocol versus guideline physiotherapy for patients with chronic low back pain: a randomised controlled trial

Intensive group training using principles of graded activity has been proven to be effective in occupational care for workers with chronic low back pain. Objective of the study was to compare the effects of an intensive group training protocol aimed at returning to normal daily activities and guideline physiotherapy for primary care patients with non-specific chronic low back pain. The study was designed as pragmatic randomised controlled trial with a setup of 105 primary care physiotherapists in 49 practices and 114 patients with non-specific low back pain of more than 12 weeks duration participated in the study. In the intensive group training protocol exercise therapy, back school and operant-conditioning behavioural principles are combined. Patients were treated during 10 individual sessions along 20 group sessions. Usual care consisted of physiotherapy according to the Dutch guidelines for Low Back Pain. Main outcome measures were functional disability (Roland Morris disability questionnaire), pain intensity, perceived recovery and sick leave because of low back pain assessed at baseline and after 6, 13, 26 and 52 weeks. Both an intention-to-treat analysis and a per-protocol analysis were performed. Multilevel analysis did not show significant differences between both treatment groups on any outcome measures during the complete follow-up period, with one exception. After 26 weeks the protocol group showed more reduction in pain intensity than the guideline group, but this difference was absent after 52 weeks. We finally conclude that an intensive group training protocol was not more effective than usual physiotherapy for chronic low back pain