Root-associated fungal communities colonizing two dominant semiarid grasses: Hilaria sp. and Stipa sp.

We conducted a preliminary survey of the fungal communities associated with roots of Stipa hymenoides and Hilaria jamesii, two grasses native to the southwestern United States. Root samples from 10 different plants were collected at a semiarid grassland in Utah. Fungal communities were assessed using microscopic and molecular methods. Roots were cleared with KOH and stained using blue ink to visualize mycorrhizal and endophytic fungi. A total of 100 root segments were surface sterilized and plated on malt extract agar with antibiotics. Fungal endophytes were identified using nrITS primers.

Results/Conclusions

Microscopic analyses showed that all root samples from both Hillaria and Stipa were colonized by dark septate and arbuscular mycorrhizal fungi. Vesicles and hyaline hyphae also were observed in all the roots. Sclerotia, a characteristic structure of some dark septate fungi were also found. Approximately 75 fungi were isolated representing at least 45 morphotypes. Molecular identification showed that both grasses are colonized by endophytes in the orders Pleosporales, Hypocreales, and Sordariales commonly found in semiarid grasses, liverworts, and mosses

Classical BI: Its Semantics and Proof Theory

We present Classical BI (CBI), a new addition to the family of bunched logics which originates in O'Hearn and Pym's logic of bunched implications BI. CBI differs from existing bunched logics in that its multiplicative connectives behave classically rather than intuitionistically (including in particular a multiplicative version of classical negation). At the semantic level, CBI-formulas have the normal bunched logic reading as declarative statements about resources, but its resource models necessarily feature more structure than those for other bunched logics; principally, they satisfy the requirement that every resource has a unique dual. At the proof-theoretic level, a very natural formalism for CBI is provided by a display calculus \`a la Belnap, which can be seen as a generalisation of the bunched sequent calculus for BI. In this paper we formulate the aforementioned model theory and proof theory for CBI, and prove some fundamental results about the logic, most notably completeness of the proof theory with respect to the semantics.Comment: 42 pages, 8 figure

Ecological distribution and population physiology defined by proteomics in a natural microbial community

Community proteomics applied to natural microbial biofilms resolves how the physiology of different populations from a model ecosystem change with measured environmental factors in situ.The initial colonists, Leptospirillum Group II bacteria, persist throughout ecological succession and dominate all communities, a pattern that resembles community assembly patterns in some macroecological systems.Interspecies interactions, and not abiotic environmental factors, demonstrate the strongest correlation to physiological changes of Leptospirillum Group II.Environmental niches of subdominant populations seem to be determined by combinations of specific sets of abiotic environmental factors

Soil seal development under simulated rainfall: structural, physical and hydrological dynamics

This study delivers new insights into rainfall-induced seal formation through a novel approach in the use of X-ray Computed Tomography (CT). Up to now seal and crust thickness have been directly quantified mainly through visual examination of sealed/crusted surfaces, and there has been no quantitative method to estimate this important property. X-ray CT images were quantitatively analysed to derive formal measures of seal and crust thickness. A factorial experiment was established in the laboratory using open-topped microcosms packed with soil. The factors investigated were soil type (three soils: silty clay loam - ZCL, sandy silt loam - SZL, sandy loam - SL) and rainfall duration (2-14 minutes). Surface seal formation was induced by applying artificial rainfall events, characterised by variable duration, but constant kinetic energy, intensity, and raindrop size distribution. Soil porosities derived from CT scans were used to quantify the thickness of the rainfall-induced surface seals and reveal temporal seal micro-morphological variations with increasing rainfall duration. In addition, the water repellency and infiltration dynamics of the developing seals were investigated by measuring water drop penetration time (WDPT) and unsaturated hydraulic conductivity (Kun). The range of seal thicknesses detected varied from 0.6 - 5.4 mm. Soil textural characteristics and OM content played a central role in the development of rainfall-induced seals, with coarser soil particles and lower OM content resulting in thicker seals. Two different trends in soil porosity vs. depth were identified: i) for SL soil porosity was lowest at the immediate soil surface, it then increased constantly with depth till the median porosity of undisturbed soil was equalled; ii) for ZCL and SL the highest reduction in porosity, as compared to the median porosity of undisturbed soil, was observed in a well-defined zone of maximum porosity reduction c. 0.24 - 0.48 mm below the soil surface. This contrasting behaviour was related to different dynamics and processes of seal formation which depended on the soil properties. The impact of rainfall-induced surface sealing on the hydrological behaviour of soil (as represented by WDTP and Kun) was rapid and substantial: an average 60% reduction in Kun occurred for all soils between 2 and 9 minutes rainfall, and water repellent surfaces were identified for SZL and ZCL. This highlights that the condition of the immediate surface of agricultural soils involving rainfall-induced structural seals has a strong impact in the overall ability of soil to function as water reservoir

Alcohol Consumption Trajectory Patterns in Adult Women with HIV Infection

HIV-infected women with excessive alcohol consumption are at risk for adverse health outcomes, but little is known about their long-term drinking trajectories. This analysis included longitudinal data, obtained from 1996–2006, from 2791 women with HIV from the Women’s Interagency HIV Study. Among these women, the proportion in each of five distinct drinking trajectories was: continued heavy drinking (3%), reduction from heavy to non-heavy drinking (4%), increase from non-heavy to heavy drinking (8%), continued non-heavy drinking (36%), and continued non-drinking (49%). Depressive symptoms, other substance use (crack/cocaine, marijuana, and tobacco), co-infection with HCV, and heavy drinking prior to enrollment were associated with trajectories involving future heavy drinking. In conclusion, many women with HIV change their drinking patterns over time. Clinicians and those providing alcohol-related interventions might target those with depression, current use of tobacco or illicit drugs, HCV infection, or a previous history of drinking problems

The Enterovirus 71 A-particle Forms a Gateway to Allow Genome Release: A CryoEM Study of Picornavirus Uncoating

Since its discovery in 1969, enterovirus 71 (EV71) has emerged as a serious worldwide health threat. This human pathogen of the picornavirus family causes hand, foot, and mouth disease, and also has the capacity to invade the central nervous system to cause severe disease and death. Upon binding to a host receptor on the cell surface, the virus begins a two-step uncoating process, first forming an expanded, altered "A-particle", which is primed for genome release. In a second step after endocytosis, an unknown trigger leads to RNA expulsion, generating an intact, empty capsid. Cryo-electron microscopy reconstructions of these two capsid states provide insight into the mechanics of genome release. The EV71 A-particle capsid interacts with the genome near the icosahedral two-fold axis of symmetry, which opens to the external environment via a channel ~10 Å in diameter that is lined with patches of negatively charged residues. After the EV71 genome has been released, the two-fold channel shrinks, though the overall capsid dimensions are conserved. These structural characteristics identify the two-fold channel as the site where a gateway forms and regulates the process of genome release. © 2013 Shingler et al

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC