The genus Aspergillus comprises a few hundred species sharing a common asexual spore forming structure, the aspergillum. Approximately one-third of these species also produce a sexual stage, all but ...five of which are known to be homothallic. Sexual stages associated with Aspergillus fall into approximately ten different genera, reflecting a tremendous degree of phylogenetic and biological diversity. Sexual stages in Aspergillus are plectomycetous, typical for the order in which it resides, the Eurotiales. Theoretically, a homothallic Aspergillus species can produce both asexual conidia and sexual ascospores in both clonal and recombinant fashion, although the actual significance of these potential modes of reproduction is unclear. Aspergillus species with known sexual stages tend to be minor players in infections of humans, perhaps because of their tendency to produce fewer asexual spores compared to their non-teleomorphic congeners. The discovery of population genetic and genomic evidence for sex in species with no known sexual stage indicates that no assumptions can be made about the clonal versus recombinant life histories of a species based on its known mitotic and/or meiotic reproductive modes.
► The state, development donors and Taliban attempted to effect social change in Pakistan’s Swat valley. ► To understand these dynamics, I compare the explanatory power of deliberative and radical ...theorising. ► Both approaches fail to provide analytical, procedural or normative insights due to their eurocentric ontologies. ► I advocate for a change of focus from ontologised explanation to an analysis of the actual ‘how’ of politics. ► This focus on ‘politics as practice’ provides differentiated insights into Swat, being a postcolonial arena.
In recent years, the Swat valley in North-West Pakistan has witnessed various waves of ‘politics’. Different groups have attempted to change socio-economic conditions, each according to their clear visions of a better future. After a period of top-down attempts at modernisation by the state, development projects inspired by deliberative democracy have attempted to increase political space for ‘local people’, but failed. Swat has also witnessed agonistic politics, with the emergence of a fundamentalist social movement that constructed a radical discourse of otherisation, entering into an antagonism with the state that created war and havoc. Thus, Swat offers a challenging learning ground to reflect on practices for producing change, as well as on theoretical currents in academia. I argue that deliberative and radical theorising provide insights into the political life of Swat, but fall short analytically (missing social complexities), procedurally (favouring specific techniques of social negotiation), and normatively (due to preconceived understandings of a ‘better future’). I substantiate my argument by showing that both positions take euro-centric conceptualisation of ‘citizens’, a (modern) ‘state’, and ‘citizen/state relations’ as universals – basic conditions that are not met in the post-colonial setting of Swat. I therefore argue that our curiosity should be redirected from ontologised explanation to an analysis of actual practices of societal negotiation and the norms within which these are embedded. Such insights will make it possible for us to appreciate the enormous challenges people in Swat face in their struggle to negotiate aspirations among disparate voices and to imagine some common understanding of a ‘better future’ – challenges that go beyond what deliberative or agonistic theorising can offer.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Abstract
RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The bacterial RhlE-like DEAD-box RNA helicases are among ...the least well studied of these enzymes. They are widespread especially among Proteobacteria, whose genomes often encode multiple homologs. The significance of the expansion and diversification of RhlE-like proteins for bacterial fitness has not yet been established. Here, we study the two RhlE homologs present in the opportunistic pathogen Pseudomonas aeruginosa. We show that, in the course of evolution, RhlE1 and RhlE2 have diverged in their biological functions, molecular partners and RNA-dependent enzymatic activities. Whereas RhlE1 is mainly needed for growth in the cold, RhlE2 also acts as global post-transcriptional regulator, affecting the level of hundreds of cellular transcripts indispensable for both environmental adaptation and virulence. The global impact of RhlE2 is mediated by its unique C-terminal extension, which supports the RNA unwinding activity of the N-terminal domain as well as an RNA-dependent interaction with the RNase E endonuclease and the cellular RNA degradation machinery. Overall, our work reveals how the functional and molecular divergence between two homologous RNA helicases can contribute to bacterial fitness and pathogenesis.
Graphical Abstract
Graphical Abstract
Schematic representation of RhlE1 and RhlE2 biological role in Pseudomonas aeruginosa.
To derive reference points (RPs) for health-based guidance values, the benchmark dose (BMD) approach increasingly replaces the no-observed-adverse-effect level approach. In the BMD approach, the RP ...corresponds to the benchmark dose lower confidence bounds (BMDLs) of a mathematical dose–response model derived from responses of animals over the entire dose range applied. The use of the entire dose range is seen as an important advantage of the BMD approach. This assumes that responses over the entire dose range are relevant for modeling low-dose responses, the basis for the RP. However, if part of the high-dose response was unnoticed triggered by a mechanism of action (MOA) that does not work at low doses, the high-dose response distorts the modeling of low-dose responses. Hence, we investigated the effect of high-dose specific responses on BMDLs by assuming a low- and a high-dose MOA. The BMDLs resulting from modeling fictitious quantal data were scattered over a broad dose range overlapping with the toxic range. Hence, BMDLs are sensitive to high-dose responses even though they might be irrelevant to low-dose response modeling. When applying the BMD approach, care should be taken that high-dose specific responses do not unduly affect the BMDL that derives from low doses.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
The kinetic analysis of irreversible protein reactions requires an analytical technique that provides access to time-dependent infrared spectra in a single shot. Here, we present a spectrometer based ...on dual-frequency-comb spectroscopy using mid-infrared frequency combs generated by quantum cascade lasers. Attenuation of the intensity of the combs by molecular vibrational resonances results in absorption spectra covering 55 cm–1 in the fingerprint region. The setup has a native resolution of 0.3 cm–1, noise levels in the μOD range, and achieves sub-microsecond time resolution. We demonstrate the simultaneous recording of both spectra and transients of the photoactivated proton pump bacteriorhodopsin. More importantly, a single shot, i.e., a single visible light excitation, is sufficient to extract spectral and kinetic characteristics of several intermediates in the bacteriorhodopsin photocycle. This development paves the way for the noninvasive analysis of enzymatic conversions with high time resolution, broad spectral coverage, and minimal sample consumption.
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IJS, KILJ, NUK, PNG, UL, UM
A Theory of States and Traits-Revised Steyer, Rolf; Mayer, Axel; Geiser, Christian ...
Annual review of clinical psychology,
01/2015, Volume:
11, Issue:
1
Journal Article
Peer reviewed
Open access
We present a revision of latent state-trait (LST-R) theory with new definitions of states and traits. This theory applies whenever we study the consistency of behavior, its variability, and its ...change over time. States and traits are defined in terms of probability theory. This allows for a seamless transition from theory to statistical modeling of empirical data. LST-R theory not only gives insights into the nature of latent variables but it also takes into account four fundamental facts: Observations are fallible, they never happen in a situational vacuum, they are always made using a specific method of observations, and there is no person without a past. Although the first fact necessitates considering measurement error, the second fact requires allowances for situational fluctuations. The third fact implies that, in the first place, states and traits are method specific. Furthermore, compared to the previous version of LST theory (see, e.g.,
Steyer et al. 1992
,
1999
), our revision is based on the notion of a person-at-time-t. The new definitions in LST-R theory have far-reaching implications that not only concern the properties of states, traits, and the associated concepts of measurement errors and state residuals, but also are related to the analysis of states and traits in longitudinal observational and intervention studies.
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CMK, FFLJ, NUK, UL, UM, UPUK
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from ...traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.
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BFBNIB, GIS, IJS, KISLJ, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
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•Simple, low cost and easy to prepare electrochemical device.•Shellac natural polymer.•Detection of sulfamethoxazole in real samples.•Miniaturized paper-based device.
The growth in ...the demand for mass analysis, in a fast and safe way, with good reliability and low cost has aroused great scientific interest in the search for new devices that prioritize precision and time. In this sense, this work presents a simple, disposable, and easy-to-use electrochemical sensor, developed on a waterproof paper substrate with a conductive ink based on shellac, a resin of natural origin, and graphite. The conductive ink was obtained through a simple mixture of its components and deposited on the paper substrate, being ready to use after a drying period. The new sensor was employed for the electrochemical detection of sulfamethoxazole (SMX), an antibiotic belonging to the class of sulfonamides, which presents great importance due to its direct impact on the flow of the food chain and is, therefore, commonly found as a metabolic residue in environmental and food samples. Using the differential pulse voltammetry technique, a linear range of 5.0 μmol L−1–100 μmol L−1 and a limit of detection of 0.4 μmol L−1 were obtained. The electrochemical sensor was also employed for the analysis of SMX in water and milk samples, and recovery values between 91 and 110% were obtained, proving that the development and application of the new conductive ink proposed for the fabrication of disposable devices provided an efficient electrochemical detection of SMX in the applied samples.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Giardia intestinalis is a non-invasive, protozoan parasite infecting the upper small intestine of most mammals. Symptomatic infections cause the diarrhoeal disease giardiasis in humans and animals, ...but at least half of the infections are asymptomatic. However, the molecular underpinnings of these different outcomes of the infection are still poorly defined. Here, we studied the early transcriptional response to G. intestinalis trophozoites, the disease-causing life-cycle stage, in human enteroid-derived, 2-dimensional intestinal epithelial cell (IEC) monolayers. Trophozoites preconditioned in media that maximise parasite fitness triggered only neglectable inflammatory transcription in the IECs during the first hours of co-incubation. By sharp contrast, "non-fit" or lysed trophozoites induced a vigorous IEC transcriptional response, including high up-regulation of many inflammatory cytokines and chemokines. Furthermore, "fit" trophozoites could even suppress the stimulatory effect of lysed trophozoites in mixed infections, suggesting active G. intestinalis suppression of the IEC response. By dual-species RNA-sequencing, we defined the IEC and G. intestinalis gene expression programs associated with these differential outcomes of the infection. Taken together, our results inform on how G. intestinalis infection can lead to such highly variable effects on the host, and pinpoints trophozoite fitness as a key determinant of the IEC response to this common parasite.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A large collection of strains belonging to the Fusarium solani species complex (FSSC) was isolated from soil and perithecia in primary forests in Sri Lanka (from fallen tree bark) and tropical ...Australia (Queensland, from fallen tree fruits and nuts). Portions of the translation elongation factor 1-alpha (tef1) gene, the nuclear large subunit (NLSU) and internal transcribed spacer regions (ITS) of the nuclear ribosomal RNA genes were sequenced in 52 isolates from soil and perithecia. The FSSC was divided previously into three clades with some biogeographic structure, termed Clades 1, 2 and 3. All Sri Lankan and Australian soil isolates were found to be members of Clade 3, most grouping with the cosmopolitan soil-associated species F. falciforme. All but two Sri Lankan perithecial isolates were associated with a set of five divergent phylogenetic lineages that were associated with Clade 2. Australian perithecial isolates resided in a subclade of Clade 3 where most of the previously defined mating populations of the FSSC reside. Isolates from perithecia and those cultured from soil were always members of different species lineages, even when derived from proximal locations. The previous biogeographic assignment of Clade 2 to South America is now expanded to the worldwide tropics. Sri Lanka appears to be an important center of diversity for the FSSC. Nectria haematococca is epitypified with a collection from the type locality in Sri Lanka; its anamorph is described as a new species, Fusarium haematococcum. Neocosmospora E.F. Smith is adopted as the correct genus for Nectria haematococca. These new species are described: F. kurunegalense/Neo. kurunegalensis, F. rectiphorus/Neo. rectiphora/, F. mahasenii/Neo. mahasenii/, F. kelerajum/Neo. keleraja.
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BFBNIB, GIS, IJS, KISLJ, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
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