What is Microthrix parvicella ?

Microthrix parvicella is one of the filamentous bacteria that is known to create problems in the operation of activated sludge plants. Its physiology has already been investigated, although primarily in the context of its being a bulking species. It is now recognized that it is one of the major foam-forming organisms and, as such, needs further study. The initial isolation of M. parvicella did not prove to be as easy as would be expected from the earlier work and, eventually, micromanipulation was required. Growth studies showed that it exhibited several morphological forms, only one of which was that described previously. This has led to doubts about the classification of this species which does not yet have a clearly defined bacteriological designation.     

The unexpected long period of elevated CH4 emissions from an inundated fen meadow ended only with the occurrence of cattail (Typha latifolia)

Drainage and agricultural use transform natural peatlands from a net carbon (C) sink to a net C source. Rewetting of peatlands, despite of high methane (CH₄) emissions, holds the potential to mitigate climate change by greatly reducing CO₂ emissions. However, the time span for this transition is unknown because most studies are limited to a few years. Especially, nonpermanent open water areas often created after rewetting, are highly productive. Here, we present 14 consecutive years of CH₄ flux measurements following rewetting of a formerly long-term drained peatland in the Peene valley. Measurements were made at two rewetted sites (non-inundated vs. inundated) using manual chambers. During the study period, significant differences in measured CH₄ emissions occurred. In general, these differences overlapped with stages of ecosystem transition from a cultivated grassland to a polytrophic lake dominated by emergent helophytes, but could also be additionally explained by other variables. This transition started with a rapid vegetation shift from dying cultivated grasses to open water floating and submerged hydrophytes and significantly increased CH₄ emissions. Since 2008, helophytes have gradually spread from the shoreline into the open water area, especially in drier years. This process was periodically delayed by exceptional inundation and eventually resulted in the inundated site being covered by emergent helophytes. While the period between 2009 and 2015 showed exceptionally high CH₄ emissions, these decreased significantly after cattail and other emergent helophytes became dominant at the inundated site. Therefore, CH₄ emissions declined only after 10 years of transition following rewetting, potentially reaching a new steady state. Overall, this study highlights the importance of an integrative approach to understand the shallow lakes CH₄ biogeochemistry, encompassing the entire area with its mosaic of different vegetation forms. This should be ideally done through a study design including proper measurement site allocation as well as long-term measurements.     

A review of methods to trace material flows into final products in dynamic material flow analysis: From industry shipments in physical units to monetary input–output tables,Part 1

Dynamic material flow analysis (dMFA) is widely used to model stock-flow dynamics. To appropriately represent material lifetimes, recycling potentials, and service provision, dMFA requires data about the allocation of economy-wide material consumption to different end-use products or sectors, that is, the different product stocks, in which material consumption accumulates. Previous estimates of this allocation only cover few years, countries, and product groups. Recently, several new methods for estimating end-use product allocation in dMFA were proposed, which so far lack systematic comparison. We review and systematize five methods for tracing material consumption into end-use products in inflow-driven dMFA and discuss their strengths and limitations. Widely used data on industry shipments in physical units have low spatio-temporal coverage, which limits their applicability across countries and years. Monetary input–output tables (MIOTs) are widely available and their economy-wide coverage makes them a valuable source to approximate material end-uses. We find four distinct MIOT-based methods: consumption-based, waste input–output MFA (WIO-MFA), Ghosh absorbing Markov chain, and partial Ghosh. We show that when applied to a given MIOT, the methods’ underlying input–output models yield the same results, with the exception of the partial Ghosh method, which involves simplifications. For practical applications, the MIOT system boundary must be aligned to those of dMFA, which involves the removal of service flows, sector (dis)aggregation, and re-defining specific intermediate outputs as final demand. Theoretically, WIO-MFA, applied to a modified MIOT, produces the most accurate results as it excludes massless and waste transactions. In part 2 of this work, we compare methods empirically and suggest improvements for aligning MIOT-dMFA system boundaries.     

PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design

The ability to design customized proteins to perform specific tasks is of great interest. We are particularly interested in the design of sensitive and specific small molecule ligand-binding proteins for biotechnological or biomedical applications. Computational methods can narrow down the immense combinatorial space to find the best solution and thus provide starting points for experimental procedures. However, success rates strongly depend on accurate modeling and energetic evaluation. Not only intra- but also intermolecular interactions have to be considered. To address this problem, we developed PocketOptimizer, a modular computational protein design pipeline, that predicts mutations in the binding pockets of proteins to increase affinity for a specific ligand. Its modularity enables users to compare different combinations of force fields, rotamer libraries, and scoring functions. Here, we present a much-improved version––PocketOptimizer 2.0. We implemented a cleaner user interface, an extended architecture with more supported tools, such as force fields and scoring functions, a backbone-dependent rotamer library, as well as different improvements in the underlying algorithms. Version 2.0 was tested against a benchmark of design cases and assessed in comparison to the first version. Our results show how newly implemented features such as the new rotamer library can lead to improved prediction accuracy. Therefore, we believe that PocketOptimizer 2.0, with its many new and improved functionalities, provides a robust and versatile environment for the design of small molecule-binding pockets in proteins. It is widely applicable and extendible due to its modular framework. PocketOptimizer 2.0 can be downloaded at https://github.com/Hoecker-Lab/pocketoptimizer .     

Letter from the Editors

Transgenic Research -     

Pulmonary maturation in the hypophysectomised ovine fetus. Differential responses to adrenocorticotrophin and cortisol

Pulmonary maturation in six ovine fetuses hypophysectomised by a cryosurgical method at 0.7-0.8 of pregnancy and delivered by hysterotomy at 152.2 +/- 2.9 (SD) days was compared with that in seven control fetuses delivered at 144.5 +/- 3.5 days. Both the wet and the dry weight of the lungs was less in the hypophysectomised fetuses but total DNA did not differ. Lung volumes at 40 cm of H2O and at 5 cm of H2O on deflation in hypophysectomised fetuses were less than one-third that of controls. Saturated phosphatidylcholine, as an estimate of surfactant, was lower in both lung tissue and lavage fluid. A further group of hypophysectomised fetuses was infused intravenously either with cortisol at 1 mg/h for 72 h (n = 6), or with ACTH1-24 at 5 microgram/h for 84 h (n = 6) before delivery at 155.0 +/- 2.1 days and 154.2 +/- 3.9 days respectively. None of the indices of pulmonary maturation in the cortisol-treated fetuses differed from those in untreated hypophysectomised fetuses whereas values for lung volumes at 40 and 5 cm of H2O in ACTH-treated fetuses were more than twice those of untreated hypophysectomised fetuses and did not differ significantly from controls. In addition, the amount of saturated phosphatidylcholine in lavage fluid was greater in ACTH-treated fetuses (0.13 +/- 0.10 mg/g) than in untreated hypophysectomised fetuses (0.04 +/- 0.48 mg/g). Lung volume at 40 cm of H2O in four fetuses that were thyroidectomised at the time of hypophysectomy responded to ACTH as in hypophysectomised fetuses with intact thyroids but other indices were unaffected. We conclude that hypophysectomy retards pulmonary maturation in fetal sheep. Since ACTH restores distensibility and increases alveolar surfactant in the absence of other pituitary hormones it is likely that ACTH has a major role in lung maturation. The lack of response to cortisol suggests that the effect of ACTH is not mediated only by circulating cortisol.     

Polyhydroxyphenyläther aus der phaeophycee Sargassum muticum

From an acetylated fraction of Sargassum muticum (Yendo) Fensholt were isolated: phloroglucinol tri-acetate; diphlorethol pentaacetate (2,4,6,3′,5′-pentaacetoxydiphenyl ether), bifuhalol hexaacetate (2,4,6,3′,4′,5′-hexaacetoxydiphenyl ether), trifuhalol A octaacetate (2,6-diacetoxy-1-(3,4,5-triacetoxyphenoxy)-4-(2,4,6-triacetoxy- phenoxy)-benzene), and the new trifuhalol B octaacetate(3,5-diacetoxy -1-(2,4,6-triacetoxyphenoxy)-2-(3,4,5- triacetoxyphenoxy)-benzene).     

Statistical analysis of a linkage experiment in barley involving quantitative trait loci for height and ear-emergence time and two genetic markers on chromosome 4

Summary The quantitative traits height and ear-emergence date were analyzed in the F₂ progeny of a cross between a tall winter barley cultivar (Gerbel) and a short spring barley cultivar (Heriot). The trait distributions were found to be related to the genotypes at two biochemical loci, -amylase (Bmy1) and water-soluble protein (Wsp3), which are known to lie on the long arm of chromosome 4. Linkages between each trait and the markers were investigated using normal mixture models. The two parental phenotypes and the heterozygote phenotype of Bmy1 were distinguishable so the model could be used directly to estimate linkage between Bmy1 and a quantitative trait locus (QTL) for height (Height). The Gerbel homozygote and heterozygote phenotype of Wsp3 could not be distinguished and the model was adapted accordingly. The proportion of plants requiring vernalization was consistent with control by two independent genes acting epistatically, and a normal mixture model based on a two-gene hypothesis was fitted to the distribution of ear-emergence date to estimate linkage between the marker loci and a QTL for ear-emergence date (Vrn1). The parameters of each model were the recombination fraction between the marker locus and the QTL and the means and standard deviations associated with each QTL genotype; these were estimated by maximum likelihood. The fitted distributions correspond well to those observed and the order of the loci along the chromosome is inferred to be Height — Vrn1 — Bmy1 — Wsp3, with Wsp3 being the most distal.