Nitrogen budgets and soil nitrogen stocks of organic and conventional cropping systems: how reconcile efficiency and sustainability of nitrogen use?

Organic and conventional cropping systems differ in the nature and amounts of nitrogen (N) inputs, which may affect efficiency and sustainability of N use. In the DOK (bio-Dynamic, bio-Organic, Konventionell) field experiment, organic and conventional cropping systems have been compared since 1978 at two fertilization levels (with level 2 being typical for the respective system and level 1 receiving half of this dose)

Standard methods for molecular research in Apis mellifera

From studies of behaviour, chemical communication, genomics and developmental biology, among many others, honey bees have long been a key organism for fundamental breakthroughs in biology. With a genome sequence in hand, and much improved genetic tools, honey bees are now an even more appealing target for answering the major questions of evolutionary biology, population structure, and social organization. At the same time, agricultural incentives to understand how honey bees fall prey to disease, or evade and survive their many pests and pathogens, have pushed for a genetic understanding of individual and social immunity in this species. Below we describe and reference tools for using modern molecular-biology techniques to understand bee behaviour, health, and other aspects of their biology. We focus on DNA and RNA techniques, largely because techniques for assessing bee proteins are covered in detail in Hartfelder et al. (2013). We cover practical needs for bee sampling, transport, and storage, and then discuss a range of current techniques for genetic analysis. We then provide a roadmap for genomic resources and methods for studying bees, followed by specific statistical protocols for population genetics, quantitative genetics, and phylogenetics. Finally, we end with three important tools for predicting gene regulation and function in honey bees: Fluorescence in situ hybridization (FISH), RNA interference (RNAi), and the estimation of chromosomal methylation and its role in epigenetic gene regulation.Fundação para a Ciência e Tecnologi

Folding-competent and folding-defective forms of Ricin A chain have different fates following retrotranslocation from the endoplasmic reticulum

We report that a toxic polypeptide retaining the potential to refold upon dislocation from the endoplasmic reticulum (ER) to the cytosol (ricin A chain; RTA) and a misfolded version that cannot (termed RTAΔ), follow ER-associated degradation (ERAD) pathways in Saccharomyces cerevisiae that substantially diverge in the cytosol. Both polypeptides are dislocated in a step mediated by the transmembrane Hrd1p ubiquitin ligase complex and subsequently degraded. Canonical polyubiquitylation is not a prerequisite for this interaction because a catalytically inactive Hrd1p E3 ubiquitin ligase retains the ability to retrotranslocate RTA, and variants lacking one or both endogenous lysyl residues also require the Hrd1p complex. In the case of native RTA, we established that dislocation also depends on other components of the classical ERAD-L pathway as well as an ongoing ER–Golgi transport. However, the dislocation pathways deviate strikingly upon entry into the cytosol. Here, the CDC48 complex is required only for RTAΔ, although the involvement of individual ATPases (Rpt proteins) in the 19S regulatory particle (RP) of the proteasome, and the 20S catalytic chamber itself, is very different for the two RTA variants. We conclude that cytosolic ERAD components, particularly the proteasome RP, can discriminate between structural features of the same substrate

BAT3 Guides Misfolded Glycoproteins Out of the Endoplasmic Reticulum

Secretory and membrane proteins that fail to acquire their native conformation within the lumen of the Endoplasmic Reticulum (ER) are usually targeted for ubiquitin-dependent degradation by the proteasome. How partially folded polypeptides are kept from aggregation once ejected from the ER into the cytosol is not known. We show that BAT3, a cytosolic chaperone, is recruited to the site of dislocation through its interaction with Derlin2. Furthermore, we observe cytoplasmic BAT3 in a complex with a polypeptide that originates in the ER as a glycoprotein, an interaction that depends on the cytosolic disposition of both, visualized even in the absence of proteasomal inhibition. Cells depleted of BAT3 fail to degrade an established dislocation substrate. We thus implicate a cytosolic chaperone as an active participant in the dislocation of ER glycoproteins.United States. National Institutes of HealthBoehringer Ingelheim Fond

Phosphorus dynamics in a tropical forest soil restored after strip mining

Background and aims We hypothesized that successful early ecosystem and soil development in these P-deficient soil materials will initially depend on effective re-establishment of P storage and cycling through organic matter. This hypothesis was tested in a 26-year chronosequence of seven lightly fertilized, oxidic soil materials restored to eucalypt forest communities after bauxite mining. Methods Total P (Pt) status, Hedley P fractions and partial chemical speciation (NaOH-EDTA extraction and analysed using solution 31P NMR spectroscopy) were determined in the restored soils. Results Concentrations of Pt and most Hedley fractions changed with restoration period, declined with depth and were strongly positively correlated with C and N concentrations. Biological P dominated the Labile and Intermediate P fractions while Long-term P was dominantly inorganic. Organic P concentrations in NaOH-EDTA extracts and their chemical natures were similar in restored and unburned native forest sites. Phosphomonoesters were the dominant class of organic P. Conclusions Surprisingly rapid P accretion and fractional changes occurred over 26 years, largely in the surface soils and closely associated with organic matter status. Alkaline hydrolysis products of phosphodiesters and pyrophosphate indicated the importance of microbial P cycling. The important consequences for long-term ecosystem development and biological diversity require further study

Mycoplasma hyorhinis-contaminated cell lines activate primary innate immune cells via a protease-sensitive factor

Mycoplasma are a frequent and occult contaminant of cell cultures, whereby these prokaryotic organisms can modify many aspects of cell physiology, rendering experiments that are conducted with such contaminated cells problematic. Chronic Mycoplasma contamination in human monocytic cells lines has been associated with suppressed Toll-like receptor (TLR) function. In contrast, we show here that components derived from a Mycoplasma hyorhinis-infected cell line can activate innate immunity in non-infected primary immune cells. Release of pro-inflammatory cytokines such as IL-6 by dendritic cells in response to Mycoplasma hyorhinis-infected cell components was critically dependent on the adapter protein MyD88 but only partially on TLR2. Unlike canonical TLR2 signaling that is triggered in response to the detection of Mycoplasma infection, innate immune activation by components of Mycoplasma-infected cells was inhibited by chloroquine treatment and sensitive to protease treatment. We further show that in plasmacytoid dendritic cells, soluble factors from Mycoplasma hyorhinis-infected cells induce the production of large amounts of IFN-α. We conclude that Mycoplasma hyorhinis-infected cell lines release protein factors that can potently activate co-cultured innate immune cells via a previously unrecognized mechanism, thus limiting the validity of such co-culture experiments

Biogenesis and functions of bacterial S-layers.

The outer surface of many archaea and bacteria is coated with a proteinaceous surface layer (known as an S-layer), which is formed by the self-assembly of monomeric proteins into a regularly spaced, two-dimensional array. Bacteria possess dedicated pathways for the secretion and anchoring of the S-layer to the cell wall, and some Gram-positive species have large S-layer-associated gene families. S-layers have important roles in growth and survival, and their many functions include the maintenance of cell integrity, enzyme display and, in pathogens and commensals, interaction with the host and its immune system. In this Review, we discuss our current knowledge of S-layer and related proteins, including their structures, mechanisms of secretion and anchoring and their diverse functions

NPK Bilanzen von ökologischer und konventioneller Landwirtschaft im Vergleich: Ergebnisse eines 35-jährigen Feldversuches

Die Ausreichende Verfügbarkeit von Stickstoff (N), Phosphor (P) und Kalium (K) ist essentiell für einen konstanten Ernteertrag in landwirtschaftlichen Systemen. Im DOK-Versuch in Therwil (Schweiz) wird seit 1978 ein Systemvergleich zwischen ökologischer und konventioneller Landwirtschaft im Rahmen eines Feldversuches betrieben. Die Verfahren biologisch-dynamisch (DYN) und organisch-biologisch (ORG) werden nur mit Stallmist gedüngt, während im konventionellen Verfahren (KON) zusätzlich mit Mineraldünger ausgeglichen wird. Im mineralisch gedüngten Verfahren (MIN) wird nur Mineraldünger ausgebracht, in der ungedüngten Kontrollfläche (NON) erfolgt seit Versuchsbeginn keine Düngung. Die Verfahren DYN, ORG und KON werden auf zwei Düngestufen geführt (2 = praxisübliche Düngung; 1 = halbe praxisübliche Dündung), Verfahren MIN nur auf Düngestufe 2. Ziel der Arbeit war es eine NPK Bilanz für den DOK-Versuch zu errechnen, um eine Abschätzung des Verlustpotentials bzw. von Nährstoffmangel der Feldfrüchte im jeweiligen Bewirtschaftungssystem zu ermöglichen. Die Nährstoffbilanz errechnete sich aus dem Vergleich jährlicher Eintrag minus jährlicher Austrag pro Versuchsparzelle. Berücksichtigte Einträge für die Elemente N, P und K waren: 1) Düngung, 2) Deposition, 3) Saatgut. Für N wurde zusätzlich die 4) symbiotische N-fixierung durch Leguminosen sowie der 5) Transfer von fixiertem N zu Gräsern, basierend auf vorhergehenden Studien im DOK Versuch, geschätzt. Berücksichtigte Austräge für die Elemente N, P und K waren: 6) Entzug durch Ernteprodukte sowie 7) Auswaschungsversluste. Für die Elemente N und P wurden zusätzlich die Bodenvorräte aus jährlichen (N) oder 7-jährlichen (P) Messungen in Ober- und Unterboden errechnet und mit den Ergebnissen der Bilanzierung in Beziehung gesetzt. Die wichtigsten Parameter der Nährstoffbilanzen waren die Faktoren Düngung sowie Entzug durch Ernteprodukte, wobei in der N-Bilanz auch die symbiotische N-fixierung und deren Transfer zu Gräsern eine gewichtige Rolle spielte. Die Ergebnisse der NPK-Bilanzierung deuten auf unterschiedliche Nährstofflimitierungen sowohl im Bezug auf die Verfahren, als auch auf den unterschiedlichen Düngestufen hin. Die Resultate werden in Bezug auf eine nachhaltige Bodennutzung in verschiedenen landwirtschaftlichen Systemen diskutiert

Determining Contaminant Distribution and Migration by Integrating Data from Multiple Cone Penetrometer-Based Tools

The cone penetrometer has been used for geologic characterization at the U.S. Department of Energy-owned Savannah River Site for the past seven years