Soil microbial diversity affects soil organic matter decomposition in a silty grassland soil

Soil microorganisms play a pivotal role in soil organic matter (SOM) turn-over and their diversity is discussed as a key to the function of soil ecosystems. However, the extent to which SOM dynamics may be linked to changes in soil microbial diversity remains largely unknown. We characterized SOM degradation along a microbial diversity gradient in a two month incubation experiment under controlled laboratory conditions. A microbial diversity gradient was created by diluting soil suspension of a silty grassland soil. Microcosms containing the same sterilized soil were re-inoculated with one of the created microbial diversities, and were amended with ¹³C labeled wheat in order to assess whether SOM decomposition is linked to soil microbial diversity or not. Structural composition of wheat was assessed by solid-state ¹³C nuclear magnetic resonance, sugar and lignin content was quantified and labeled wheat contribution was determined by ¹³C compound specific analyses. Results showed decreased wheat O-alkyl-C with increasing microbial diversity. Total non-cellulosic sugar-C derived from wheat was not significantly influenced by microbial diversity. Carbon from wheat sugars (arabinose-C and xylose-C), however, was highest when microbial diversity was low, indicating reduced wheat sugar decomposition at low microbial diversity. Xylose-C was significantly correlated with the Shannon diversity index of the bacterial community. Soil lignin-C decreased irrespective of microbial diversity. At low microbial diversity the oxidation state of vanillyl–lignin units was significantly reduced. We conclude that microbial diversity alters bulk chemical structure, the decomposition of plant litter sugars and influences the microbial oxidation of total vanillyl–lignins, thus changing SOM composition.     

Modeling the estrogen receptor to growth factor receptor signaling switch in human breast cancer cells

Breast cancer cells develop resistance to endocrine therapies by shifting between estrogen receptor (ER)-regulated and growth factor receptor (GFR)-regulated survival signaling pathways. To study this switch, we propose a mathematical model of crosstalk between these pathways. The model explains why MCF7 sub-clones transfected with HER2 or EGFR show three GFR-distribution patterns, and why the bimodal distribution pattern can be reversibly modulated by estrogen. The model illustrates how transient overexpression of ER activates GFR signaling and promotes estrogen-independent growth. Understanding this survival-signaling switch can help in the design of future therapies to overcome resistance in breast cancer.     

LCA as an element in environmental management systems—comparison of conditions in selected organisations in Poland, Sweden and Germany

Purpose

In this two-part paper (Background and Initial Assumptions (part 1) and Results of Survey Research (part 2)), we present surveys whose main objective is to determine whether, and to what extent, the life cycle assessment (LCA) technique is used for the identification and assessment of environmental aspects in environmental management systems (EMS) and whether there are any differences in this respect between the companies and countries analysed.

Methods

The survey research was carried out using the computer assisted self-administered interviewing method among selected Polish, German and Swedish organisations which implement EMS in accordance with the requirements of ISO 14001 and/or the EMAS regulation.

Results

The organisations investigated, regardless of their country, are dominated by qualitative and semi-quantitative techniques of assessment and identification of environmental aspects. LCA was used sporadically, although some differences can be observed between the countries analysed.

Conclusions

The environmental managers accustomed to traditional qualitative and semi-quantitative solutions have not been given preparation to enable them to understand and adopt different approaches such as LCA. On the other hand, representatives of the organisations investigated declared that they were ready to accept an even longer timescale for the identification and assessment processes relating to environmental aspects, which represents a potential opportunity for LCA. The more precise understanding and definition of environmental problems that are precisely defined in LCA would represent a novelty for environmental managers. In practice, environmental problems are defined in a general sense and rather ambiguously, as this level of detail is sufficient in the context of qualitative and semi-quantitative techniques commonly used for the identification and assessment of environmental aspects.     

Comprehensive Evaluation of 11 Cytokines in Premature Infants with Surgical Necrotizing Enterocolitis

Objective

A prospective study to investigate the pattern of pro- and anti-inflammatory cytokine responses in neonates with surgical necrotizing enterocolitis (NEC) and identify those cytokines being the most promising for future research.

Methods

A panel of 11 different cytokines were measured in 9 infants with proven NEC and compared with 18 age-matched healthy neonates.

Results

The serum concentrations of the interleukins (IL)-6, IL-8, and IL-10 were significantly (32–fold to 56-fold) higher in NEC infants compared with controls. In contrast, IL-5, IFN gamma, IL-4 and IL-2 showed slightly (1.4-fold to 5.9-fold) lower levels in the NEC samples. However, these cytokines showed a very low absolute concentration in infants with NEC and in controls. The sum of the serum concentrations of IL-6, IL-8 and IL-10 was able to clearly separate infants with NEC from control samples. IL-1 beta and TNF-alpha showed no statistically different levels. The serum levels of TNF-beta and IL-12p70 were below the detection limit in more than 50% of all samples per group.

Conclusion

In spite of strong local inflammation only three out of eleven cytokines (IL-6, IL-8, and IL-10) showed strongly increased serum levels indicating an important role of them in the pathogenesis of NEC. At least two of these three cytokines were elevated in every single NEC patient. Thus, longitudinal monitoring of combined IL-8, IL-6, and IL-10 levels could reveal their potency in being clinical relevant markers in NEC.     

Haemosporidian Parasites of Antelopes and Other Vertebrates from Gabon,Central Africa

Re-examination, using molecular tools, of the diversity of haemosporidian parasites (among which the agents of human malaria are the best known) has generally led to rearrangements of traditional classifications. In this study, we explored the diversity of haemosporidian parasites infecting vertebrate species (particularly mammals, birds and reptiles) living in the forests of Gabon (Central Africa), by analyzing a collection of 492 bushmeat samples. We found that samples from five mammalian species (four duiker and one pangolin species), one bird and one turtle species were infected by haemosporidian parasites. In duikers (from which most of the infected specimens were obtained), we demonstrated the existence of at least two distinct parasite lineages related to Polychromophilus species (i.e., bat haemosporidian parasites) and to sauropsid Plasmodium (from birds and lizards). Molecular screening of sylvatic mosquitoes captured during a longitudinal survey revealed the presence of these haemosporidian parasite lineages also in several Anopheles species, suggesting a potential role in their transmission. Our results show that, differently from what was previously thought, several independent clades of haemosporidian parasites (family Plasmodiidae) infect mammals and are transmitted by anopheline mosquitoes.     

Heterotrophy mitigates the response of the temperate coral Oculina arbuscula to temperature stress

Anthropogenic increases in atmospheric carbon dioxide concentration have caused global average sea surface temperature (SST) to increase by approximately 0.11°C per decade between 1971 and 2010 – a trend that is projected to continue through the 21st century. A multitude of research studies have demonstrated that increased SSTs compromise the coral holobiont (cnidarian host and its symbiotic algae) by reducing both host calcification and symbiont density, among other variables. However, we still do not fully understand the role of heterotrophy in the response of the coral holobiont to elevated temperature, particularly for temperate corals. Here, we conducted a pair of independent experiments to investigate the influence of heterotrophy on the response of the temperate scleractinian coral Oculina arbuscula to thermal stress. Colonies of O. arbuscula from Radio Island, North Carolina, were exposed to four feeding treatments (zero, low, moderate, and high concentrations of newly hatched Artemia sp. nauplii) across two independent temperature experiments (average annual SST (20°C) and average summer temperature (28°C) for the interval 2005–2012) to quantify the effects of heterotrophy on coral skeletal growth and symbiont density. Results suggest that heterotrophy mitigated both reduced skeletal growth and decreased symbiont density observed for unfed corals reared at 28°C. This study highlights the importance of heterotrophy in maintaining coral holobiont fitness under thermal stress and has important implications for the interpretation of coral response to climate change.     

A note on the selection of priority rules in software packages for project management

Various software packages for project management include a procedure for resource-constrained scheduling. In several packages, the user can influence this procedure by selecting a priority rule. However, the resource-allocation methods that are implemented in the procedures are proprietary information; therefore, the question of how the priority-rule selection impacts the performance of the procedures arises. We experimentally evaluate the resource-allocation methods of eight recent software packages using the 600 instances of the PSPLIB J120 test set. The results of our analysis indicate that applying the default rule tends to outperform a randomly selected rule, whereas applying two randomly selected rules tends to outperform the default rule. Applying a small set of more than two rules further improves the project durations considerably. However, a large number of rules must be applied to obtain the best possible project durations.     

In-Situ Observation of Membrane Protein Folding during Cell-Free Expression

Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando) at molecular resolution.     

Molecular basis of ion permeability in a voltage‐gated sodium channel

Voltage‐gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na⁺ ≈ Li⁺ ≫ K⁺, Ca²⁺, Mg²⁺) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.     

Identification and molecular characterization of the nicotianamine synthase gene family in bread wheat

Nicotianamine (NA) is a non‐protein amino acid involved in fundamental aspects of metal uptake, transport and homeostasis in all plants and constitutes the biosynthetic precursor of mugineic acid family phytosiderophores (MAs) in graminaceous plant species. Nicotianamine synthase (NAS) genes, which encode enzymes that synthesize NA from S‐adenosyl‐L‐methionine (SAM), are differentially regulated by iron (Fe) status in most plant species and plant genomes have been found to contain anywhere from 1 to 9 NAS genes. This study describes the identification of 21 NAS genes in the hexaploid bread wheat (Triticum aestivum L.) genome and their phylogenetic classification into two distinct clades. The TaNAS genes are highly expressed during germination, seedling growth and reproductive development. Fourteen of the clade I NAS genes were up‐regulated in root tissues under conditions of Fe deficiency. Protein sequence analyses revealed the presence of endocytosis motifs in all of the wheat NAS proteins as well as chloroplast, mitochondrial and secretory transit peptide signals in four proteins. These results greatly expand our knowledge of NAS gene families in graminaceous plant species as well as the genetics underlying Fe nutrition in bread wheat.