Shake-up and shake-off excitations with associated electron losses in X-ray studies of proteins

Photoionization of an atom by X-rays usually removes an inner shell electron from the atom, leaving behind a perturbed "hollow ion" whose relaxation may take different routes. In light elements, emission of an Auger electron is common. However, the energy and the total number of electrons released from the atom may be modulated by shake-up and shake-off effects. When the inner shell electron leaves, the outer shell electrons may find themselves in a state that is not an eigen-state of the atom in its surroundings. The resulting collective excitation is called shake-up. If this process also involves the release of low energy electrons from the outer shell, then the process is called shake-off. It is not clear how significant shake-up and shake-off contributions are to the overall ionization of biological materials like proteins. In particular, the interaction between the outgoing electron and the remaining system depends on the chemical environment of the atom, which can be studied by quantum chemical methods. Here we present calculations on model compounds to represent the most common chemical environments in proteins. The results show that the shake-up and shake-off processes affect approximately 20% of all emissions from nitrogen, 30% from carbon, 40% from oxygen, and 23% from sulfur. Triple and higher ionizations are rare for carbon, nitrogen, and oxygen, but are frequent for sulfur. The findings are relevant to the design of biological experiments at emerging X-ray free-electron lasers.     

Columnar denitrification of water by immobilized Pseudomonas denitrificans cells

Summary Whole cells of Pseudomonas denitrificans, immobilized in alginate gel, were used for columnar denitrification of ground water. Ethanol was selected as a suitable carbon source and the C/N-ratio necessary for satisfactory nitrate reduction was established (1.6 mg ethanol-C/mg nitrate-N). The course of the reaction and the diffusional limitations were investigated during columnar denitrification. The mechanical integrity of the gel matrix, as judged from leakage of cells was studied. The release of cells into the effluent was effectively inhibited (<10² cells/ml) by the use of different filter devices. The operational characteristics were determined by studying a column operating for nearly four months. Theoretically, the alginate gel column should, from high nitrate drinking water (22 mg NO ₃ ^– -N/1), produce 3 1 of denitrified water/kg gel/h (wet wt.) during a period of two months. The regeneration of nitrate reduction activity by means of activation in nutrient media proved a useful tool for restoring initial activity, the gel column having shown no loss in activity at the end of the operation period.     

Population structure and dynamics of wood mouse Apodemus sylvaticus in Iceland

Five-year-studies of two wood mouse populations (Apodemus sylvaticus L.) were carried out outside the village Vík. S. Iceland, and in a birch forest close to the lake Mývatn, N. Iceland. The population at Vík was studied on a 1.10 ha grid on a slope covered with Angelica archangelica L., the seeds of which constituted a major food resource for the mice. Altogether 948 individuals were caught, marked and followed during 1973–1978. No other free-living small mammals occur in Iceland, and predator pressure is low and considered non-existent on the Angelica slope. The population density was extremely high; highest autumn density recorded was 150 ind ha^?1. Like other Apodemus populations, the one at Vík showed a typical seasonal pattern in numbers: a winter decrease, relatively stable numbers in late summer, and an autumn peak. Breeding started in late April or early May and ended in late September; no winter breeding was observed. Three or four litters were produced, and the last litter(s) of the season greatly contributed to the autumn increase. The output of young per reproductive female throughout the year was negatively correlated with spring density, and autumn peak density with the number of females in August. Also overwinter success and weight changes appeared to be associated with population density (and weather). Survival rates did not vary much between years and seasons and were consistently rather high. Autumn survival of juveniles was positively correlated with mean minimum temperatures. Juvenile survival was, at least at times, negatively affected by the presence of adult males. Trapping outside the main grid did not indicate any marked dispersal, though some immigration to the grid must have occurred, especially in spring and early summer. Among the factors governing the population density and dynamics of wood mouse at Vík we emphasize the absence of interspecific competition and predation, the rich and dependable food resources (mainly Angelica seeds), the mild (though moist and windy) climate, the shelter of dense Angelica stands, the abundance of crevices (e.g. nest-sites), and the social interactions. The birch forest in northern Iceland was low productive and the wood mouse population differed from the Vík population by exhibiting low density, short breeding season, and high vagility; characteristics we consider to be representative for most Apodemus populations in Iceland.     

Monitoring Sub-Saharan African Physician Migration and Recruitment Post-Adoption of the WHO Code of Practice: Temporal and Geographic Patterns in the United States

Data monitoring is a key recommendation of the WHO Global Code of Practice on the International Recruitment of Health Personnel, a global framework adopted in May 2010 to address health workforce retention in resource-limited countries and the ethics of international migration. Using data on African-born and African-educated physicians in the 2013 American Medical Association Physician Masterfile (AMA Masterfile), we monitored Sub-Saharan African (SSA) physician recruitment into the physician workforce of the United States (US) post-adoption of the WHO Code of Practice. From the observed data, we projected to 2015 with linear regression, and we mapped migrant physicians’ locations using GPS Visualizer and ArcGIS. The 2013 AMA Masterfile identified 11,787 active SSA-origin physicians, representing barely 1.3% (11,787/940,456) of the 2013 US physician workforce, but exceeding the total number of physicians reported by WHO in 34 SSA countries (N = 11,519). We estimated that 15.7% (1,849/11,787) entered the US physician workforce after the Code of Practice was adopted. Compared to pre-Code estimates from 2002 (N = 7,830) and 2010 (N = 9,938), the annual admission rate of SSA émigrés into the US physician workforce is increasing. This increase is due in large part to the growing number of SSA-born physicians attending medical schools outside SSA, representing a trend towards younger migrants. Projection estimates suggest that there will be 12,846 SSA migrant physicians in the US physician workforce in 2015, and over 2,900 of them will be post-Code recruits. Most SSA migrant physicians are locating to large urban US areas where physician densities are already the highest. The Code of Practice has not slowed the SSA-to-US physician migration. To stem the physician “brain drain”, it is essential to incentivize professional practice in SSA and diminish the appeal of US migration with bolder interventions targeting primarily early-career (age ≤ 35) SSA physicians.     

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii' KT0803

Members of the phylum Bacteroidetes are abundant in many marine ecosystems and are known to have a pivotal role in the mineralization of complex organic substrates such as polysaccharides and proteins. We studied the decomposition of the algal glycans laminarin and alginate by ‘Gramella forsetii'' KT0803, a bacteroidetal isolate from North Sea surface waters. A combined application of isotope labeling, subcellular protein fractionation and quantitative proteomics revealed two large polysaccharide utilization loci (PULs) that were specifically induced, one by alginate and the other by laminarin. These regulons comprised genes of surface-exposed proteins such as oligomer transporters, substrate-binding proteins, carbohydrate-active enzymes and hypothetical proteins. Besides, several glycan-specific TonB-dependent receptors and SusD-like substrate-binding proteins were expressed also in the absence of polysaccharide substrates, suggesting an anticipatory sensing function. Genes for the utilization of the beta-1,3-glucan laminarin were found to be co-regulated with genes for glucose and alpha-1,4-glucan utilization, which was not the case for the non-glucan alginate. Strong syntenies of the PULs of ‘G. forsetii'' with similar loci in other Bacteroidetes indicate that the specific response mechanisms of ‘G. forsetii'' to changes in polysaccharide availability likely apply to other Bacteroidetes. Our results can thus contribute to an improved understanding of the ecological niches of marine Bacteroidetes and their roles in the polysaccharide decomposition part of carbon cycling in marine ecosystems.     

A bridge between original and novel states: ontogeny and function of "suction discs" in the Branchiura (Crustacea)

The emergence of novel structures in the course of evolution faces an explanatory problem, leaving the gap from the ancestral structures difficult to bridge. This difficulty is caused by the lack of intermediate stages. Branchiurans are ectoparasitic crustaceans which use a pair of "suction discs" to attach to their host. These structures are modified first maxillae. During ontogeny, the first maxillae transform from a normal cephalic appendage to the specialized suction disc. However, supposedly ancestral branchiurans lack the suction discs in the adults and the first maxilla remains a normal appendage throughout. We describe the muscular arrangements in the developing first maxillae in Argulus coregoni. The suction discs originate as a fusion of the first and second podomeres. The sucker muscles of the suction discs are homologous to the muscles that insert in the second podomere at the early larval stages. The developmental process of the suction disc can be seen as a "recapitulation" of the evolutionary process. We thus show how the first maxilla can maintain not just the biological role but also a functional continuity during the evolution of the novel structure. From this example it is obvious that the intermediate stages of the emerging novelty, if present in the ontogeny, can help solve at least some of the enigmatic appearances of novel structures.