Jay Bailey as mentor--the students' perspective

Professor James E. Bailey was not only a world-renowned leader and pioneer in biochemical engineering but also a mentor to the many graduate students and postdoctoral researchers in his group. To provide non-"Bailey-ites" with an impression of Jay as a mentor, we begin with a brief review of his career, focusing on the dynamics of the research group. Typical student experiences of being part of the Bailey group are then discussed, including the recognition of a particular research style and Jay's expectations for hard work. Finally, we provide some thoughts on Jay's mentoring style, which was marked by an ability to foster independence, a sense of quality, and passion for research. Jay's contributions as a mentor can perhaps be recognized as being as significant as his research achievements.     

Spatial and temporal variability in reproductive timing of Antarctic krill (Euphausia superba Dana)

Spawning dates of Antarctic krill, Euphausia superba Dana, were calculated from larval stage compositions, and corrected using data on maturity stage composition of the adult krill. Both original and literature data obtained from the Antarctic Peninsula-Bellingshausen Sea area and around the Antarctic continent were used. A time series (1975/76–1986/87) for several subareas of the Antarctic Peninsula-Bellingshausen Sea area indicates considerable variation in the krill spawning start, maxima and completion. In particular years (1975/76, 1980/81), krill spawning in the western Atlantic sector began relatively early, was intensive, and completed early. Some years (1977/78, 1981/82) were characterised by long and non-synchronised krill spawning. Compiled data sets for the Atlantic sector (1980/81), the entire Antarctic (1983/84) and the east Indian-west Pacific Antarctic waters (1981–85) reveal some spatial patterns in krill reproductive timing. In relation to spawning timing variation, the habitats of the krill population fall into five categories: (1) areas with an early beginning (late Novemberearly December) and a variable, but normally long, duration (3–3.5 months) of krill spawning; this is generally the southern boundary of the Antarctic Circumpolar Current, (2) areas with an early beginning, but a short duration of krill spawning (Gerlache Strait), (3) areas with a highly variable (within 1–1.5 months) beginning and a relatively long duration (ca. 3 months) of krill spawning (Bransfield Strait, Palmer Archipelago), (4) areas with a late beginning (late December–January) and a long duration of krill spawning (Bellingshausen Sea, D'Urville Sea, and Balleny Islands area), and (5) areas with a delayed beginning, but a very short duration (ca. 1.5 months) of krill spawning (Ross Sea slope, probably the Coastal Current area off the Lasarev Sea shelf and in the south-eastern Weddell Sea. These patterns can be partly explained by peculiarities of the ice regime in particular areas and by routes of krill movement within water circulation systems.     

A new species of the genus Paralomis (Crustacea: Decapoda: Lithodidae) from the Spiess seamount near Bouvet Island (Southern Ocean), with notes on habitat and ecology

A new species of the genus Paralomis, Paralomis elongata, has been collected from the Spiess seamount near Bouvet Island in the Southern Ocean. The species shows close affinity with P. anamerae Macpherson, 1988, from the Patagonian Shelf, P. africana Macpherson, 1987, from the south-western African shelf, and P. aculeata Henderson, 1888, from Crozet Islands. Morphological differences among the species and ecological characteristics are discussed.     

Phosphate deposition capacity of athletes during hypokinesia, phosphate loading, and ambulation

Hypokinesia (diminished movement) induces significant phosphate (P) excretion; however, little is known about the P deposition ability of the body during hypokinesia (HK). Using P loads, the aim of this study was to establish the deposition ability of the body to retain P during prolonged HK. Studies were done during a 30-d period of pre-HK and a 364-d period of HK. Forty male trained athletes aged 24.7 ± 8.0 yr were chosen as subjects. They were equally divided into four groups: unloaded ambulatory control subjects (UACS), unloaded hypokinetic subjects (UHKS), loaded ambulatory control subjects (LACS), and loaded hypokinetic subjects (LHKS). All hypokinetic subjects were limited to an average walking distance of 0.7 km/d. Loading tests with 85.0 mg of calcium phosphate/kg body weight were performed on the LACS and LHKS. Fecal P loss, urinary calcium (Ca) and P loss, serum P, Ca, and the ionized calcium (Ca_I) levels increased significantly (p≤0.05) in the LHKS and UHKS groups when compared with the LACS and UACS groups, respectively. Serum intact parathyroid hormone (iPTH) and the 1,25-dihydroxyvitamin D₃ [1,25-(OH)₂ D₃] levels decreased significantly (p≤0.05) in the LHKS and UHKS groups when compared with the LACS and UACS groups, respectively. After the P load, significant (p≤0.05) differences were observed between LHKS and UHKS groups regarding serum, urinary, and fecal P changes. Thus, the deposition capacity of P decreased significantly (p≤0.05) more in the LHKS group than in the UHKS group. The deposition of P, fecal P, urinary P and Ca, serum Ca_I, P, Ca, 1,25-(OH)₂ D₃, and iPTH changed insignificantly (p>0.05) in control groups when compared with their baseline values. It was shown that after the P load, significant differences were observed between the loaded and unloaded hypokinetic subjects regarding serum, urinary, and fecal P values and P retention. The oral P load intensified P loss from the body. It was concluded that the higher the P intake increased the greater P loss and the lower P deposition and thus the less likely it is for the P load to benefit hypokinetic subjects.     

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Toxoplasma gondii is a human pathogen prevalent worldwide that poses a challenging and unmet need for novel treatment of toxoplasmosis. Using a semi-automated reconstruction algorithm, we reconstructed a genome-scale metabolic model, ToxoNet1. The reconstruction process and flux-balance analysis of the model offer a systematic overview of the metabolic capabilities of this parasite. Using ToxoNet1 we have identified significant gaps in the current knowledge of Toxoplasma metabolic pathways and have clarified its minimal nutritional requirements for replication. By probing the model via metabolic tasks, we have further defined sets of alternative precursors necessary for parasite growth. Within a human host cell environment, ToxoNet1 predicts a minimal set of 53 enzyme-coding genes and 76 reactions to be essential for parasite replication. Double-gene-essentiality analysis identified 20 pairs of genes for which simultaneous deletion is deleterious. To validate several predictions of ToxoNet1 we have performed experimental analyses of cytosolic acetyl-CoA biosynthesis. ATP-citrate lyase and acetyl-CoA synthase were localised and their corresponding genes disrupted, establishing that each of these enzymes is dispensable for the growth of T. gondii, however together they make a synthetic lethal pair.     

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

The metabolic capabilities of the species and the local environment shape the microbial interactions in a community either through the exchange of metabolic products or the competition for the resources. Cells are often arranged in close proximity to each other, creating a crowded environment that unevenly reduce the diffusion of nutrients. Herein, we investigated how the crowding conditions and metabolic variability among cells shape the dynamics of microbial communities. For this, we developed CROMICS, a spatio-temporal framework that combines techniques such as individual-based modeling, scaled particle theory, and thermodynamic flux analysis to explicitly incorporate the cell metabolism and the impact of the presence of macromolecular components on the nutrients diffusion. This framework was used to study two archetypical microbial communities (i) Escherichia coli and Salmonella enterica that cooperate with each other by exchanging metabolites, and (ii) two E. coli with different production level of extracellular polymeric substances (EPS) that compete for the same nutrients. In the mutualistic community, our results demonstrate that crowding enhanced the fitness of cooperative mutants by reducing the leakage of metabolites from the region where they are produced, avoiding the resource competition with non-cooperative cells. Moreover, we also show that E. coli EPS-secreting mutants won the competition against the non-secreting cells by creating less dense structures (i.e. increasing the spacing among the cells) that allow mutants to expand and reach regions closer to the nutrient supply point. A modest enhancement of the relative fitness of EPS-secreting cells over the non-secreting ones were found when the crowding effect was taken into account in the simulations. The emergence of cell-cell interactions and the intracellular conflicts arising from the trade-off between growth and the secretion of metabolites or EPS could provide a local competitive advantage to one species, either by supplying more cross-feeding metabolites or by creating a less dense neighborhood.     

Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks

Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy of biochemical reactions have long been established. However, a concept for incorporation of cross-membrane transport in these calculations is still missing, although the theory for calculating thermodynamic properties of transport processes is long known. Here, we have developed two equivalent equations to calculate the change in Gibbs energy of combined transport and reaction processes based on two different ways of treating biochemical thermodynamics. We illustrate the need for these equations by showing that in some cases there is a significant difference between the proposed correct calculation and using an approximative method. With the developed equations, thermodynamic analysis of metabolic networks spanning over multiple physical compartments can now be correctly described.