Density‐dependent parasitism in biological control of soil‐borne insects,nematodes, fungi and bacteria

Temporal density‐dependent parasitism appears to explain the development of some pest‐ and pathogen‐suppressive soils. In many examples, an enrichment of hosts (soil‐borne pests or pathogens) precedes and supports a build up of beneficial parasites in perennial crops or in monocultures, and the population dynamics of hosts and parasites may be described in epidemiological terms. Although the examples support the concept of a balance of nature based on density‐dependent regulation, we lack detailed understanding of the processes that drive these beneficial epidemics. In addition, the epidemics develop slowly and often do not provide the control expected by farmers. Current research, therefore, emphasizes inundative release of beneficial agents. Nevertheless, we should study epidemics in soil in order to learn how they might be enhanced; to learn how better to utilize inoculum that is inundatively added to soil; and to contribute to the general discussion of population biology and regulation.     

Selective incorporation of 5-hydroxytryptophan blocks long range electron transfer in oxalate decarboxylase

Oxalate decarboxylase from Bacillus subtilis is a binuclear Mn-dependent acid stress response enzyme that converts the mono-anion of oxalic acid into formate and carbon dioxide in a redox neutral unimolecular disproportionation reaction. A π-stacked tryptophan dimer, W96 and W274, at the interface between two monomer subunits facilitates long-range electron transfer between the two Mn ions and plays an important role in the catalytic mechanism. Substitution of W96 with the unnatural amino acid 5-hydroxytryptophan leads to a persistent EPR signal which can be traced back to the neutral radical of 5-hydroxytryptophan with its hydroxyl proton removed. 5-Hydroxytryptophan acts as a hole sink preventing the formation of Mn(III) at the N-terminal active site and strongly suppresses enzymatic activity. The lower boundary of the standard reduction potential for the active site Mn(II)/Mn(III) couple can therefore be estimated as 740 mV against the normal hydrogen electrode at pH 4, the pH of maximum catalytic efficiency. Our results support the catalytic importance of long-range electron transfer in oxalate decarboxylase while at the same time highlighting the utility of unnatural amino acid incorporation and specifically the use of 5-hydroxytryptophan as an energetic sink for hole hopping to probe electron transfer in redox proteins.     

Real-time monitoring of biomass during Escherichia coli high-cell-density cultivations by in-line photon density wave spectroscopy

An efficient monitoring and control strategy is the basis for a reliable production process. Conventional optical density (OD) measurements involve superpositions of light absorption and scattering, and the results are only given in arbitrary units. In contrast, photon density wave (PDW) spectroscopy is a dilution-free method that allows independent quantification of both effects with defined units. For the first time, PDW spectroscopy was evaluated as a novel optical process analytical technology tool for real-time monitoring of biomass formation in Escherichia coli high-cell-density fed-batch cultivations. Inline PDW measurements were compared to a commercially available inline turbidity probe and with offline measurements of OD and cell dry weight (CDW). An accurate correlation of the reduced PDW scattering coefficient µ_s′ with CDW was observed in the range of 5–69 g L⁻¹ (R² = 0.98). The growth rates calculated based on µ_s′ were comparable to the rates determined with all reference methods. Furthermore, quantification of the reduced PDW scattering coefficient µ_s′ as a function of the absorption coefficient µ_a allowed direct detection of unintended process trends caused by overfeeding and subsequent acetate accumulation. Inline PDW spectroscopy can contribute to more robust bioprocess monitoring and consequently improved process performance.     

Bioprocess development to produce a hyperthermostable S-methyl-5′-thioadenosine phosphorylase in Escherichia coli

Nucleoside phosphorylases are important biocatalysts for the chemo-enzymatic synthesis of nucleosides and their analogs which are, among others, used for the treatment of viral infections or cancer. S-methyl-5′-thioadenosine phosphorylases (MTAP) are a group of nucleoside phosphorylases and the thermostable MTAP of Aeropyrum pernix (ApMTAP) was described to accept a wide range of modified nucleosides as substrates. Therefore, it is an interesting biocatalyst for the synthesis of nucleoside analogs for industrial and therapeutic applications. To date, thermostable nucleoside phosphorylases were produced in shake flask cultivations using complex media. The drawback of this approach is low volumetric protein yields which hamper the wide-spread application of the thermostable nucleoside phosphorylases in large scale. High cell density (HCD) cultivations allow the production of recombinant proteins with high volumetric yields, as final optical densities >100 can be achieved. Therefore, in this study, we developed a suitable protocol for HCD cultivations of ApMTAP. Initially, optimum expression conditions were determined in 24-well plates using a fed-batch medium. Subsequently, HCD cultivations were performed using E. coli BL21-Gold cells, by employing a glucose-limited fed-batch strategy. Comparing different growth rates in stirred-tank bioreactors, cultivations revealed that growth at maximum growth rates until induction resulted in the highest yields of ApMTAP. On a 500-mL scale, final cell dry weights of 87.1–90.1 g L⁻¹ were observed together with an overproduction of ApMTAP in a 1.9%–3.8% ratio of total protein. Compared to initially applied shake flask cultivations with terrific broth (TB) medium the volumetric yield increased by a factor of 136. After the purification of ApMTAP via heat treatment and affinity chromatography, a purity of more than 90% was determined. Activity testing revealed specific activities in the range of 0.21 ± 0.11 (low growth rate) to 3.99 ± 1.02 U mg⁻¹ (growth at maximum growth rate). Hence, growth at maximum growth rate led to both an increased expression of the target protein and an increased specific enzyme activity. This study paves the way towards the application of thermostable nucleoside phosphorylases in industrial applications due to an improved heterologous expression in Escherichia coli.     

The prevalence of root surface caries amongst Irish adults

In a national survey of adult dental health conducted in the Republic of Ireland in 1989/90 a total of 1,527 subjects aged 25 and older were examined for root surface caries. It was found that the prevalence of root surface caries was highest in older age groups and also amongst males, residents of non-fluoridated communities and those earning low incomes. Tooth loss masked the potential prevalence of root surface caries. With more persons retaining their natural teeth into middle and old age the prevalence of root surface caries is likely to increase in the future.     

Process intensification strategies toward cell culture-based high-yield production of a fusogenic oncolytic virus

We present a proof-of-concept study for production of a recombinant vesicular stomatitis virus (rVSV)-based fusogenic oncolytic virus (OV), rVSV-Newcastle disease virus (NDV), at high cell densities (HCD). Based on comprehensive experiments in 1 L stirred tank reactors (STRs) in batch mode, first optimization studies at HCD were carried out in semi-perfusion in small-scale cultivations using shake flasks. Further, a perfusion process was established using an acoustic settler for cell retention. Growth, production yields, and process-related impurities were evaluated for three candidate cell lines (AGE1.CR, BHK-21, HEK293SF)infected at densities ranging from 15 to 30 × 10⁶ cells/mL. The acoustic settler allowed continuous harvesting of rVSV-NDV with high cell retention efficiencies (above 97%) and infectious virus titers (up to 2.4 × 10⁹ TCID₅₀/mL), more than 4–100 times higher than for optimized batch processes. No decrease in cell-specific virus yield (CSVY) was observed at HCD, regardless of the cell substrate. Taking into account the accumulated number of virions both from the harvest and bioreactor, a 15–30 fold increased volumetric virus productivity for AGE1.CR and HEK293SF was obtained compared to batch processes performed at the same scale. In contrast to all previous findings, formation of syncytia was observed at HCD for the suspension cells BHK 21 and HEK293SF. Oncolytic potency was not affected compared to production in batch mode. Overall, our study describes promising options for the establishment of perfusion processes for efficient large-scale manufacturing of fusogenic rVSV-NDV at HCD for all three candidate cell lines.     

Population dynamics,productivity and biomass allocation ofZizania latifolia in an aquatic-terrestrial ecotone

The population and production ecology of aZizania latifolia stand at a sheltered shore of the Hitachi-Tone River were investigated. Shoot emergence was observed twice a year; the fist was a synchronized shoot emergence in April and the second was from August to October. Aboveground biomass was mostly occupied by leaves and peaked at 1500 g dry weight m⁻² in August. The belowground biomass also reached its peak, 750 g dry weight m⁻², in August. The secondary shoots were small in spite of their high density. Leaves were produced continuously throughout the season. The leaf life span was as short as 55.6 days for cohorts that emerged from May through to September. Total annual net production ofZ. latifolia could be more than 3400 g dry weight m⁻². Shoot clusters of several centimeters were observed in April. The following self-thinning caused a regular distribution of the remaining shoots in August. Most shoots produced in August to October were found near a shoot persisting since April. They showed more concentrated distribution than shoots in April. A large biomass allocation to leaves and the ability to produce many clump shoots during the late growing period may facilitate dominance ofZ. latifolia in relatively sheltered sites.     

Studies on low-level MDR cells

Acquired or spontaneous resistance is a major clinical problem in the treatment of cancer. Low levels of MDR gene expression or P-glycoprotein have been correlated with a high level of drug resistance in vitro and a poor response to chemotherapy in some tumors. A strong correlation between MDR mRNA, P-glycoprotein levels and degree of drug resistance has not been found in several resistant model tumor cell lines. In some cell lines at low and high level of resistance different mechanisms seem to be involved.     

Population dynamics of japanese serow in relation to social organization and habitat conditions. I. Stability of Japanese serow density in stable habitat conditions

The density of a Japanese serow (Capricornis crispus) population, which has been in stable habitat conditions and free from hunting and predation, was investigated by direct observation of serows at Kusoudomari (336 ha), Wakinosawa village, Aomori Prefecture, Japan, during 1977–89. The vegetation, composed of mature mixed forest ofThujopsis with deciduous trees (43.2%), secondary forest of deciduous trees (23.4%) and a plantation of coniferous trees (30.0%) showed little change during the study period. The serows were counted 17 times each winter for 14 consecutive years. The serow population maintained a stable density with a mean of 12.5 individuals km⁻² (SD=1.4) ranging from 8.6 to 14.6 km⁻². The ratio of the proportion of kids (<1 year old) to serows more than 1 year old decreased, but density did not decrease during the study period. Though extremely severe winters with heavy snowfall in 1984–86 caused a decline in serow density, the density recovered within a few years. It was considered that the stability of the serow density resulted mainly from the stable food supply and the lack of human disturbance, such as forest cutting in the habitat. Stable population density for a long period is probably related to the social organization of the serow.     

CryoRes: Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning

Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in different regions of a map. Currently available methods for local resolution estimation require manual adjustment of parameters and in some cases necessitate acquisition or de novo generation of so-called “half maps”. Here, we developed CryoRes, a deep-learning algorithm to estimate local resolution directly from a single final cryo-EM density map, specifically by learning resolution-aware patterns of density map voxels through supervised training on a large dataset comprising 1,174 experimental cryo-EM density maps. CryoRes significantly outperforms all of the state-of-the-art competing resolution estimation methods, achieving an average RMSE of 2.26 Å for local resolution estimation relative to the currently most reliable FSC-based method blocres, yet requiring only the single final map as input. Further, CryoRes is able to generate a molecular mask for each map, with accuracy 12.12% higher than the masks generated by ResMap. CryoRes is ultra-fast, fully automatic, parameter-free, applicable to cryo-EM subtomogram data, and freely available at https://cryores.zhanglab.net.