Toward intensifying design of experiments in upstream bioprocess development: An industrial Escherichia coli feasibility study

In this study, step variations in temperature, pH, and carbon substrate feeding rate were performed within five high cell density Escherichia coli fermentations to assess whether intraexperiment step changes, can principally be used to exploit the process operation space in a design of experiment manner. A dynamic process modeling approach was adopted to determine parameter interactions. A bioreactor model was integrated with an artificial neural network that describes biomass and product formation rates as function of varied fed‐batch fermentation conditions for heterologous protein production. A model reliability measure was introduced to assess in which process region the model can be expected to predict process states accurately. It was found that the model could accurately predict process states of multiple fermentations performed at fixed conditions within the determined validity domain. The results suggest that intraexperimental variations of process conditions could be used to reduce the number of experiments by a factor, which in limit would be equivalent to the number of intraexperimental variations per experiment. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1343–1352, 2016     

Selection and optimization of a suitable pretreatment method for miscanthus and poplar raw material

Miscanthus and poplar are very promising second‐generation feedstocks due to the high growth rates and low nutrient demand. The aim of the study was to develop a systematic approach for choosing suitable pretreatment methods evaluated with the modified severity factor (log ). Optimal pretreatment results in a high delignification grade, low cellulose solubilization and increased accessibility for enzymatic hydrolysis while revealing minimal log values. In order to do so, several reaction approaches were compared. Acid‐catalyzed organosolv processing carried out for miscanthus and poplar revealed the highest delignification grade leading to a relatively high glucose yield after enzymatic saccharification. In both cases, a design of experiments approach was used to study the influence of relevant parameters. Modeling the data resulted in the identification of optimum pretreatment conditions for miscanthus with concentrations of 0.16% H₂SO₄ and 50% EtOH at 185°C for a retention time of 60 min. Experimental validation of these conditions revealed an even higher delignification degree (88%) and glucose yield (85%) than predicted. 0.19% H₂SO₄ and 50% EtOH were determined as optimum concentrations, 182°C and 48 min identified as optimum pretreatment conditions for poplar; the delignification degree was 84% and the resulting glucose yield 70%.     

Polyphyly,asexual reproduction and dual trophic mode in Buchwaldoboletus

Most Boletaceae form ectomycorrhizas but species in two sister groups (subfamily Chalciporoideae and the genus Pseudoboletus) have unclear trophic modes and are putatively mycoparasitic. Chalciporoideae is the earliest diverging lineage in Boletaceae and includes Chalciporus and Buchwaldoboletus. Buchwaldoboletus species fruit on wood and were thought to be saprobes, but the type species Buchwaldoboletus lignicola is mycoparasitic on the wood decay fungus Phaeolus schweinitzii. However, the nutritional mode and host range of B. lignicola and other Buchwaldoboletus remain unclear. We obtained fresh collections and axenic cultures of B. lignicola, B. hemichrysus and B. sphaerocephalus from the southeastern USA. We use cultures to examine the phylogenetic relationships among taxa in Chalciporoideae, elucidate the trophic mode of Buchwaldoboletus species and test the effect that Buchwaldoboletus species have on wood decay. Our analysis supports the hypothesis that the Chalciporus lineage is sister to all other Boletaceae but suggests that Buchwaldoboletus is not monophyletic. Confrontation experiments on agar suggest that Buchwaldoboletus species might parasitize a wide range of decay fungi. Buchwaldoboletus hemichrysus and B. sphaerocephalus produce abundant conidia in culture whereas the more distantly related B. lignicola produces sclerotia. Wood decay assays show that Buchwaldoboletus species did not have a significant effect on the decay caused by wood decay fungi. Interestingly, when B. lignicola or B. hemichrysus were inoculated alone on wood both species decayed wood, producing a brown rot that can cause 35–65% mass loss over 6 months. Our results suggest that Buchwaldoboletus species have a dual trophic mode as saprobes and mycoparasites.     

1H, 13C and 15N resonance assignments of YajG, an Escherichia coli protein of unknown structure and function

The ampG gene codes for a permease required to uptake anhydro-muropeptides into bacterial cytoplasm. Located upstream in the same operon, is another 579-base-pair-long open reading frame encoding a putative lipoprotein YajG, whose nearly complete ¹H,¹³C,¹⁵N assignments are reported here.     

Optimization of compressive loading parameters to mimic in vivo cervical spine kinematics in vitro

The human cervical spine supports substantial compressive load in vivo. However, the traditional in vitro testing methods rarely include compressive loads, especially in investigations of multi-segment cervical spine constructs. Previously, a systematic comparison was performed between the standard pure moment with no compressive loading and published compressive loading techniques (follower load – FL, axial load – AL, and combined load – CL). The systematic comparison was structured a priori using a statistical design of experiments and the desirability function approach, which was chosen based on the goal of determining the optimal compressive loading parameters necessary to mimic the segmental contribution patterns exhibited in vivo. The optimized set of compressive loading parameters resulted in in vitro segmental rotations that were within one standard deviation and 10% of average percent error of the in vivo mean throughout the entire motion path. As hypothesized, the values for the optimized independent variables of FL and AL varied dynamically throughout the motion path. FL was not necessary at the extremes of the flexion–extension (FE) motion path but peaked through the neutral position, whereas, a large negative value of AL was necessary in extension and increased linearly to a large positive value in flexion. Although further validation is required, the long-term goal is to develop a “physiologic” in vitro testing method, which will be valuable for evaluating adjacent segment effect following spinal fusion surgery, disc arthroplasty instrumentation testing and design, as well as mechanobiology experiments where correct kinematics and arthrokinematics are critical.     

Identification and characterization of carbapenem binding sites within the RND-transporter AcrB

Understanding the molecular determinants for recognition, binding and transport of antibiotics by multidrug efflux systems is important for basic research and useful for the design of more effective antimicrobial compounds. Imipenem and meropenem are two carbapenems whose antibacterial activity is known to be poorly and strongly affected by MexAB-OprM, the major efflux pump transporter in Pseudomonas aeruginosa. However, not much is known regarding recognition and transport of these compounds by AcrAB-TolC, which is the MexAB-OprM homologue in Escherichia coli and by definition the paradigm model for structural studies on efflux pumps. Prompted by this motivation, we unveiled the molecular details of the interaction of imipenem and meropenem with the transporter AcrB by combining computer simulations with biophysical experiments. Regarding the interaction with the two main substrate binding regions of AcrB, the so-called access and deep binding pockets, molecular dynamics simulations revealed imipenem to be more mobile than meropenem in the former, while comparable mobilities were observed in the latter. This result is in line with isothermal titration calorimetry, differential scanning experiments, and binding free energy calculations, indicating a higher affinity for meropenem than imipenem at the deep binding pocket, while both sharing similar affinities at the access pocket. Our findings rationalize how different physico-chemical properties of compounds reflect on their interactions with AcrB. As such, they constitute precious information to be exploited for the rational design of antibiotics able to evade efflux pumps.     

Egg development and hatching success in alpine chironomids

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Comparison of microbially induced calcium carbonate precipitation eligibility using sporosarcina pasteurii and bacillus licheniformis on two different sands

The use of biological means for ground improvement have become popular, which generally works through the process called microbially-induced calcium carbonate precipitation (MICP). Many studies indicate successful application of MICP based improvement with multiple bacteria and on several soils. Given the proven performance of MICP, this study aims to examine the MICP process by comparing the calcium carbonate precipitation ability of widely studied bacteria, i.e., Sporosarcina pasteurii and relatively under-recognized bacteria, i.e., Bacillus licheniformis to outline the formation success. For this purpose, two different sands were tested for observing precipitation behavior using a series of syringe tests. Furthermore, the effect of concentration and inclusion of calcium chloride for nutrition of bacteria, saturation with water, and hybrid use of two bacteria were investigated in some tests for diversification. X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive x-ray spectroscopy (EDS) were used for the interpretation of results. Results indicated that Sporosarcina pasteurii had performed superior over Bacillus licheniformis when achieving calcium carbonate precipitation in tests for both sands. In addition, many intriguing SEM images contributed to the literature of MICP monitoring, highlighting the effects of the variables investigated.