Synthesis of diketopiperazines with on-resin N-methylation and cyclative release.

Enantiomerically pure N-methylated diketopiperazines (DKP) can be obtained by treating a N-methylated resin-bound dipeptide with 20% piperidine in dimethylformamide via a process known as cyclative release. N-methylated resin-bound dipeptides can be formed from N-methylated precursors or N-methylation can be selectively performed on the resin. When on-resin N-methylation was performed on the C-terminal side of the dipeptide, diastereomers were formed. Yet the cyclative release is shown to be a stereoselective process, as seen using preformed N-methylated amino acids. The procedure was also applied to synthesize the pseudodiketopiperazine cyclo(Phepsi[CH2NH]Leu). When comparing nonmethylated, monomethylated and bismethylated derivatives, we find that N-methylation results in a dramatic increase in solubility.     

A comparative study of eubacterial communities by PCR-DGGE fingerprints in anoxic and aerobic biotrickling filters used for biogas desulfurization

Bioprocess and Biosystems Engineering - Biological desulfurization has proven to be a process that is technically and economically feasible on using biotrickling filters that can be performed under...     

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     

Dynamic modeling and analyses of simultaneous saccharification and fermentation process to produce bio-ethanol from rice straw

The rice straw, an agricultural waste from Asians’ main provision, was collected as feedstock to convert cellulose into ethanol through the enzymatic hydrolysis and followed by the fermentation process. When the two process steps are performed sequentially, it is referred to as separate hydrolysis and fermentation (SHF). The steps can also be performed simultaneously, i.e., simultaneous saccharification and fermentation (SSF). In this research, the kinetic model parameters of the cellulose saccharification process step using the rice straw as feedstock is obtained from real experimental data of cellulase hydrolysis. Furthermore, this model can be combined with a fermentation model at high glucose and ethanol concentrations to form a SSF model. The fermentation model is based on cybernetic approach from a paper in the literature with an extension of including both the glucose and ethanol inhibition terms to approach more to the actual plants. Dynamic effects of the operating variables in the enzymatic hydrolysis and the fermentation models will be analyzed. The operation of the SSF process will be compared to the SHF process. It is shown that the SSF process is better in reducing the processing time when the product (ethanol) concentration is high. The means to improve the productivity of the overall SSF process, by properly using aeration during the batch operation will also be discussed.     

Identification of crystals in joint fluids

The inflammatory process present in synovial arthritic specimens can be diagnosed by crystal-type identification performed in cytopathology laboratories by the use of simple methods. These methods involve wet coverslipped preparations of fresh fluid specimens or sediments and compensated polarizing microscopy, which can be performed with a routine microscope equipped with polarizing filters and a substitute compensator. Details of the methodology are described. The morphologic characteristics of the crystals are described in cases of gout, pseudogout and arthritis of other types in which secondary calcifications are present.     

Dry first, measure later: a new procedure to preserve and measure zooplankton for ecophysiological studies

The processing of freshwater crustaceans for ecophysiologicalstudies can be simplified considerably if species determination,selection and measurements of the specimens are performed afterfreezing and lyophilization. As the zooplankters do not changeshape during this process, reliable taxonomic determinationcan be performed with dried animals. Besides easy handling,this procedure ensures minimization of metabolic losses dueto prolonged exposure to room temperature, and significantlyreduces losses of radiotracer material in grazing studies.     

Peptide identification quality control

Identification of large proteomics data sets is routinely performed using sophisticated software tools called search engines. Yet despite the importance of the identification process, its configuration and execution is often performed according to established lab habits, and is mostly unsupervised by detailed quality control. In order to establish easily obtainable quality control criteria that can be broadly applied to the identification process, we here introduce several simple quality control methods. An unbiased quality control of identification parameters will be conducted using target/decoy searches providing significant improvement over identification standards. MASCOT identifications were for instance increased by 13% at a constant level of confidence. The target/decoy approach can however not be universally applied. We therefore also quality control the application of this strategy itself, providing useful and intuitive metrics for evaluating the precision and robustness of the obtained false discovery rate.     

Catalytic upgrading of bio-oil by HZSM-5 in sub- and super-critical ethanol

The pyrolysis bio-oil from rice husk was upgraded in sub- and super-critical ethanol using HZSM-5 as catalyst. The results showed that super-critical upgrading process performed more effectively than sub-critical upgrading process. Acidic HZSM-5 facilitates esterification in super-critical ethanol to convert acids contained in crude bio-oil into various kinds of esters. Stronger acidic HZSM-5 (low Si/Al ratio) can facilitate cracking of heavy components of crude bio-oil more effectively in super-critical upgrading process. The residue of distillated upgraded bio-oil from super-critical upgrading process decreased evidently, compared with that of distillated crude bio-oil. This work proved that crude bio-oil can be effectively upgraded in super-critical upgrading process with the aid of acidic catalyst.     

Additive‐Multiplicative Regression Models for Spatio‐Temporal Epidemics

An extension of the stochastic susceptible–infectious–recovered (SIR) model is proposed in order to accommodate a regression context for modelling infectious disease data. The proposal is based on a multivariate counting process specified by conditional intensities, which contain an additive epidemic component and a multiplicative endemic component. This allows the analysis of endemic infectious diseases by quantifying risk factors for infection by external sources in addition to infective contacts. Inference can be performed by considering the full likelihood of the stochastic process with additional parameter restrictions to ensure non‐negative conditional intensities. Simulation from the model can be performed by Ogata's modified thinning algorithm. As an illustrative example, we analyse data provided by the Federal Research Centre for Virus Diseases of Animals, Wusterhausen, Germany, on the incidence of the classical swine fever virus in Germany during 1993–2004.     

Principle and method of kinetic microphotometric enzyme activity determination in situ

Summary An advanced apparative set-up is described for multipositional microphotometric recording of histochemical enzyme reactions in cryostat sections. It consists of a computer controlled microscope photometer with scanning stage. Measurements on the same tissue section may be performed at 12 preselected positions. These are repeatedly brought into the measuring beam in several measuring cycles. The complete measuring process, storage of measuring position coordinates, movements of the stage and statistical evaluation of the data is under computer control. By use of the gel film technique, extinction changes in tetrazolium coupled enzyme reactions can be measured continuously at initial rate conditions. Measurements are performed at identical conditions and can thus be analysed as relative enzyme activities.     

Principle and method of kinetic microphotometric enzyme activity determination in situ

An advanced apparative set-up is described for multipositional microphotometric recording of histochemical enzyme reactions in cryostat sections. It consists of a computer controlled microscope photometer with scanning stage. Measurements on the same tissue section may be performed at 12 preselected positions. These are repeatedly brought into the measuring beam in several measuring cycles. The complete measuring process, storage of measuring position coordinates, movements of the stage and statistical evaluation of the data is under computer control. By use of the gel film technique, extinction changes in tetrazolium coupled enzyme reactions can be measured continuously at initial rate conditions. Measurements are performed at identical conditions and can thus be analysed as relative enzyme activities.     

Low-level aspects of segmentation and recognition.

This paper discusses two problems related to three-dimensional object recognition. The first is segmentation and the selection of a candidate object in the image, the second is the recognition of a three-dimensional object from different viewing positions. Regarding segmentation, it is shown how globally salient structures can be extracted from a contour image based on geometrical attributes, including smoothness and contour length. This computation is performed by a parallel network of locally connected neuron-like elements. With respect to the effect of viewing, it is shown how the problem can be overcome by using the linear combinations of a small number of two-dimensional object views. In both problems the emphasis is on methods that are relatively low level in nature. Segmentation is performed using a bottom-up process, driven by the geometry of image contours. Recognition is performed without using explicit three-dimensional models, but by the direct manipulation of two-dimensional images.     

Parallel sample preparation of proteins,from crude samples to crystals ready for MALDI-MS,in an integrated microfluidic system

A microfluidic structure is presented where selective capture of proteins in complex samples, followed by clean-up, enzymatic processing, and MALDI-MS sample preparation of peptides generated, can be performed. The structure uses an affinity column to capture the protein while all other components in the sample are disposed of. The protein of interest is then eluted from the affinity column and captured on a second column on which the enzymatic processing is performed. Salts and hydrophilic contaminants are then removed before the products from the enzymatic reaction are eluted together with a suitable MALDI matrix and the solvent evaporated in a designated MALDI target structure. All steps can be performed automatically in 54 parallel microstructures on a microfluidic compact disc. The process is demonstrated by the selective capture and tryptic digest of recombinant IgG molecules from samples containing other proteins: an excess of bovine serum albumin or spent cell culture media.     

Characterization of cell‐banking parameters for the cryopreservation of mammalian cell lines in 100‐mL cryobags

This article describes a cell banking process for rBHK cell lines in 100‐mL cryobags. As the use of larger volume cell banks requires greater cell numbers and longer preparation time, extensive characterization of key process parameters beyond the conventional ranges was performed to support a cGMP banking process. All experiments were conducted using two recombinant BHK21 cell lines, one of them cotransfected with Hsp70. The results show that the entire cell banking process for these BHK cell lines can be performed at room temperature. A DMSO exposure time up to 5 h either directly in a bioreactor or in shaker flasks did not result in any significant negative effect after cell thaw, when the cryocontainers were frozen immediately after filling. Extensive characterization did not indicate any significant apoptotic effects after thaw. However, the Hsp70 cotransfected cell line did show a slightly better protection from potential cryopreservation‐induced apoptosis. Surprisingly, it was found that cells transferred into cryobags showed a low recovery rate after thaw if the incubation time exceeded 1.5 h before freezing. Additional experiments confirmed that the DMSO exposure time inside the cryocontainer in contrast to the DMSO exposure in a reactor or shaker flasks is much more critical. The cryobag cell banking process should therefore be performed within a 1½–2 h window; a banking process for vials should not exceed 2½ h. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Elimination of T lymphocytes from the bone marrow in HLA-incompatible bone marrow transplantation

The method presented is very well suited to eliminate T-lymphocytes from great amounts of bone-marrow. The stem cells required to reconstitute the bone-marrow are enriched in this way. It can be completely performed in a closed system. Any contamination with germs is excluded. It can be reproduced well and learnt quickly. It takes 10 hours for two trained co-workers to process 1,500 ml of bone-marrow. The vitality of cells is very good (100%). Its suitability for transplantation has still to be checked.     

The role of formulation in insulin comparability assessments.

The concept of comparability can be applied when changes are made to manufacturing processes for biotechnology products subsequent to pivotal clinical trial studies. For many process changes, comparability can be demonstrated based entirely on relevant in vitro data provided that a detailed knowledge of the process/product exists, suitable analytical methodology is employed, and historical data are available for the assessment. Insulin provides an excellent model system to illustrate many important considerations when dealing with comparability exercises for biotechnology products. The physicochemical properties of insulin demonstrate the numerous chemical reactions and physical transformations that are exclusive to proteins. These properties are heavily influenced by formulation conditions and must be carefully evaluated when process changes are made. In addition, physical and chemical testing performed on representative formulations can provide valuable insight when assessing the comparability between pre- and post-change materials. This paper reviews our experience with manufacturing changes involving insulin emphasizing the important role of formulation in the comparability exercise for protein biopharmaceuticals.     

Microfluidic biolector—microfluidic bioprocess control in microtiter plates

In industrial‐scale biotechnological processes, the active control of the pH‐value combined with the controlled feeding of substrate solutions (fed‐batch) is the standard strategy to cultivate both prokaryotic and eukaryotic cells. On the contrary, for small‐scale cultivations, much simpler batch experiments with no process control are performed. This lack of process control often hinders researchers to scale‐up and scale‐down fermentation experiments, because the microbial metabolism and thereby the growth and production kinetics drastically changes depending on the cultivation strategy applied. While small‐scale batches are typically performed highly parallel and in high throughput, large‐scale cultivations demand sophisticated equipment for process control which is in most cases costly and difficult to handle. Currently, there is no technical system on the market that realizes simple process control in high throughput. The novel concept of a microfermentation system described in this work combines a fiber‐optic online‐monitoring device for microtiter plates (MTPs)—the BioLector technology—together with microfluidic control of cultivation processes in volumes below 1 mL. In the microfluidic chip, a micropump is integrated to realize distinct substrate flow rates during fed‐batch cultivation in microscale. Hence, a cultivation system with several distinct advantages could be established: (1) high information output on a microscale; (2) many experiments can be performed in parallel and be automated using MTPs; (3) this system is user‐friendly and can easily be transferred to a disposable single‐use system. This article elucidates this new concept and illustrates applications in fermentations of Escherichia coli under pH‐controlled and fed‐batch conditions in shaken MTPs. Biotechnol. Bioeng. 2010;107: 497–505. © 2010 Wiley Periodicals, Inc.     

UPSEC: an algorithm for classifying unaligned protein sequences into functional families.

To classify proteins into functional families based on their primary sequences, popular algorithms such as the k-NN-, HMM-, and SVM-based algorithms are often used. For many of these algorithms to perform their tasks, protein sequences need to be properly aligned first. Since the alignment process can be error-prone, protein classification may not be performed very accurately. To improve classification accuracy, we propose an algorithm, called the Unaligned Protein SEquence Classifier (UPSEC), which can perform its tasks without sequence alignment. UPSEC makes use of a probabilistic measure to identify residues that are useful for classification in both positive and negative training samples, and can handle multi-class classification with a single classifier and a single pass through the training data. UPSEC has been tested with real protein data sets. Experimental results show that UPSEC can effectively classify unaligned protein sequences into their corresponding functional families, and the patterns it discovers during the training process can be biologically meaningful.     

Identifyability measures to select the parameters to be estimated in a solid‐state fermentation distributed parameter model

Process modeling can lead to of advantages such as helping in process control, reducing process costs and product quality improvement. This work proposes a solid‐state fermentation distributed parameter model composed by seven differential equations with seventeen parameters to represent the process. Also, parameters estimation with a parameters identifyability analysis (PIA) is performed to build an accurate model with optimum parameters. Statistical tests were made to verify the model accuracy with the estimated parameters considering different assumptions. The results have shown that the model assuming substrate inhibition better represents the process. It was also shown that eight from the seventeen original model parameters were nonidentifiable and better results were obtained with the removal of these parameters from the estimation procedure. Therefore, PIA can be useful to estimation procedure, since it may reduce the number of parameters that can be evaluated. Further, PIA improved the model results, showing to be an important procedure to be taken. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:905–917, 2016     

Modulation of brain activity during action observation: influence of perspective, transitivity and meaningfulness

The coupling process between observed and performed actions is thought to be performed by a fronto-parietal perception-action system including regions of the inferior frontal gyrus and the inferior parietal lobule. When investigating the influence of the movements' characteristics on this process, most research on action observation has focused on only one particular variable even though the type of movements we observe can vary on several levels. By manipulating the visual perspective, transitivity and meaningfulness of observed movements in a functional magnetic resonance imaging study we aimed at investigating how the type of movements and the visual perspective can modulate brain activity during action observation in healthy individuals. Importantly, we used an active observation task where participants had to subsequently execute or imagine the observed movements. Our results show that the fronto-parietal regions of the perception action system were mostly recruited during the observation of meaningless actions while visual perspective had little influence on the activity within the perception-action system. Simultaneous investigation of several sources of modulation during active action observation is probably an approach that could lead to a greater ecological comprehension of this important sensorimotor process.