Kinetic analyses and structure-activity relationship studies of synthetic lysine acetylation catalysts

Lysine acylation of proteins is a crucial chemical reaction, both as a post-translational modification and as a method for bioconjugation. We previously developed a chemical catalyst, DSH, which activates a chemically stable thioester including acyl-CoA, allowing the site-selective lysine acylation of histones under physiological conditions. However, a more active catalyst is required for efficient lysine acylation in more complex biological milieu, such as in living cells, but there are no rational guidelines for developing efficient lysine acylation catalysts for use under physiological conditions as opposed to in organic solvents. We, herein, conducted a kinetic analysis of the ability of DSH and several derivatives to mediate lysine acetylation to better understand the structural elements essential for high acetylation activity under physiological conditions. Interestingly, the obtained trend in reactivity was different from that observed in organic solvents, suggesting that a different principle is necessary for designing chemical catalysts specifically for use under physiological conditions compared to catalysts for use in organic solvents. Based on the obtained information, we identified a new catalyst scaffold with high activity and structural flexibility for further modification to improve this catalyst system.     

Serum-free culture conditions for analysis of secretory proteinases during myogenic differentiation of mouse C2C12 myoblasts.

We have been studying extracellular proteins such as proteinases and attachment factors under serum-free culture conditions. A number of studies on myogenesis using an in vitro culture system have reported that proteinases and ECM components play significant roles in muscle differentiation. However, most of the studies were performed in the presence of serum. Serum is abundant in the aforementioned proteins and its use in serum-free culture affects many cellular functions significantly. In this study, we tried to establish serum-free culture conditions for analyzing extracellular proteins involved in mouse myogenic differentiation. By evaluating media, supplements, and procedure of cell inoculation under serum-free conditions and by comparing the resultant conditions with conventional conditions on differentiated characteristics of the cells, it was revealed that serum-free Dulbecco's modified Eagle's medium/Ham's F-12 plus insulin more efficiently supported myogenesis morphologically and biochemically than conventional 2% horse serum-containing culture and that secretory proteinases obtained from our serum-free culture were different from those obtained utilizing conventional serum-free cultures in their activities and patterns. Since our serum-free medium consists of simple components, the medium is low cost and easy to prepare. Furthermore, the results suggest that our culture conditions are superior to conventional conditions biochemically and morphologically and will provide more precise and accurate information on extracellular proteins involved in myogenesis.     

The bioclimatic model: a method of palaeoclimatic qualitative inference based on mammal associations

Aim The bioclimatic model is a new method for palaeoclimatic reconstruction built on the assumption of a significant correlation between climate and mammal community composition. The goal of this approach is to infer past climatic conditions using mammal fossil associations as source data. Location The study used mammal faunas from all over the world to develop the bioclimatic model. As an example of the potential of the model, we have applied it to Quaternary faunas from Eurasia. Methods The proposed model was constructed by applying multivariate discriminant analysis to modern mammal faunas and climates from throughout the world. The model was validated with a different set of modern faunas than those used in the discriminant analysis, including some from transitional zones between different climates (ecotones). To test the reliability of the method in the Pleistocene, the results have been compared to those obtained with data from other disciplines, such as palaeobotany. Results The results obtained in the validation of the model show that more than 90% of the localities have been classified correctly. Comparisons of results in the late Pleistocene‐Holocene of Barová between a palaeobotanical study and the bioclimatic analysis show the latter to be highly accurate. The results for early Pleistocene faunas show somewhat drier and more open climatic conditions for Europe than the present day, with larger areas of steppe environments. Main Conclusions The bioclimatic model could be used to infer climatic conditions from mammal faunas. The results presented in this work provide a preliminary example of the potential that bioclimatic analysis has as a tool for palaeoclimatic inference. Finally, this method offers the opportunity to standardize data coming from vertebrate palaeontology for use in the construction and evaluation of climatic models.     

Protein synthesis in Petunia hybrida chloroplasts isolated from leaves and cell cultures

Isolation and incubation conditions were established for Petunia hybrida chloroplasts capable of performing in vitro protein and RNA synthesis. Under these conditions, chloroplasts from leaves as well as from the non-photoautotrophic mutant green cell culture AK-2401 are able to incorporate labeled amino acids into polypeptides. Intact chloroplasts can use light as an energy source; photosynthetically-inactive chloroplasts require the addition for ATP for this protein synthesis. Sodium dodecylsulphate polyacrylamide slab gel electrophoresis shows that in isolated leaf chloroplasts at least twenty-five radioactive polypeptide species are synthesized. The three major products synthesized have molecular weights of 52,000, 32,000 and 17,000. Coomassie brilliant-bluestained polypeptide patterns from plastids isolated from the mutant green cell culture AK-2401 differ considerably from those obtained from leaf chloroplasts. The pattern of radioactive polypeptides synthesized in these isolated cell culture plastids also shows differences. These results indicate that the difference in developmental stage observed between plastids from the cell culture AK-2401 and leaves is reflected in an altered expression of the chloroplast DNA.Abbreviations CAP D-threo-chloramphenicol - 2,4-D 2,4-dichlorophenoxyacetic acid - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - RuBPCase ribulose-1,5-bisphosphate carboxylase - SDS sodium dodecylsulphate     

Competition – Supporting or preventing an increased use of bioenergy?

The intensified use of biomass as an energy source is an often-repeated goal of the German and European climate protection policy. Therefore, framework conditions have been created in recent years, which allow for a wider use of biomass within the energy system especially for a provision of electricity and fuels. Due to this policy, Germany, for example, has emerged as the leading producer of biogas from energy crops and fatty methyl ester (FAME) in Europe. However, due to the high energy price level, the use of biomass for heating purposes and as a renewable raw material have increased at the same time. To supply the obviously increased demand for biomass or biobased energy carriers cost efficiently, nationwide and to some extend even global markets are under development at present. As the demand for biomass is expected to continue to increase strongly, it is feared that an increasing competition with the use for food and fodder as well as a raw material might occur in the years to come. Against this background we have analyzed the competitions that can be expected, and the influence that they may have on the further expansion of the use of biomass for energy production. Experiences from Germany are provided exemplarily. Based on this, it is concluded that measures need to be taken to support an efficient and sustainable use of bioenergy in the future.     

Classification of Different Tympanic Membrane Conditions Using Fused Deep Hypercolumn Features and Bidirectional LSTM

Objectives: Middle ear inflammatory diseases are global health problem that can have serious consequences such as hearing loss and speech disorders. The high cost of medical devices such as oto-endoscope and oto-microscope used by the specialists for the diagnosis of the disease prevents its widespread use. In addition, the decisions of otolaryngologists may differ due to the subjective visual examinations. For this reason, computer-aided middle ear disease diagnosis systems are needed to eliminate subjective diagnosis and high cost problems. To this aim, a hybrid deep learning approach was proposed for automatic recognition of different tympanic membrane conditions such as earwax plug, myringosclerosis, chronic otitis media and normal from the otoscopy images.Materials and methods: In this study we used public Ear Imagery dataset containing 880 otoscopy images. The proposed approach detects keypoints from the otoscopy images and following the obtained keypoint positions, extracts hypercolumn deep features from 5 different layers of the VGG 16 model. Classification of tympanic membrane conditions were realized by feeding the deep hypercolumn features to Bi-LSTM network in the form of non-time related data.Results: The performance of the proposed model was evaluated in three different color spaces as Red-Green-Blue (RGB), Hue-Saturation-Value (HSV) and Haematoxylin-Eosin-Diaminobenzidine (HED). The proposed model achieved acceptable results in all color spaces, moreover it showed a very successful performance in classifying tympanic membrane conditions especially in RGB space. Experimental studies showed that the proposed model achieved Acc of 99.06%, Sen of 98.13% and Spe of 99.38%.Conclusion: As a result, a robust model with high sensitivity was obtained for classification of tympanic membrane conditions and it was shown that Bi-LSTM network, which is generally used with time-related data, could also be used successfully with non-time related data for diagnosis of tympanic membrane conditions.     

Über die Nachrichtenaufnahme durch biologische Receptoren

Summary The Hodgkin-Huxley theory of ion fluxes across membranes during excitation is extended to explain the graduated depolarisation (receptor potential) of sensory cell membranes. Electric circuit equivalents of living membranes are developed. Driving forces and velocity coefficients are represented by means of electric parameters. From this model active and passive ionic fluxes can be calculated quantitatively on the basis of transport equations derived from irreversible thermodynamics. Thus the circuit equivalent may be used as an analog computer. Electric receptor models allow a reproduction of all potential curves which have been derived in electrophysiological experiments on PD-receptors. The results obtained by the use of this model agree with the results obtained in biological experiments under various conditions of stimuli. The significance of solution compartments for intra-and extracellular ions in relation to the time functions of various conditions are discussed in detail. This models are of heuristic value in experimental research. In combination with neuron networks they can be used for the analysis of information theoretical problems.     

Protein instability during HIC: describing the effects of mobile phase conditions on instability and chromatographic retention

Hydrophobic interaction chromatography (HIC) is known to be potentially denaturing to proteins, but the effects of mobile phase conditions on chromatographic behavior are not well understood. In this study, we apply a model describing the effects of secondary protein unfolding equilibrium on chromatographic behavior, including the effects of salt concentration on both stability and adsorption. We use alpha-lactalbumin as a model protein that in the presence and absence of calcium, allows evaluation of adsorption parameters for folded and unfolded species independently. The HIC adsorption equilibrium under linear binding conditions and solution phase protein stability have been obtained from a combination of literature and new experiments. The effect of salt concentration on protein stability and the rate constant for unfolding on the chromatographic surface have been determined by fitting the model to isocratic chromatography data under marginally stable conditions. The model successfully describes the effects of added calcium and ammonium sulfate. The results demonstrate the importance of considering the effects on stability of mobile phase modifiers when applying HIC to marginally stable     

hiPSC‐derived iMSCs: NextGen MSCs as an advanced therapeutically active cell resource for regenerative medicine

Mesenchymal stem cells (MSCs) are being assessed for ameliorating the severity of graft‐versus‐host disease, autoimmune conditions, musculoskeletal injuries and cardiovascular diseases. While most of these clinical therapeutic applications require substantial cell quantities, the number of MSCs that can be obtained initially from a single donor remains limited. The utility of MSCs derived from human‐induced pluripotent stem cells (hiPSCs) has been shown in recent pre‐clinical studies. Since adult MSCs have limited capability regarding proliferation, the quantum of bioactive factor secretion and immunomodulation ability may be constrained. Hence, the alternate source of MSCs is being considered to replace the commonly used adult tissue‐derived MSCs. The MSCs have been obtained from various adult and foetal tissues. The hiPSC‐derived MSCs (iMSCs) are transpiring as an attractive source of MSCs because during reprogramming process, cells undergo rejuvination, exhibiting better cellular vitality such as survival, proliferation and differentiations potentials. The autologous iMSCs could be considered as an inexhaustible source of MSCs that could be used to meet the unmet clinical needs. Human‐induced PSC‐derived MSCs are reported to be superior when compared to the adult MSCs regarding cell proliferation, immunomodulation, cytokines profiles, microenvironment modulating exosomes and bioactive paracrine factors secretion. Strategies such as derivation and propagation of iMSCs in chemically defined culture conditions and use of footprint‐free safer reprogramming strategies have contributed towards the development of clinically relevant cell types. In this review, the role of iPSC‐derived mesenchymal stromal cells (iMSCs) as an alternate source of therapeutically active MSCs has been described. Additionally, we also describe the role of iMSCs in regenerative medical applications, the necessary strategies, and the regulatory policies that have to be enforced to render iMSC's effectiveness in translational medicine.     

Isolation and propagation of keratinocytes derived from Cashmere goat fetus

The study was conducted to isolate epidermal keratinocytes from Cashmere goat fetus with the aim to develop suitable conditions for keratinocyte cultivation and propagation. The methods developed for keratinocyte culture include (i) use of a feeder-layer of mitotically inactivated fibroblasts obtained from goat and mouse fetal skin, (ii) use of a substrate such as collagen IV, or (iii) without use of any substrate. Epidermal cell removal was established by enzymatically separating keratinocytes from 12 to 16 weeks aged fetal skin tissues treated with 0.125% trypsin solution overnight at 4 degrees C. The cells were maintained in all culture conditions with serum containing medium. Keratinocyte multiplication and proliferation were comparable in different culture conditions and the improved cellular attachment and growth have been obtained in cultures on feeder layers. Colony forming keratinocytes on feeder layer were heterogeneous in their growth potential. In feeder free conditions, high cellular density was required at plating for sub-cultivation as their poor attachment in culture dishes. This study reports the comparative efficacy of different culture conditions for keratinocyte isolation and in vitro propagation originating from Cashmere goat fetus.     

Conditions for initiating Lake Victoria haplochromine (Oreochromis esculentus) primary cell cultures from caudal fin biopsies

The global decline of freshwater fishes has created a need to cryopreserve biological materials from endangered species in an effort to conserve the biodiversity within this taxon. Since maternal gametes and embryos from fish are difficult to cryopreserve, somatic cells obtained from caudal fins have become an increasingly popular resource as they contain both maternal and paternal DNA ensuring valuable traits are not lost from the population. Somatic cells stored in cryobanks can be used to supplement endangered populations with genetically valuable offspring with the use of assisted reproductive technologies. However, initiating primary cell cultures from caudal fin biopsies of endangered species can be challenging as standardized protocols have not yet been developed. The objective of this study was to identify culture conditions, including antibiotic supplementation, biopsy size, and culture temperature, suitable for establishing primary cell cultures of ngege (Oreochromis esculentus), a critically endangered African cichlid. Six-millimeter caudal fin biopsies provided sufficient material to develop a primary cell culture when incubated at 25°C using standard fish cell culture medium containing 1× Primocin. Further investigation and application of these culture conditions for other endangered freshwater fishes is necessary.     

Natural cellulose fibers from switchgrass with tensile properties similar to cotton and linen

We report the production and characteristics of natural cellulose fibers obtained from the leaves and stems of switchgrass. In this paper, the composition, structure and properties of fibers obtained from the leaves and stem of switchgrass have been studied in comparison to the common natural cellulose fibers, such as cotton, linen and kenaf. The leaves and stems of switchgrass have tensile properties intriguingly similar to that of linen and cotton, respectively. Fibers were obtained from the leaves and stems of switchgrass using a simple alkaline extraction and the structure and properties of the fibers were studied. Fibers obtained from switchgrass leaves have crystallinity of 51%, breaking tenacity of 5.5 g per denier (715 MPa) and breaking elongation of 2.2% whereas the corresponding values for fibers obtained from switchgrass stems are 46%, 2.7 g per denier and 6.8%, respectively. Switchgrass is a relatively easy to grow and high yield biomass crop that can be source to partially substitute the natural and synthetic fibers currently in use. We hope that this research will stimulate interests in using switchgrass as a novel fiber crop in addition to being promoted as a potential source for biofuels.     

Dynamic muscle force predictions from EMG: an artificial neural network approach

EMG signals of dynamically contracting muscle have never been used to predict experimentally known muscle forces across subjects. Here, we use an artificial neural network (ANN) approach to first derive an EMG–force relationship from a subset of experimentally determined EMGs and muscle forces; second, we use this relationship to predict individual muscle forces for different contractile conditions and in subjects whose EMG and force data were not used in the derivation of the EMG–force relationship; and third, we validate the predicted muscle forces against the known forces recorded in vivo. EMG and muscle forces were recorded from the cat soleus for a variety of locomotor conditions giving a data base from three subjects, four locomotor conditions, and 8–16 steps per subject and condition. Considering the conceptual differences in the tasks investigated (e.g. slow walking vs. trotting), the intra-subject results obtained here are superior to those published previously, even though the approach did not require a muscle model or the instantaneous contractile conditions as input for the force predictions. The inter-subject results are the first of this kind to be presented in the literature and they typically gave cross-correlation coefficients between actual and predicted forces of >0.90 and root mean square errors of <15%, thus they were considered excellent.

From the results of this study, it was concluded that ANNs represent a powerful tool to capture the essential features of EMG–force relationships of dynamically contracting muscle, and that ANNs might be used widely to predict muscle forces based on EMG signals.     

Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli.

The very high concentration of macromolecules within cells can potentially have an overwhelming effect on the thermodynamic activity of cellular components because of excluded volume effects. To estimate the magnitudes of such effects, we have made an experimental study of the cytoplasm of Escherichia coli. Parameters from cells and cell extracts are used to calculate approximate activity coefficients for cytoplasmic conditions. These calculations require a representation of the sizes, concentrations and effective specific volumes of the macromolecules in the extracts. Macromolecule size representations are obtained either by applying a two-phase distribution assay to define a related homogeneous solution or by using the molecular mass distribution of macromolecules from gel filtration. Macromolecule concentrations in cytoplasm are obtained from analyses of extracts by applying a correction for the dilution that occurs during extraction. That factor is determined from experiments based upon the known impermeability of the cytoplasmic volume to sucrose in intact E. coli. Macromolecule concentrations in the cytoplasm of E. coli in either exponential or stationary growth phase are estimated to be approximately 0.3 to 0.4 g/ml. Macromolecule specific volumes are inferred from the composition of close-packed precipitates induced by polyethylene glycol. Several well-characterized proteins which bind to DNA (lac repressor, RNA polymerase) are extremely sensitive to changes in salt concentration in studies in vitro, but are insensitive in studies in vivo. Application of the activity coefficients from the present work indicates that at least part of this discrepancy arises from the difference in excluded volumes in these studies. Applications of the activity coefficients to solubility or to association reactions are also discussed, as are changes associated with cell growth phase and osmotic or other effects. The use of solutions of purified macromolecules that emulate the crowding conditions inferred for cytoplasm is discussed.     

Inhibition of the in vitro outgrowth of Epstein-Barr virus-infected lymphocytes by TG lymphocytes.

Human T lymphocytes subpopulations from subjects not acutely infected with EBV have been selected and examined for ability to inhibit the outgrowth of autologous B lymphocytes that have undergone in vitro infection with EB virus. The results show that only TG lymphocytes are inhibitory. TG lymphocytes from subjects who are EBV antibody-negative inhibit as well as those from subjects who have EBV antibody. TG lymphocyte populations, as well as other T cell fractions obtained from neonatal subjects, fail to inhibit the outgrowth of infected, autologous lymphocytes under the conditions tested. We propose that NK cells are responsible for the inhibitory effects described in this report.     

Prediction of amyloid aggregation in vivo

Many human diseases owe their pathology, to some degree, to the erroneous conversion of proteins from their soluble state into fibrillar, β-structured aggregates, often referred to as amyloid fibrils. Neurodegenerative diseases, such as Alzheimer and spongiform encephalopathies, as well as type 2 diabetes and both localized and systemic amyloidosis, are among the conditions that are associated with the formation of amyloid fibrils. Several mathematical tools can rationalize and even predict important parameters of amyloid fibril formation. It is not clear, however, whether such algorithms have predictive powers for in vivo systems, in which protein aggregation is affected by the presence of other biological factors. In this review, we briefly describe the existing algorithms and use them to predict the effects of mutations on the aggregation of specific proteins, for which in vivo experimental data are available. The comparison between the theoretical predictions and the experimental data obtained in vivo is shown for each algorithm and experimental data set, and statistically significant correlations are found in most cases.     

A novel chromatography system to isolate active ribosomes from pathogenic bacteria

We have developed a novel chromatography for the rapid isolation of active ribosomes from bacteria without the use of harsh conditions or lengthy procedures that damage ribosomes. Ribosomes interact with an alkyl linker attached to the resin, apparently through their RNA component. Examples are given with ribosomes from Escherichia coli, Deinococcus radiodurans, and with clinical isolates of Streptococcus pneumoniae and methicillin-resistant Staphylococcus aureus (MRSA). The ribosomes obtained by this method are unusually intact, so that highly active ribosomes can now be isolated from the clinical isolates, enabling significantly improved in vitro functional assays that will greatly assist the discovery and development of new ribosomally targeted antibiotics.     

Simulation of photon transport in a three-dimensional leaf: implications for photosynthesis

A model to evaluate photon transport within leaves and the implications for photosynthesis are investigated. A ray tracing model, Raytran, was used to produce absorption profiles within a virtual dorsiventral plant leaf oriented in two positions (horizontal/vertical) and illuminated on one of its two faces (adaxial/abaxial). Together with chlorophyll profiles, these absorption profiles feed a simple photosynthesis model that calculates the gross photosynthetic rate as a function of the incident irradiance. The differences observed between the four conditions are consistent with the literature: horizontal‐adaxial leaves, which are commonly found in natural conditions, have the greatest light use efficiency. The absorption profile obtained with horizontal‐abaxial leaves lies below this, but above those obtained for vertical leaves. The latter present similar gross photosynthetic rates when irradiated on either the adaxial or abaxial surfaces. Vertical profiles of photosynthetic rates across the leaf confirm that carbon fixation occurs mainly in the palisade parenchyma, that the leaf anatomy is integral to its function and that leaves cannot be considered as a single homogeneous unit. Finally, the relationships between leaf structure, orientation and photosynthesis are discussed.     

An ensemble analysis of electromyographic activity during whole body pointing with the use of support vector machines

We explored the use of support vector machines (SVM) in order to analyze the ensemble activities of 24 postural and focal muscles recorded during a whole body pointing task. Because of the large number of variables involved in motor control studies, such multivariate methods have much to offer over the standard univariate techniques that are currently employed in the field to detect modifications. The SVM was used to uncover the principle differences underlying several variations of the task. Five variants of the task were used. An unconstrained reaching, two constrained at the focal level and two at the postural level. Using the electromyographic (EMG) data, the SVM proved capable of distinguishing all the unconstrained from the constrained conditions with a success of approximately 80% or above. In all cases, including those with focal constraints, the collective postural muscle EMGs were as good as or better than those from focal muscles for discriminating between conditions. This was unexpected especially in the case with focal constraints. In trying to rank the importance of particular features of the postural EMGs we found the maximum amplitude rather than the moment at which it occurred to be more discriminative. A classification using the muscles one at a time permitted us to identify some of the postural muscles that are significantly altered between conditions. In this case, the use of a multivariate method also permitted the use of the entire muscle EMG waveform rather than the difficult process of defining and extracting any particular variable. The best accuracy was obtained from muscles of the leg rather than from the trunk. By identifying the features that are important in discrimination, the use of the SVM permitted us to identify some of the features that are adapted when constraints are placed on a complex motor task.