Improving the representation of peptide‐like inhibitor and antibiotic molecules in the Protein Data Bank

With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide‐like inhibitor and antibiotic molecules so that they can be easily identified and analyzed. Peptide‐like inhibitors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single‐component molecules, their peptide‐like composition was captured in a new representation, called the subcomponent sequence. A novel concept called “group” was developed for representing complex peptide‐like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide‐like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide‐like inhibitors and antibiotics accurately and consistently. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 659–668, 2014.     

Macromolecular complexes of BSA with gelatin

This work studies the effect of the helix-coil transition in gelatin on the structure development in the complex forming water-gelatin-BSA system using dynamic light scattering, environment scanning electron microscopy, rheometry, differential scanning microcalorimetry, circular dichroism, fluorescence, and absorption measurements. It was established that the structure of the complexes formed and the mechanism of intermacromolecular interaction are different in the case of two conformation states of gelatin. Above the temperature of the conformational transition (40 °C) intermacromolecular interaction leads to collapse gelatin macromolecules and formation compact (30 nm in radius) BSA-gelatin complexes (～6:1, mole/mole), partial stabilization of the secondary structure (increase the mean helix content), and stabilization of BSA molecules against thermo aggregation. At the same time it does not leads to an appreciable change in the thermodynamic parameters of the thermal transitions for BSA and gelatin. Below the temperature of the conformation transition (at 18 °C) the interaction results in formation of the large (600-1000 nm in radius) complex particles due to trapping BSA molecules into the meshes of the gelatin network and, as consequence, a substantial increase in the storage and loss moduli of the system.     

Use of inert gas jets to measure the forces required for mechanical gene transfection

Background

Abnormal blood glucose (BG) concentrations have been associated with increased morbidity and mortality in both critically ill adults and infants. Furthermore, hypoglycaemia and glycaemic variability have both been independently linked to mortality in these patients. Continuous Glucose Monitoring (CGM) devices have the potential to improve detection and diagnosis of these glycaemic abnormalities. However, sensor noise is a trade-off of the high measurement rate and must be managed effectively if CGMs are going to be used to monitor, diagnose and potentially help treat glycaemic abnormalities.

Aim

To develop a tool that will aid clinicians in identifying unusual CGM behaviour and highlight CGM data that potentially need to be interpreted with care.

Methods

CGM data and BG measurements from 50 infants at risk of hypoglycaemia were used. Unusual CGM measurements were classified using a stochastic model based on the kernel density method and historical CGM measurements from the cohort. CGM traces were colour coded with very unusual measurements coloured red, highlighting areas to be interpreted with care. A 5-fold validation of the model was Monte Carlo simulated 25 times to ensure an adequate model fit.

Results

The stochastic model was generated using ~67,000 CGM measurements, spread across the glycaemic range ~2-10?mmol/L. A 5-fold validation showed a good model fit: the model 80% confidence interval (CI) captured 83% of clinical CGM data, the model 90% CI captured 91% of clinical CGM data, and the model 99% CI captured 99% of clinical CGM data. Three patient examples show the stochastic classification method in use with 1) A stable, low variability patient which shows no unusual CGM measurements, 2) A patient with a very sudden, short hypoglycaemic event (classified as unusual), and, 3) A patient with very high, potentially un-physiological, glycaemic variability after day 3 of monitoring (classified as very unusual).

Conclusions

This study has produced a stochastic model and classification method capable of highlighting unusual CGM behaviour. This method has the potential to classify important glycaemic events (e.g. hypoglycaemia) as true clinical events or sensor noise, and to help identify possible sensor degradation. Colour coded CGM traces convey the information quickly and efficiently, while remaining computationally light enough to be used retrospectively or in real-time.     

Study of transplanted lichens with the use of physical methods: the case of <Emphasis Type="Italic">Xanthoria parietina</Emphasis> (L.) Th. Fr.

Electron paramagnetic resonance spectroscopy and inductively coupled plasma optical emission spectrometry were used to study the epiphytic lichen Xanthoria parietina (L.) Th. Fr. transplanted to natural and urbanized zones in the Moscow region. The combination of physical and lichenindication methods allowed us to determine periods as well as the magnitude of changes in the biophysical characteristics of the transplanted lichen in different environmental conditions. Electron paramagnetic resonance spectroscopy demonstrated that the number of paramagnetic centers in lichens transplanted to the natural zone did not change in comparison with initial value (2.6 ± 0.4)·10¹⁷ spin/mg) and remained stable after four weeks after transplantation. The number of paramagnetic centers in lichens transplanted to the urbanized zone increased by 1.1·10¹⁷ spin/mg by the end of the third week as compared with its initial value ((2.6 ± 0.4)·10¹⁷ spin/mg). Inductively coupled plasma optical emission spectrometry was used to measure concentration of iron, copper, manganese, magnesium, and zinc. We detected substantial changes in concentration of these elements during first four weeks after transplantation. For instance, concentration of copper in lichens transplanted to the urbanized zone increased from 7.5 ± 2.7 μg/g to 56.4 ± 8.6 μg/g by the end of the third week of the experiment.     

Developmental cycle and the cytomorphological characteristics of the oleandomycin producer Streptomyces antibioticus

The developmental cycle and cytomorphological features of the industrial strain OL-1 and its variant 0968 of the oleandomycin-producing organism were studied. Variant 0968 was obtained as a result of exposure of the spores of strain OL-1 to UV light. When grown under submerged conditions in flasks with the rich medium, the strains were characterized by a complete developmental cycle consisting of three generations of the hyphae. Every generation had a tendency for formation of submerged spores. The UV-induced variant differed from the industrial strain by higher levels of the antibiotic accumulation which correlated with higher rates of the spore germination. The strains were characterized by polymorphism of the mycelium and formation of submerged spores during their cultivation which is likely to prolong the antibiotic synthesis from 120 to 216 hours from the inoculation moment. The long-term selection of the oleandomycin-producing organism on the rich medium markedly changed the culture genotype and resulted in significant changes in the developmental cycle under submerged cultivation conditions. The data may be used for the microscopic control of the process of oleandomycin production.     

Increasing the effectiveness of ampicillin in combination with lysozyme

The effect of lysozyme (2 mg/kg) on pharmacokinetics of ampicillin (60 mg/kg) and the lymph nodes was studied in a model of experimental diffuse peritonitis in 52 dogs. The drugs were administered intramuscularly in single doses simultaneously with simulation of the pathological process. Under such conditions, lysozyme promoted an increase in the ampicillin concentration in the lymphatic system, blood and tissues and prolonged the antibacterial activity to 18 hours of the experiment. This resulted in retarding lympho- and hematogenic dissemination of the infection from the primary focus and lowered the infectious and toxic affection of the regional lymph nodes, thus securing their barrier and immunological function. With lysozyme used in combination with the antibiotic the immunomorphological zones of the lymph nodes appeared to be preserved and the volumetric proportion of macrophages increased. Then the volumetric proportion of the blast cells and the frequency of macrophagal and lymphocytic interactions also increased. The most pronounced cell interactions were observed in the distal (tracheobronchial) lymph nodes whose functions before the infection generalization were mainly immunological.     

Zinc-iodine-osmium impregnation of giant synaptosomes obtained from the hippocampal formation of the rabbit]

The fraction of giant synaptosomes from the r. inferior of the rabbit hippocampus was studied using impregnation with zinc iodide-osmium tetroxide (XIO) reagent and electron microscopy. In this fraction, light and dark synaptosomes were observed. The reaction product was found in the clear-centered synaptic vesicles (200-400 A) as electron-dense structures of different forms and small osmiophilic particles on the vesicular membranes. Dense-cored vesicles and postsynaptic structures were not revealed with ZIO-reagent. The structures revealed with ZIO-reagent in the giant synaptosomes of the hippocampus are supposedly related to stroage of the neurotransmitter-glutamate.     

Rate of benyzylpenicillin inactivation in native solutions during extraction]

The constants of benzylpenicillin inactivation in acidified fermentation broth filtrates were different in various filtrate batches. Marked inactivation of the antibiotic in the filtrates immediately after their acidification was observed. Possible losses of the antibiotic due to inactivation under conditions of extraction were estimated.     

N-acetyl-beta-D-hexosaminidase secreted by the marine fungus Phoma glomerata

Among the ten strains of marine fungi studied, the mycelial fungus Phoma glomerata showed maximum potency in producing N-acetyl-beta-D-glucosaminidase. The conditions for fungal growth and enzyme biosynthesis were evaluated. N-acetyl-beta-D-hexosaminidase was isolated from the culture liquid of Phoma glomerata by ion-exchange chromatography (on DEAE-cellulose and DEAE-Sephacell) and gel filtration (on Toyopearl HW-55) with a yield of 35%; the enzyme, purified 36.4-fold, had a molecular weight of 20 kDa. The homogeneity of the enzyme was confirmed by gel filtration and SDS-PAGE. Transglycosylation reactions catalyzed by the enzyme produced N-acetyl-D-glucosamine and N-acetyl-D-galactosamine with respective yields of 38 and 46%.     

Phenotypic differentiation of neurons in intraocular transplants

Neurochemical differentiation of neurons in transplants developing in rat anterior eye chamber was studied. Pieces of the somatosensory neocortex area, isolated from 17-day fetuses of Wistar rats, were used for the transplantation. The general cytological analysis and immunochemical identification of GABAergic neurons in neocortical transplants and in the appropriate brain area of the recipient rats (control) were carried out after 6 months. Cytoarchitectonics typical for neocortex was not revealed in the transplants. Furthermore, a 1.4-fold decrease in numerical density of the entire neuron population was found compared to the control. The proportion of GABAergic nerve cells in the transplanted tissue was reduced even more dramatically— by 13.1 times. The dimensions of all types of neurons, especially GABAergic cells, were greater in the transplants in oculo compared to neocortex in situ. The increase in size occurred mostly due to the cytoplasm. Thus, the nuclei of GABA-positive neurons in the transplants were larger by 1.2 times compared to the control and their perikarya were larger by 1.5 times. The obtained results showed that the conditions in the anterior eye chamber the most dramatically affect the differentiation of GABAergic neurons, and cell hypertrophy, probably, is the functional compensation of the decrease in their number. Considering the literature data on the increased excitability and synchronized neuronal activity in the intraocular transplants, it can be assumed that these transplants can be used as a model for studying the cellular mechanisms of nervous tissue epileptization under disinhibition conditions.