TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction

Among new protein structure predictors, the recently developed AlphaFold predictor relies on contact map in line with contact map potential based threading model that basically relies on fold recognition. In parallel, sequence similarity based homology model relies on homologue recognition. Both of these methods rely on sequence-structure or sequence-sequence similarity with protein with known structure in absence of which, as argued in the development of AlphaFold, the structure prediction becomes quite challenging. However, the term, "known structure" depends on the similarity method adopted to identify it, for example, through sequence match yielding homologue or sequence-structure match yielding a fold. Also, quite often, AlphaFold structures are found to be not acceptable by the structure evaluating gold standard parameters. In this context, this work utilized the concept of ordered local physicochemical property, ProtPCV by Pal et al (2020) providing a new similarity criteria to identify the template protein with known structure. Finally a template search engine, TemPred was developed using the ProtPCV similarity criteria. It was intriguing to find that quite often templates generated by TemPred were better than that produced by the conventional search engines. It pointed out the need of combined approach to get better structural model for a protein.

Application of sequence semantic and integrated cellular geography approach to study alternative biogenesis of exonic circular RNA

BACKGROUND

Concurrent existence of lncRNA and circular RNA at both nucleus and cytosol within a cell at different proportions is well reported. Previous studies showed that circular RNAs are synthesized in nucleus followed by transportation across the nuclear membrane and the export is primarily defined by their length. lncRNAs primarily originated through inefficient splicing and seem to use NXF1 for cytoplasm export. However, it is not clear whether circularization of lncRNA happens only in nucleus or it also occurs in cytoplasm. Studies indicate that circular RNAs arise when the splicing apparatus undergoes a phenomenon of back splicing. Minor spliceosome (U12 type) mediated splicing occurs in cytoplasm and is responsible for the splicing of 0.5% of introns of human cells. Therefore, possibility of cRNA biogenesis mediated by minor spliceosome at cytoplasm cannot be ruled out. Secondly, information on genes transcribing both circular and lncRNAs along with total number of RBP binding sites for both of these RNA types is extractable from databases. This study showed how these apparently unconnected pieces of reports could be put together to build a model for exploring biogenesis of circular RNA.

RESULTS

As a result of this study, a model was built under the premises that, sequences with special semantics were molecular precursors in biogenesis of circular RNA which occurred through catalytic role of some specific RBPs. The model outcome was further strengthened by fulfillment of three logical lemmas which were extracted and assimilated in this work using a novel data analytic approach, Integrated Cellular Geography. Result of the study was found to be in well agreement with proposed model. Furthermore this study also indicated that biogenesis of circular RNA was a post-transcriptional event.

CONCLUSIONS

Overall, this study provides a novel systems biology based model under the paradigm of Integrated Cellular Geography which can assimilate independently performed experimental results and data published by global researchers on RNA biology to provide important information on biogenesis of circular RNAs considering lncRNAs as precursor molecule. This study also suggests the possible RBP-mediated circularization of RNA in the cytoplasm through back-splicing using minor spliceosome.

APT: An Automated Probe Tracker From Gene Expression Data

Out of currently available semi-automatic tools for detecting diagnostic probes relevant to a pathophysiological condition, ArrayMining and GEO2R of NCBI are most popular. The shortcomings of ArrayMining and GEO2R are that both tools list the probes ordering them on the basis of their individual statistical level of significances with only difference of statistical methods used by them. While the latest tool GEO2R outputs either top 250 or all genes following its own ranking mechanism, ArrayMining requires number of probes to be inputted by the user. This study provided a way for automatic selection of probe-set that can be obtained from the voting of outputs resulted from statistical methods, t-Test, Mann-Whitney Test and Empirical Bayes Moderated t-test. It was also intriguing to find that the parameters of these statistical methods can be represented as a mathematical function of group fisher's discriminant ratio of a disease-control expression data-pair. Result of this fully automatic method, APT shows 88.97 percent success in comparison to 80.40 and 87.60 percent successes of ArrayMining and GEO2R respectively to include reported probes. Furthermore, out of 10 fold cross validation and 5 new test cases, APT shows a better performance than both ArrayMining and GEO2R in regards to sensitivity and specificity.

An improved protein structure evaluation using a semi-empirically derived structure property

BACKGROUND

In the backdrop of challenge to obtain a protein structure under the known limitations of both experimental and theoretical techniques, the need of a fast as well as accurate protein structure evaluation method still exists to substantially reduce a huge gap between number of known sequences and structures. Among currently practiced theoretical techniques, homology modelling backed by molecular dynamics based optimization appears to be the most popular one. However it suffers from contradictory indications of different validation parameters generated from a set of protein models which are predicted against a particular target protein. For example, in one model Ramachandran Score may be quite high making it acceptable, whereas, its potential energy may not be very low making it unacceptable and vice versa. Towards resolving this problem, the main objective of this study was fixed as to utilize a simple experimentally derived output, Surface Roughness Index of concerned protein of unknown structure as an intervening agent that could be obtained using ordinary microscopic images of heat denatured aggregates of the same protein.

RESULT

It was intriguing to observe that direct experimental knowledge of the concerned protein, however simple it may be, might give insight on acceptability of its particular structural model out of a confusion set of models generated from database driven comparative technique for structure prediction. The result obtained from a widely varying structural class of proteins indicated that speed of protein structure evaluation can be further enhanced without compromising with accuracy by recruiting simple experimental output.

CONCLUSION

In this work, a semi-empirical methodological approach was provided for improving protein structure evaluation. It showed that, once structure models of a protein were obtained through homology technique, the problem of selection of a best model out of a confusion set of Pareto-optimal structures could be resolved by employing a structure agent directly obtainable through experiment with the same protein as experimental ingredient. Overall, in the backdrop of getting a reasonably accurate protein structure of pathogens causing epidemics or biological warfare, such approach could be of use as a plausible solution for fast drug design.

EcircPred: Sequence and secondary structural property based computational identification of exonic circular RNAs

Circular RNAs are new class of stable non-coding RNAs, whose expressions are specific to tissues as well as developmental stages and reported to act as gene regulators. Conspicuous presences of some of them as biomarkers for cancers, aging etc. are well reported. Biogenesis of circular RNA competes with Pre-mRNA splicing using the same splicing machinery and gene loci. Also, some circular RNAs are reported to have open reading frames and internal ribosome entry site for ribosome binding, which increases the chance of overlapping features among circular and mRNA transcripts. Therefore, discriminating the Exonic circular RNAs and mRNAs solely through sequence properties is challenging. However, possible discriminating factors, such as, reports on non-canonical arrangement of exons in circular RNAs were cited. This study was dedicated to classify Circular RNAs from mRNAs by recruiting features extracted from sequences as well as predicted secondary structures and ANN classifier models for all these feature types. The features were statistics of di-nucleotide index, emission probability of RNA sequences and entropy of di-nucleotides. Finally a simple decision voting was applied to combine decisions obtained from multiple classifiers. After performing 10 fold cross validation we obtained average values of efficiency, sensitivity, specificity and Mathews correlation coefficient as 0.8374, 0.8544, 0.8203 and 0.6753 respectively. In the backdrop of few reports of identification of circular RNAs from constitutive exons and other long non-coding RNAs, this is the first report of discriminating exonic circular RNAs from mRNAs using sequence and sequence-derived properties.

An Improved Protein Surface Extraction Method Using Rotating Cylinder Probe

For extraction of information on binding sites of a protein, the commonly known geometry-based methods utilize the corresponding PDB file to extract its surface as a first step. Finally, the surface is used to find the binding site atoms. As shown in this paper work, since none of the mostly used surface extraction methods can retrieve a sizeable percentage of the binding site atoms, the scope of development of a better method remains. In this direction, this paper presents a new benchmarking criteria based on utilization of binding site information to compare performance of these surface extraction methods. Also, a new surface extraction method is introduced based on the use of a rotating cylinder probe adapting from the work of Weisel et al. (Chem Cent J 1:7-23, 2007. doi: 10.1186/1752-153X-1-7 ). The result of the new method shows a significant improvement of performance in comparison to the existing methods.

Occupational benzene exposure from vehicular sources in India and its effect on hematology, lymphocyte subsets and platelet P-selectin expression

Benzene exposure from vehicular sources and its health impact are relatively unexplored in India. We have investigated in this study hematology and lymphocyte subsets of 25 petrol pump attendants, 25 automobile service station workers and 35 controls matched for age, sex and socioeconomic conditions. The participants were non-smoking males of Kolkata (former Calcutta) in eastern India. Compared with controls, the workers had 3.8- times more trans,trans-muconic acid in urine, suggesting higher level of benzene exposure. The exposed subjects had decreased erythrocyte, hemoglobin, lymphocyte and platelet levels, but increased neutrophil, band cells, RBC aniso-poikilocytosis and target cells. In addition, CD4+, CD8+ and CD19+ cells were decreased by 37, 20 and 47% respectively, but CD 16+ 56+ NK cells were increased by 20%. P-selectin expression on platelet surface of the workers was significantly elevated ( P < 0.05), indicating upregulation of platelet activity. In summary, the study revealed high level of benzene exposure from vehicular sources in India, and the exposed subjects had hematological and immunological alterations. Toxicology and Industrial Health 2007; 23: 167—175.

Protein structure validation using a semi-empirical method

Current practice of validating predicted protein structural model is knowledge-based where scoring parameters are derived from already known structures to obtain decision on validation out of this structure information. For example, the scoring parameter, Ramachandran Score gives percentage conformity with steric-property higher value of which implies higher acceptability. On the other hand, Force-Field Energy Score gives conformity with energy-wise stability higher value of which implies lower acceptability. Naturally, setting these two scoring parameters as target objectives sometimes yields a set of multiple models for the same protein for which acceptance based on a particular parameter, say, Ramachandran score, may not satisfy well with the acceptance of the same model based on other parameter, say, energy score. The confusion set of such models can further be resolved by introducing some parameters value of which are easily obtainable through experiment on the same protein. In this piece of work it was found that the confusion regarding final acceptance of a model out of multiple models of the same protein can be removed using a parameter Surface Rough Index which can be obtained through semi-empirical method from the ordinary microscopic image of heat denatured protein.

Exploring geometric properties of gold nanoparticles using TEM images to explain their chaperone like activity for citrate synthase

Study on geometric properties of nanoparticles and their relation with biomolecular activities, especially protein is quite a new field to explore. This work was carried out towards this direction where images of gold nanoparticles obtained from transmission electron microscopy were processed to extract their size and area profile at different experimental conditions including and excluding a protein, citrate synthase. Since the images were ill-posed, texture of a context-window for each pixel was used as input to a back-propagation network architecture to obtain decision on its membership as nanoparticle. The segmented images were further analysed by k-means clustering to derive geometric properties of individual nanoparticles even from their assembled form. The extracted geometric information was found to be crucial to give a model featuring porous cage like configuration of nanoparticle assembly using which the chaperone like activity of gold nanoparticles can be explained.

An ANN-GA model based promoter prediction in Arabidopsis thaliana using tilling microarray data

Identification of promoter region is an important part of gene annotation. Identification of promoters in eukaryotes is important as promoters modulate various metabolic functions and cellular stress responses. In this work, a novel approach utilizing intensity values of tilling microarray data for a model eukaryotic plant Arabidopsis thaliana, was used to specify promoter region from non-promoter region. A feed-forward back propagation neural network model supported by genetic algorithm was employed to predict the class of data with a window size of 41. A dataset comprising of 2992 data vectors representing both promoter and non-promoter regions, chosen randomly from probe intensity vectors for whole genome of Arabidopsis thaliana generated through tilling microarray technique was used. The classifier model shows prediction accuracy of 69.73% and 65.36% on training and validation sets, respectively. Further, a concept of distance based class membership was used to validate reliability of classifier, which showed promising results. The study shows the usability of micro-array probe intensities to predict the promoter regions in eukaryotic genomes.

Neurocognitive derivation of protein surface property from protein aggregate parameters

Current work targeted to predicate parametric relationship between aggregate and individual property of a protein. In this approach, we considered individual property of a protein as its Surface Roughness Index (SRI) which was shown to have potential to classify SCOP protein families. The bulk property was however considered as Intensity Level based Multi-fractal Dimension (ILMFD) of ordinary microscopic images of heat denatured protein aggregates which was known to have potential to serve as protein marker. The protocol used multiple ILMFD inputs obtained for a protein to produce a set of mapped outputs as possible SRI candidates. The outputs were further clustered and largest cluster centre after normalization was found to be a close approximation of expected SRI that was calculated from known PDB structure. The outcome showed that faster derivation of individual protein's surface property might be possible using its bulk form, heat denatured aggregates.

A comparative study on the molecular descriptors for predicting drug-likeness of small molecules

Screening of " drug-like" molecule from the molecular database produced through high throughput techniques and their large repositories requires robust classification. In our work, a set of heuristically chosen nine molecular descriptors including four from Lipinski's rule, were used as classification parameter for screening "drug-like" molecules. The robustness of classification was compared with four fundamental descriptors of Lipinski. Back propagation neural network based classifier was applied on a database of 60000 molecules for classification of, " drug-like" and "non drug-like" molecules. Classification result using nine descriptors showed high classification accuracy of 96.1% in comparison to that using four Lipinski's descriptors which yielded an accuracy of 82.48%. Also a significant decrease of false positives resulted while using nine descriptors causing a sharp 18% increase of specificity of classification. From this study it appeared that Lipinski's descriptors which mainly deal with pharmacokinetic properties of molecules form the basis for identification of "drug-like" molecules that can be substantially improved by adding more descriptors representing pharmaco-dynamics properties of molecules.

Functional group based Ligand binding affinity scoring function at atomic environmental level

Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for protein-ligand complexes which takes atomic environment in to account hence functional group as a singular entity. The proposed knowledge based scoring function is fast, simple to construct, easy to use and moreover it tackle the existing problem of handling molecular orientation in active site pocket. We have designed and used Functional group based Ligand retrieval (FBLR) system which can identify and detect the orientation of functional groups in ligand. This decoy searching was used to build the above KBSF to quantify the activity and affinity of high resolution protein-ligand complexes. We have proposed the probable use of these decoys in molecular build-up as a de-novo drug designing approach. We have also discussed the possible use of the said KSBF in pharmacophore fragment detection and pseudo center based fragment alignment procedure.

Surface characterization of proteins using multi-fractal property of heat-denatured aggregates

Multi-fractal property of heat-denatured protein aggregates (HDPA) is characteristic of its individual form. The visual similarity between digitally generated microscopic images of HDPA with that of surface-image of its individual X-ray structures in protein databank (PDB) displayed using Visual Molecular Dynamics (VMD) viewer is the basis of the study. We deigned experiments to view the fractal nature of proteins at different aggregate scales. Intensity based multi-fractal dimensions (ILMFD) extracted from various planes of digital microscopic images of protein aggregates were used to characterize HDPA into different classes. Moreover, the ILMFD parameters extracted from aggregates show similar classification pattern to digital images of protein surface displayed by VMD viewer using PDB entry. We discuss the use of irregular patterns of heat-denatured aggregate proteins to understand various surface properties in native proteins.

FGO: a novel ontology for identification of ligand functional group

Small molecules play crucial role in the modulation of biological functions by interacting with specific macromolecules. Hence small molecule interactions are captured by a variety of experimental methods to estimate and propose correlations between molecular structures to their biological activities. The tremendous expanse in publicly available small molecules is also driving new efforts to better understand interactions involving small molecules particularly in area of drug docking and pharmacogenomics. We have studied and designed a functional group identification system with the associated ontology for it. The functional group identification system can detect the functional group components from given ligand structure with specific coordinate information. Functional group ontology (FGO) proposed by us is a structured classification of chemical functional group which acts as an important source of prior knowledge that may be automatically integrated to support identification, categorization and predictive data analysis tasks. We have used a new annotation method which can be used to construct the original structure from given ontological expression using exact coordinate information. Here, we also discuss about ontology-driven similarity measure of functional groups and uses of such novel ontology for pharmacophore searching and de-novo ligand designing.

Platelet activation, upregulation of CD11b/ CD18 expression on leukocytes and increase in circulating leukocyte-platelet aggregates in Indian women chronically exposed to biomass smoke

The majority of households in rural India still rely on unprocessed solid biomass for domestic energy. The aim of this study was to investigate whether chronic exposure to biomass smoke causes activation of leukocytes and the formation of leukocyte-platelet aggregates. We conducted flow cytometric analysis of beta2 Mac-1 integrin (CD11b/CD18) expression on polymorphonuclear leukocytes (PMN) and monocytes, and P-selectin (CD62P) expression on the platelets of 165 women from eastern India, who cook solely with wood, dung and agricultural wastes, and 155 age- and socio-economic condition-matched control subjects, who used relatively cleaner fuel, liquefied petroleum gas (LPG). Leukocyte-platelet aggregates were defined as CD11b-positive PMN and monocytes co-expressing platelet-specific markers CD41 or CD62P. A significant increase in leukocyte-platelet aggregates was found in women who used biomass as cooking fuel. In addition, they showed increased surface expression of CD11b/CD18 in circulating PMN and monocytes and CD62P expression on platelets. The mean fluorescence intensity (MFI) of CD11b on the surface of circulating monocytes and PMN of biomass users increased by 50 and 68%, respectively. Similarly, a 62 and 48% increase in MFI was observed in CD18 expression on the surface of these cells in biomass users. The results show that chronic biomass smoke exposure activates circulating platelets, PMN and monocytes, and increases the number of leukocyte-platelet aggregates, which are considered a risk factor for thrombosis.

Endoscopic sinus surgery in cystic fibrosis: do patients benefit from surgery?

OBJECTIVE

To examine the effects of endoscopic sinus surgery on the pulmonary status of cystic fibrosis (CF) patients through the objective parameters of steroid use, pulmonary function tests (PFTs), and inpatient hospital days (IHDs).

METHODS

Retrospective chart review of all patients with CF who underwent endoscopic sinus surgery from 1993 to 1999 at a tertiary care children's hospital. Preoperative pulmonary function, inhaler and steroid use, and IHDs were compared to postoperative parameters within a 1-year period.

RESULTS

Sixty-six patients, including eight lung transplant patients, underwent a total of 112 endoscopic sinus surgery procedures; 25 patients underwent more than one procedure. Patients were taking oral steroids preoperatively in 28% of procedures and inhaled steroids in 40%. Postoperatively, there was no statistically significant change in oral or inhaled steroid use, or in postoperative pulmonary function. If the index hospitalization, which was often for reasons not related to sinus disease, was considered part of the preoperative time period, endoscopic sinus surgery (ESS) was noted to result in a marked reduction (9.5 days (adjusted), P=0.001) in hospital days during the subsequent 6 months. If the date of the procedure alone was used to define pre- and postoperative time periods, the reduction in postoperative days was more modest and not statistically significant (3.5 days (adjusted), P=0.21).

CONCLUSIONS

Although we found no statistically significant difference in PFTs, or steroid requirements following ESS, ESS may have resulted in a reduced need for hospitalization in the 6 months following the procedure. Future prospective studies in a larger number of patients and using more detailed outcome measures are needed to better evaluate the effects of endoscopic sinus surgery in pediatric patients with CF.

Abundance of siderophages in sputum: indicator of an adverse lung reaction to air pollution

OBJECTIVE

To investigate the lung response to traffic-related air pollution by enumerating hemosiderin-laden alveolar macrophages (AM) in sputum.

STUDY DESIGN

Sputum samples were collected from 103 urban adult males from Calcutta chronically exposed to automobile exhaust. Forty-nine rural individuals served as controls. AM were identified by nonspecific esterase staining. Perl's Prussian blue technique was employed for the detection of hemosiderin-laden AM (siderophages).

RESULTS

The urban group, consisting of 31 traffic officers, 25 automobile service station workers and 47 street hawkers, had seven times more AM in their sputum than did the matched controls. Besides, a remarkable rise (27-fold) in the number of siderophages in sputum was observed in urban individuals. Smoking further elevated the AM count and number of siderophages.

CONCLUSION

Abundant siderophages in the urban group may indicate the toxic effect of airborne pollutants on the lung, leading to phagocytosis of destroyed cells, including erythrocytes, and accumulation of iron in AM. Enumeration of siderophages in sputum appears to be a simple, noninvasive, inexpensive cytochemical technique well suited to preliminary assessment of the adverse effects of air pollution on the lungs in large, population-based studies, especially in developing countries.

Preimmunization anti-pneumococcal antibody levels are protective in a majority of patients with cystic fibrosis

OBJECTIVE

Although invasive pneumococcal disease is infrequent in cystic fibrosis (CF), it is recommended that all patients with CF receive pneumococcal immunization. As part of a comprehensive program to immunize our clinic population, we obtained preimmunization anti-pneumococcal antibody levels. We hypothesized that the percentage of CF patients without protective levels of anti-pneumococcal antibody levels would be high, as they are exposed to frequent antibiotic therapy that may eradicate organisms before generation of an antibody response.

METHODS

An observational study of 100 patients with CF, aged 1 to 39 years, was conducted in a regional CF center. Preimmunization anti-pneumococcal antibody levels against 6 serotypes were measured by enzyme-linked immunosorbent assay. Protective antibody levels were defined as >200 ng/mL.

RESULTS

A majority of CF patients-61% to 100%, depending on age and serotype-had protective levels of pneumococcal antibody. There was a significant positive correlation between antibody level and age for 5 of the 6 serotypes tested.

CONCLUSIONS

In contradistinction to our hypothesis, the majority of CF patients have protective preimmunization anti-pneumococcal antibody levels. However, a significant proportion-between 17% and 39%, depending on the serotype-did not exhibit adequate levels. Therefore, we concur with current recommendations for pneumococcal immunization in CF.

Selected contribution: synergism between TNF-alpha and IL-1 beta in airway smooth muscle cells: implications for beta-adrenergic responsiveness

In human cultured airway smooth muscle cells, interleukin (IL)-1 beta increases cyclooxygenase (COX)-2 expression and PGE(2) release, ultimately resulting in decreased beta-adrenergic responsiveness. In this study, we aimed to determine whether tumor necrosis factor-alpha (TNF-alpha) synergizes with IL-1 beta in the induction of these events. TNF-alpha alone, at concentrations up to 10 ng/ml, had no effect on COX-2 protein expression; at concentrations as low as 0.1 ng/ml, it significantly enhanced the ability of IL-1 beta (0.2 ng/ml) to induce COX-2 and to increase PGE(2) release. IL-1 beta and TNF-alpha in combination also significantly enhanced COX-2 promoter activity, indicating that synergism between the cytokines is mediated at the level of gene transcription. Although IL-1 beta and TNF-alpha each increased nuclear factor-kappa B activation and induced extracellular regulated kinase and p38 phosphorylation, combined administration of the cytokines did not enhance either nuclear factor-kappa B or mitogen-activated protein kinase activation. Combined administration of IL-1 beta (0.2 ng/ml) and TNF-alpha (0.1 or 1.0 ng/ml) reduced the ability of isoproterenol to decrease human airway smooth muscle cell stiffness, as measured by magnetic twisting cytometry, even though individually these cytokines, at these concentrations, had no effect on isoproterenol responses. Treatment with the selective COX-2 inhibitor NS-398 abolished the synergistic effects of TNF-alpha and IL-1 beta on beta-adrenergic responsiveness. Our results indicate that low concentrations of IL-1 beta and TNF-alpha synergize to promote beta-adrenergic hyporesponsiveness and that effects on COX-2 expression and PGE(2) are responsible for these events. The data suggest that the simultaneous release in the airway, of even very small amounts of cytokines, can have important functional consequences.

Interleukin-6 family cytokines: signaling and effects in human airway smooth muscle cells

Interleukin (IL)-1β induces cyclooxygenase (COX)-2 expression and prostanoid formation in cultured human airway smooth muscle (HASM) cells. In other cell types, IL-6 family cytokines induce COX-2 or augment IL-1β-induced COX-2 expression. The purpose of this study was to determine whether IL-6 family cytokines were involved in COX-2 expression in HASM cells. RT-PCR was used to demonstrate that the necessary receptor components for IL-6-type cytokine binding are expressed in HASM cells. IL-6 and oncostatin M (OSM) each caused a dose-dependent phosphorylation of signal transducer and activator of transcription-3, whereas IL-11 did not. IL-6, IL-11, and OSM alone had no effect on COX-2 expression. However, OSM caused dose-dependent augmentation of COX-2 expression and prostaglandin (PG) E2release induced by IL-1β. In contrast, IL-6 and IL-11 did not alter IL-1β-induced COX-2 expression. IL-6 did increase IL-1β-induced PGE2formation in unstimulated cells but not in cells stimulated with arachidonic acid (AA; 10−5M), suggesting that IL-6 effects were mediated at the level of AA release. Our results indicate that IL-6 and OSM are capable of inducing signaling in HASM cells. In addition, OSM and IL-1β synergistically cause COX-2 expression and PGE2release.

p38 MAP kinase regulates IL-1 beta responses in cultured airway smooth muscle cells

We have previously reported that interleukin (IL)-1 beta causes beta-adrenergic hyporesponsiveness in cultured human airway smooth muscle (HASM) cells by increasing cyclooxygenase (COX)-2 expression. The purpose of this study was to determine whether p38 mitogen-activated protein (MAP) kinase is involved in these events. IL-1 beta (2 ng/ml for 15 min) increased p38 phosphorylation fourfold. The p38 inhibitor SB-203580 (3 microM) decreased IL-1 beta-induced COX-2 by 70 +/- 7% (P < 0.01). SB-203580 had no effect on PGE(2) release in control cells but caused a significant (70-80%) reduction in PGE(2) release in IL-1 beta-treated cells. IL-1 beta increased the binding of nuclear proteins to the oligonucleotides encoding the consensus sequences for activator protein (AP)-1 and nuclear factor (NF)-kappa B, but SB-203580 did not affect this binding, suggesting that the mechanism of action of p38 was not through AP-1 or NF-kappa B activation. The NF-kappa B inhibitor MG-132 did not alter IL-1 beta-induced COX-2 expression, indicating that NF-kappa B activation is not required for IL-1 beta-induced COX-2 expression in HASM cells. IL-1 beta attenuated isoproterenol-induced decreases in HASM stiffness as measured by magnetic twisting cytometry, and SB-203580 abolished this effect. These results are consistent with the hypothesis that p38 is involved in the signal transduction pathway through which IL-1 beta induces COX-2 expression, PGE(2) release, and beta-adrenergic hyporesponsiveness.

Air pollution in Calcutta elicits adverse pulmonary reaction in children

BACKGROUND & OBJECTIVE

Pulmonary responses of children chronically exposed to ambient air pollution in Calcutta have been investigated.

METHODS

A total number of 153 children from Calcutta and 116 from rural West Bengal in the age group of 6-17 yr were included in this study. Respiratory symptom complex, sputum cytology and micronucleus (MN) count of buccal epithelial cells were evaluated. Blood smears were examined for WBC differential count and RBC morphology.

RESULTS

Marked rise in respiratory symptoms (43% in urban vs 14% in rural) and sputum alveolar macrophage (AM) number was observed in urban children compared to their rural counterparts (14.2 +/- 1.4 AM/hpf vs 6.7 +/- 1.4 AM/hpf, mean +/- SE, P < 0.001). The urban group also demonstrated increased numbers of neutrophils, eosinophils and iron-laden AM in their sputum. Besides, buccal epithelial cells of urban children exhibited higher MN frequency than their rural counterparts (0.22 vs 0.17%, P < 0.05). While sputum neutrophilia and eosinophilia suggest inflammatory and allergic lung reactions, elevated MN count is indicative of greater genotoxic effect on the exposed tissues of urban children. Hypochromic red cells in peripheral blood smear was a common finding in both urban and rural groups, but eosinophils and monocytes were present in elevated frequencies in the rural children.

INTERPRETATION & CONCLUSION

The study demonstrated that children inhaling grossly polluted air of Calcutta suffer from adverse lung reactions and genetic abnormality in the exposed tissues.

Onset of Percolation and Fractal Classification Scheme for Multilamellar Lipid Vesicles

Percolation, like phase transition, expresses a critical property of an assembly. The paper provides a brief description of the onset of percolation and the fractal behavior of clusters formed as a result of spontaneous assembly of multilamellar lipid vesicles (MLVs). The onset of percolation was studied using a series of mixed lipid systems. The percolation threshold showed a strong linear dependence on the net charge of the constituent lipids. Second, the vesicular clusters were characterized using a canonical coordinate frame spanned by the fractal dimension and the porosity of the cluster images. MLVs made of different lipid constituents formed different domains on such representations. The location of the individual domains relative to a simulated random cluster seemed to provide a measure of order-element present in such clusters. The specificity of the domain locations and their sensitivity to alteration in a microenvironment was studied in some detail. Copyright 1999 Academic Press.

Multilamellar vesicular clusters of phosphatidylcholine and their sensitivity to spectrin: a study by fractal analysis

The cluster patterns of multilamellar vesicles (MLV) of dimyristoylphosphatidylcholine (DMPC) were analyzed using a combination of fractal analysis and lattice simulation. Self-assembly of DMPC MLVs resulted in two types of microscopically observable clusters. The clusters were classified on the basis of their mass fractal dimension, two-dimensional porosity, and the light scattering properties. Spectrin, a cytoskeletal protein, well known for its role in determining the cellular morphology, was used to perturb such spontaneously formed clusters. The fragmentation of the clusters by hydrodynamic perturbation followed a power law, implying again a fractal behavior. A lattice-based simulation was performed generating different class of cluster patterns. The observed correspondence between the cluster patterns and their stability was discussed in the framework of the proposed lattice simulation.

Renal tubular acidosis in pregnancy: case report and literature review

Renal tubular acidosis is a rare form of chronic metabolic acidosis, which is either inherited as an autosomal dominant condition (Types 1, 2, and 3) or acquired. Its effects on pregnancy and vice versa are not known, but chronic acidosis may affect fetal bone growth and development. Chronic maternal acidosis may also lead to fetal distress, which should respond to correction of the maternal acidosis. The patient is a 20-year-old gravida 2, para 1-0-0-1, Hispanic female with distal renal tubular acidosis, diagnosed 1 year prior to this pregnancy after suffering from hypokalemic paralysis. During the pregnancy she required steadily increasing doses of potassium and bicarbonate, to maintain electrolyte balance. She delivered a healthy full-term female infant, weighing 2,892 g, with Apgars of 5 and 9 at 1 and 5 min, respectively, following an induction of labor for oligohydramnios. There was no evidence of intrapartum or neonatal distress, and the infant was discharged home with her mother on the first postpartum day in good health. Established renal tubular acidosis, which was adequately treated with bicarbonate and potassium supplementation during pregnancy, had no apparent ill effects on fetal or neonatal well-being in this case.

Alterations of brain serotonin during experimental tumor growth in mice

Concentrations of serotonin (5-HT) and its metabolite 5-hydroxyindoleacetic acid (5-HIAA) were studied in discrete areas of brain and in large intestine of Swiss mice following transplantation of Sarcoma 180 (S 180) ascites tumor. Significant increase in 5-HT levels (2 to 3.5-fold over controls, P < 0.05) was observed in raphe region of the brain throughout the period of tumor growth. Concomitant increase, although of lesser magnitude, was recorded in raphe 5-HIAA content. 5-HT content of hypothalamus, mid brain and caudate putamen, on the other hand, remained relatively unaltered except for an increase at the advanced stage of the disease. While mid brain and hypothalamic 5-HIAA were elevated at the late stage, 5-HIAA values of caudate putamen were normal or slightly reduced during the progression of tumor. Both 5-HT and 5-HIAA levels of the large intestine showed an early decline followed by a modest increase at the late stages. Brain and plasma tryptophan levels were also elevated significantly (P < 0.05) in the tumor hosts. The results suggest a close relationship between increase in serotonin concentrations in the brain, particularly in raphe region, and the progression of S-180 tumor in mice.

Uptake and biodistribution of dopamine in bone marrow, spleen and lymph nodes of normal and tumor bearing mice

Significant labelled dopamine uptake was evident in bone marrow, spleen and lymph nodes of normal murine hosts in vivo. On the contrary animals bearing solid Ehrlich carcinoma, 3H-dopamine uptake was significantly reduced. The tumor tissue itself incorporated only insignificant amount of dopamine. Bone marrow cells, splenocytes and lymphocytes from lymph nodes showed specific uptake of this monoamine. At present the peripheral role of dopamine in the regulation of heart and kidney functions are well documented and utilized clinically for treatment of congestive heart and renal failure. The present result of specific dopamine uptake by bone marrow, spleen and lymph nodes and alterations following tumor growth where hematopoesis and immune functions are disrupted, strengthens our previous idea that dopamine might also influence the functions of these peripheral organs. Knowledge of this possible effect of DA on these peripheral organs may be of future clinical significance in the management of hematological and immune abnormalities.

Decrease in dopamine and norepinephrine concentration in different brain regions of mice during progression of Sarcoma 180 tumour

The distribution and concentration of dopamine (DA) and norepinephrine (NE), the catecholamine neurotransmitters, were studied in discrete brain areas of Sarcoma 180 tumour bearing mice. With the progression of tumour, marked depletion of DA and NE concentration was observed in some brain areas richly innervated with dopaminergic and noradrenergic neurons suggesting an inverse relationship between brain CA and tumour growth. Since brain CA influence different important physiological activities like hormonal and immunological functions, it's alteration in brain areas during malignant growth suggests the possibility that the hormonal and immunological alterations during tumour growth is at the level of brain CA.

Antitumor effect of i.p. dopamine in mice bearing Ehrlich ascites carcinoma

The cancer chemotherapeutic efficacy of dopamine (DA) was evaluated in female strain A mice bearing transplantable Ehrlich ascites carcinoma. The results demonstrated significant inhibition of tumor growth with appreciable increase in the host survival time following DA treatment. Diminished activity of the growth-related respiratory enzyme succinate dehydrogenase along with stimulated activity of the lysosomal enzyme, beta-glucuronidase in DA-treated tumor cells indicated inhibition of tumor growth as well as active lysis of the tumor cells. The direct effect of this compound on tumor proliferation was demonstrated by marked inhibition of DNA synthesis. RNA synthesis was only marginally inhibited.

Studies on growth and enzymatic characteristics of human mammary tumours grown in heterologous host

Human mammary tumours were grown in diffusion chambers in the heterologous host--Charle's Foster rat. The effect of oophorectomy-induced alterations of the hormonal environment of the host in breast tumour cells grown in the diffusion chamber were studied with respect to their growth patterns and enzymatic characteristics. The tumour cells not only survived but actively proliferated as indicated by the increase in cell count and formation of cell sheets as well as by the presence of mitotic figures. Cytochemical studies of certain enzymatic activities, i.e. succinic dehydrogenase, alkaline phosphatase, acid phosphatase and beta-glucuronidase indicate--except for a slight depression of the overall activity--that the distribution patterns are more or less maintained following diffusion chamber culture. The alteration of the hormonal environment by oophorectomy influences the cell growth and the enzymatic activity of the human tumour cells inside the diffusion chambers. The results clearly indicate that D.C. culture technique provides a useful method for assessment of growth and hormonal responsiveness of human tumours.

Enhancement of DMBA induced mammary tumours by intermittent whole body hyperthermia (42 degrees C)

Wistar Female rats bearing DMBA induced mammary tumours were subjected to whole body hyperthermia 42 degrees C dry heat exposure for 15 minutes daily for 6 weeks. The control group was maintained at a room temperature of 25 degrees C. Hyperthermia induced significant growth stimulation of breast tumour compared to the controls. Plasma estradiol was slightly decreased while total T4 and TSH values remained unchanged in heat stressed rats. Plasma prolactin was significantly increased together with enhanced synthetic activity of pituitary prolactin cells. It is concluded that heat acting as stressor accelerates breast tumor growth, probably by influencing synthesis of prolactin. Therefore the hormone dependency of tumours should be considered before hyperthermia is used as an anticancer modality.

Lipid patterns in vaginal cells exfoliated from different physiologic conditions

A comprehensive study was made of the patterns of lipid granules in vaginal cells exfoliated during different hormonal states as well as under neoplastic conditions. The influence of in vitro incubation with estrogen and progesterone on the lipid patterns in cells exfoliated from normal and cancerous cervices was also investigated. The results clearly indicated the influence of sex hormones on the size and distribution of the lipid granules. While estrogen increased the fine lipid granules, as evident during the estrogenic phase of the menstrual cycle, progesterone influenced the coarse granules, which increased during the progestational phase and pregnancy. Similar responses were observed in the in vitro studies. The significance of the fine and coarse granules in different conditions is discussed in light of both the alteration of the metabolic process governing the synthesis of these components and the conversion of fine granules to coarse granules under such conditions.