Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma

ABSTRACT: BACKGROUND: Bacterial infections have been linked to malignancies due to their ability to induce chronicinflammation. We investigated the association of oral bacteria in oral squamous cellcarcinoma (OSCC/tumor) tissues and compared with adjacent non-tumor mucosa sampled 5cm distant from the same patient (n = 10). By using culture-independent 16S rRNAapproaches, denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing, weassessed the total bacterial diversity in these clinical samples. RESULTS: DGGE fingerprints showed variations in the band intensity profiles within non-tumor andtumor tissues of the same patient and among the two groups. The clonal analysis indicatedthat from a total of 1200 sequences characterized, 80 bacterial species/phylotypes weredetected representing six phyla, Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria,Actinobacteria and uncultivated TM7 in non-tumor and tumor libraries. In combined library,12 classes, 16 order, 26 families and 40 genera were observed. Bacterial species,Streptococcus sp. oral taxon 058, Peptostreptococcus stomatis, Streptococcus salivarius,Streptococcus gordonii, Gemella haemolysans, Gemella morbillorum, Johnsonella ignavaand Streptococcus parasanguinis I were highly associated with tumor site where asGranulicatella adiacens was prevalent at non-tumor site. Streptococcus intermedius waspresent in 70% of both non-tumor and tumor sites. CONCLUSIONS: The underlying changes in the bacterial diversity in the oral mucosal tissues from non-tumorand tumor sites of OSCC subjects indicated a shift in bacterial colonization. These mostprevalent or unique bacterial species/phylotypes present in tumor tissues may be associatedwith OSCC and needs to be further investigated with a larger sample size.     

Lone pair ··· π interactions between water oxygens and aromatic residues: Quantum chemical studies based on high‐resolution protein structures and model compounds

The π electron cloud of aromatic centers is known to be involved in several noncovalent interactions such as C—H···π, O—H···π, and π···π interactions in biomolecules. Lone-pair (lp) ··· π interactions have gained attention recently and their role in biomolecular structures is being recognized. In this article, we have carried out systematic analysis of high-resolution protein structures and identified more than 400 examples in which water oxygen atoms are in close contact (distance < 3.5 Å) with the aromatic centers of aromatic residues. Three different methods were used to build hydrogen atoms and we used a consensus approach to find out potential candidates for lp···π interactions between water oxygen and aromatic residues. Quantum mechanical calculations at MP2/6-311++G(d,p) level on model systems based on protein structures indicate that majority of the identified examples have energetically favorable interactions. The influence of water hydrogen atoms was investigated by sampling water orientations as a function of two parameters: distance from the aromatic center and the angle between the aromatic plane and the plane formed by the three water atoms. Intermolecular potential surfaces were constructed using six model compounds representing the four aromatic amino acids and 510 different water orientations for each model compound. Ab initio molecular orbital calculations at MP2/6-311++G(d,p) level show that the interaction energy is favorable even when hydrogen atoms are farthest from the aromatic plane while water oxygen is pointing toward the aromatic center. The strength of such interaction depends upon the distance of water hydrogen atoms from the aromatic substituents. Our calculations clearly show that the lp···π interactions due to the close approach of water oxygen and aromatic center are influenced by the positions of water hydrogen atoms and the aromatic substituents.     

Quantification of pulmonary vascular occlusion in dogs by use of the diffusing capacity

The purpose of these experiments was to quantify stagnant intrapulmonary blood caused by a pulmonary arterial occlusion (PAO). The hypothesis was that the diffusing capacity of the lung for CO (DLCO) would be altered little by PAO when measured with the usual inspired concentrations (0.3%) of CO, since stagnant blood distal to the occlusion takes up CO for 20 s or more before significant CO backpressure would develop. However, higher levels of CO (i.e., greater than or equal to 3%) would equilibrate faster with capillary blood (within 5-10 s), and DLCO measured 10-20 s subsequent to the high CO exposure would reflect only the DLCO in the unoccluded regions. Thus the fractional reduction in DLCO measured with 3% CO, with respect to that measured with 0.3% CO, should be related to the fractional occlusion of the pulmonary artery in a predictable way. We occluded the right pulmonary artery (RPAO), the left pulmonary artery (LPAO), or the left lower lobar artery (LLPAO) and found that DLCO measured during rebreathing a 0.3% CO mixture was 80, 87, and 94%, respectively, of the preocclusion value, whereas the DLCO measured during rebreathing a 3.3% CO mixture was 59, 73, and 87% of the preocclusion value. A computer model was developed to predict the reduction in DLCO at different levels of CO exposure that would be caused by varying fractions of PAO. Our data indicated that RPAO corresponded to a 42% vascular occlusion, LPAO a 35% occlusion, and LLPAO a 20% occlusion. Measurement of DLCO using low and high concentrations of CO might be useful in assessing the fraction of vascular bed occluded and in following noninvasively the course of vascular occlusion in a variety of pulmonary diseases.     

Analysis of the impact of ERK5, JNK,and P38 kinase cascades on each other: A systems approach

The classical concept of linear pathways is being increasingly challenged by network representations, which emphasize the importance of interactions between components of a biological system, and motivates for adopting a system‐level approach in biology. We have developed a dynamical system that integrates quantitative, dynamic and topological representation of network of ERK5 (Extracellular signal‐regulated kinases 5), JNK(c‐Jun N‐terminal kinases) and P38 kinase cascades. We have observered that, the transient activation of ERK5, JNK1 and P38β kinase, and the persistent activation of JNK2, JNK3 and P38 δ kinase does not get affected due to the cross‐talks between ERK5, JNK and P38 kinase cascades. But it is due to the cross ‐ talks, the transiently activated P38α kinase become inactivated, and the transiently activated P38γ kinase become persistently activated. The impacts of one‐way cross‐talks between the cascades are insignificant and differ from the impact of two‐way cross‐talks. We generate a hypothesis that, signaling pathways should be studied as a system by considering the cross‐talks between the two adjacent cascades.     

Biomineralization Abilities of Cupriavidus Strain and Bacillus subtilis Strains In Vitro Isolated from Speleothems,Rani Cave,Chhattisgarh, India

In vitro culture experiments using three bacterial strains CSJC1, CSJC2, and CSJC3 isolated from speleothems, Rani cave, Chhattisgarh, India, were studied to examine their biomineralization potential. These speleothems showed high microbial cell enumerations on nutrient agar and iron agar (9 × 10⁴ CFU/g) followed by thiosulfate agar (7 × 10⁴ CFU/g), and 60 diverse strains were isolated. The BLASTn sequence search of 16S rRNA sequences with the NCBI database to establish the identity of CSJC1, CSJC2, and CSJC3 strains yielded similarity scores of ≥99% with the respective organisms, and the strains were identified as CSJC1 – Bacillus sp., CSJC2 – Cupriavidus sp., CSJC3 – Bacillus sp. The phylogenetic analysis of CSJC2 strain suggests that it formed a separate major cluster with Cupriavidus sp. and Cupriavidus necator. The phylogenetic analysis of CSJC1 and CSJC3 strains revealed that it formed a major cluster with several strains of Bacillus sp. and Bacillus subtilis. The biominerals induced by Cupriavidus sp. CSJC2 strain imaged with an ultra high-resolution field emission scanning electron microscope (FE-SEM) were seen as calcified coccoid shells that transformed into calcified dumbbells. FE-SEM imaging of biominerals induced by B. subtilis CSJC1 and CSJC3 tested both on B4 media and sheep blood agar individually showed that the precipitates formed calcified dumbbells that were almost similar but not identical phenotypically, indicating that strain-specific morphologies and crystal formation is easier when Ca is present in the media. This is the first comprehensive report on the possible evidences about the role of Cupriavidus sp. in calcite precipitation isolated from speleothems in the Indian caves. These results allow us to postulate that the identified strains may have a role in the biogenic influences in mineral formations at Rani cave.     

Investigations on the interactions of scorpion neurotoxins with the predicted structure of D1 dopamine receptor by protein-protein docking method. A bioinformatics approach

Dopamine receptors play a critical role in the cell signalling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for disorders like Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors. Scorpion neurotoxins are unique source of structural templates from which new therapeutic agents might be developed. We report here the 3D structure of the human D1 dopamine receptor, predicted from primary sequence using computational techniques. The predicted structure of the human D1 dopamine receptor is used to understand the mechanism of interactions between scorpion neurotoxins through the protein-protein docking method. CHARMM force field was used for the energy minimization step before applying the docking method.     

CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions

Background

As an alternative to the frequently used "reference design" for two-channel microarrays, other designs have been proposed. These designs have been shown to be more profitable from a theoretical point of view (more replicates of the conditions of interest for the same number of arrays). However, the interpretation of the measurements is less straightforward and a reconstruction method is needed to convert the observed ratios into the genuine profile of interest (e.g. a time profile). The potential advantages of using these alternative designs thus largely depend on the success of the profile reconstruction. Therefore, we compared to what extent different linear models agree with each other in reconstructing expression ratios and corresponding time profiles from a complex design.

Results

On average the correlation between the estimated ratios was high, and all methods agreed with each other in predicting the same profile, especially for genes of which the expression profile showed a large variance across the different time points. Assessing the similarity in profile shape, it appears that, the more similar the underlying principles of the methods (model and input data), the more similar their results. Methods with a dye effect seemed more robust against array failure. The influence of a different normalization was not drastic and independent of the method used.

Conclusion

Including a dye effect such as in the methods lmbr_dye, anovaFix and anovaMix compensates for residual dye related inconsistencies in the data and renders the results more robust against array failure. Including random effects requires more parameters to be estimated and is only advised when a design is used with a sufficient number of replicates. Because of this, we believe lmbr_dye, anovaFix and anovaMix are most appropriate for practical use.