Strain-rate-dependent material properties of human lung parenchymal tissue using inverse finite element approach.

Automobile crashes and blunt trauma often lead to life-threatening thoracic injuries, especially to the lung tissues. These injuries can be simulated using finite element-based human body models that need dynamic material properties of lung tissue. The strain-rate-dependent material parameters of human parenchymal tissues were determined in this study using uniaxial quasi-static (1 mm/s) and dynamic (1.6, 3, and 5 m/s) compression tests. A bilinear material model was used to capture the nonlinear behavior of the lung tissue, which was implemented using a user-defined material in LS-DYNA. Inverse mapping using genetic algorithm-based optimization of all experimental data with the corresponding FE models yielded a set of strain-rate-dependent material parameters. The bilinear material parameters are obtained for the strain rates of 0.1, 100, 300, and 500 s-1. The estimated elastic modulus increased from 43 to 153 kPa, while the toe strain reduced from 0.39 to 0.29 when the strain rate was increased from 0.1 to 500 s-1. The optimized bilinear material properties of parenchymal tissue exhibit a piecewise linear relationship with the strain rate.

A Poly-vinyl Alcohol (PVA)-based phantom and training tool for use in simulated Transrectal Ultrasound (TRUS) guided prostate needle biopsy procedures.

Trans-rectal ultrasound-guided needle biopsy is a well-established diagnosis technique for prostate cancer. To enhance the needle manoeuvring skills under ultrasound (US) guidance, it is preferable to train medical practitioners in needle biopsy on tissue-mimicking phantoms. This phantom should mimic the morphology as well as mechanical and acoustic properties of the human male pelvic region to provide a surgical experience and feedback. In this study, polyvinyl alcohol (PVA) was used and evaluated for prostate phantom development, that is stiffness tunable, US-compatible and durable phantom material. Three samples, each with 5%, 10%, and 15% concentration of PVA material, were prepared, and their mechanical and shrinkage characteristics were investigated. The anatomy of male pelvic region was used to develop an anatomically correct phantom. Later US-guided needle biopsy was performed on the phantom. The range of elastic moduli of the PVA samples was 2∼146 kPa. Their elastic moduli and volumes were found to remain statistically close from seventh to eighth freeze-thaw cycle (p>0.05). Initial US scans of the phantom resulted in satisfactory B-mode images, with a clear distinction between the prostate and its surrounding organs. This study demonstrated the applicability of PVA hydrogel as a phantom material for training in US-guided needle biopsy.

Cloning, Expression and Characterization of NAD Kinase from Staphylococcus aureus Involved in the Formation of NADP (H): A Key Molecule in the Maintaining of Redox Status and Biofilm Formation.

BACKGROUND: Staphylococcus aureus has the ability to form biofilms on any niches, a key pathogenic factor of this organism and this phenomenon is directly related to the concentration of NADPH. The formation of NADP is catalyzed by NAD kinase (NADK) and this gene of S. aureus ATCC 12600 was cloned, sequenced, expressed and characterized. MATERIALS AND METHODS: The NADK gene was polymerase chain reaction amplified from the chromosomal DNA of S. aureus ATCC 12600 and cloned in pQE 30 vector, sequenced and expressed in Escherichia coli DH5α. The pure protein was obtained by passing through nickel metal chelate agarose column. The enzyme kinetics of the enzyme and biofilm assay of the S. aureus was carried out in both aerobic and anaerobic conditions. The kinetics was further confirmed by the ability of the substrates to dock to the NADK structure. RESULTS: The recombinant NADK exhibited single band with a molecular weight of 31kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the gene sequence (GenBank: JN645814) revealed presence of only one kind of NADK in all S. aureus strains. The enzyme exhibited very high affinity for NAD compared to adenosine triphosphate concurring with the docking results. A root-mean-square deviation value 14.039Å observed when NADK structure was superimposed with its human counterpart suggesting very low homology. In anaerobic conditions, higher biofilm units were found with decreased NADK activity. CONCLUSION: The results of this study suggest increased NADPH concentration in S. aureus plays a vital role in the biofilm formation and survival of this pathogen in any environmental conditions.

Phosphorylation controls the functioning of Staphylococcus aureus isocitrate dehydrogenase--favours biofilm formation.

Isocitrate dehydrogenase (IDH) gene from Staphylococcus aureus ATCC12600 was cloned, sequenced and characterized (HM067707). PknB site was observed in the active site of IDH; thus, it was predicted as IDH may be regulated by phosphorylation. Therefore, in this study, PknB, alkaline phosphatase III (SAOV 2675) and IDH genes (JN695616, JN645811 and HM067707) of S. aureus ATCC12600 were over expressed from clones PV 1, UVPALP-3 and UVIDH 1. On passing the cytosloic fractions through nickel metal chelate column, pure enzymes were obtained. Phosphorylation of pure IDH by PknB resulted in the complete loss of activity and was restored upon dephosphorylation with SAOV 2675 which indicated that phosphorylation and dephosphorylation regulate IDH activity in S. aureus. Further, when S. aureus ATCC12600 was grown in BHI broth, decreased IDH activity and increased biofilm units were observed; therefore, this regulation of IDH alters redox status in this pathogen favouring biofilm formation.

In Staphylococcus aureus the regulation of pyruvate kinase activity by serine/threonine protein kinase favors biofilm formation.

Staphylococcus aureus, a natural inhabitant of nasopharyngeal tract, survives mainly as biofilms. Previously we have observed that S. aureus ATCC 12600 grown under anaerobic conditions exhibited high rate of biofilm formation and L-lactate dehydrogenase activity. Thus, the concentration of pyruvate plays a critical role in S. aureus, which is primarily catalyzed by pyruvate kinase (PK). Analyses of the PK gene sequence (JN645815) revealed presence of PknB site in PK gene indicating that phosphorylation may be influencing the functioning of PK. To establish this hypothesis the pure enzymes of S. aureus ATCC 12600 were obtained by expressing these genes in PK 1 and PV 1 (JN695616) clones and passing the cytosolic fractions through nickel metal chelate column. The molecular weights of pure recombinant PK and PknB are 63 and 73 kDa, respectively. The enzyme kinetics of pure PK showed K M of 0.69 ± 0.02 µM, while the K M of PknB for stpks (stpks = NLCNIPCSALLSSDITASVNCAK) substrate was 0.720 ± 0.08 mM and 0.380 ± 0.07 mM for autophosphorylation. The phosphorylated PK exhibited 40 % reduced activity (PK = 0.2 ± 0.015 µM NADH/min/ml to P-PK = 0.12 ± 0.01 µM NADH/min/ml). Elevated synthesis of pyruvate kinase was observed in S. aureus ATCC 12600 grown in anaerobic conditions suggesting that the formed pyruvate is more utilized in the synthesis phase, supporting increased rate of biofilm formation.

Comparative Structural and Functional Analysis of Staphylococcus aureus Glucokinase with other Bacterial Glucokinases.

Glucokinase is classified in bacteria based upon having ATP binding site and 'repressor/open reading frames of unknown function/sugar kinases' motif, the sequence of glucokinase gene (JN645812) of Staphylococcus aureus ATCC12600 showed presence of ATP binding site and 'repressor/open reading frames of unknown function/sugar kinases' motif. We have earlier observed glucokinase of S. aureus has higher affinity towards the substrate compared to other bacterial glucokinase and under anaerobic condition with increased glucose concentration S. aureus exhibited higher rate of biofilm formation. To establish this, 3D structure of glucokinase was built using homology modeling method, the PROCHECK and ProSA-Web analysis indicated this built glucokinase structure was close to the crystal structure. This structure was superimposed with different bacterial glucokinase structures and from the root-mean-square deviation values, it is concluded that S. aureus glucokinase exhibited very close homology with Enterococcus faecalis and Clostridium difficle while with other bacteria it showed high degree of variations both in domain and nondomain regions. Glucose docking results indicated -12.3697 kcal/mol for S. aureus glucokinase compared with other bacterial glucokinase suggesting higher affinity of glucose which correlates with enzyme kinetics and higher rate of biofilm formation.

Cloning, expression and characterization of NADP-dependent isocitrate dehydrogenase from Staphylococcus aureus.

The Krebs cycle dictates oxidative and reductive conditions in Staphylococcus aureus and is mainly regulated by isocitrate dehydrogenase (IDH) which plays pivotal role in the growth and pathogenesis of the bacteria. In the present study, IDH gene from S. aureus ATCC12600 was cloned in the Sma I site of pQE 30 vector; the resultant clone was named as UVIDH1. The insert in the clone was sequenced (accession number HM067707), and the sequence showed complete homology with IDH sequence of other S. aureus strains reported in the database indicating presence of single enzyme in S. aureus, and considerable sequence homology with other bacteria was observed; however, only 24% homology was found with NADP-dependent human IDH. Phylogenetically, the S. aureus IDH showed close identity with Bacillus subtilis and high degree of variability with other bacteria and human IDH. The expression of IDH in the clone UVIDH1 was induced with 1 mM IPTG, and the recombinant IDH was purified by passing through nickel metal chelate column; the purified recombinant IDH showed a single band in SDS-PAGE with a molecular weight of 40 kDa; K(m) and V(max) for isocitrate are 8.2 ± 0.28 and 525 ± 25 µM NADPH/mg/min, respectively, and for cofactor NADP 67.5 ± 2.82 µM and V(max) 50.5 ± 2.12 µM NADPH/mg/min.