Binding of the Biogenic Polyamines to Deoxyribonucleic Acids of Varying Base Composition: Base Specificity and the Associated Energetics of the Interaction

Background

The thermodynamics of the base pair specificity of the binding of the polyamines spermine, spermidine, putrescine, and cadaverine with three genomic DNAs Clostridium perfringens, 27% GC, Escherichia coli, 50% GC and Micrococcus lysodeikticus, 72% GC have been studied using titration calorimetry and the data supplemented with melting studies, ethidium displacement and circular dichroism spectroscopy results.

Methodology/Principal Findings

Isothermal titration calorimetry, differential scanning calorimetry, optical melting studies, ethidium displacement, circular dichroism spectroscopy are the various techniques employed to characterize the interaction of four polyamines, spermine, spermidine, putersine and cadaverine with the DNAs. Polyamines bound stronger with AT rich DNA compared to the GC rich DNA and the binding varied depending on the charge on the polyamine as spermine>spermidine >putrescine>cadaverine. Thermodynamics of the interaction revealed that the binding was entropy driven with small enthalpy contribution. The binding was influenced by salt concentration suggesting the contribution from electrostatic forces to the Gibbs energy of binding to be the dominant contributor. Each system studied exhibited enthalpy-entropy compensation. The negative heat capacity changes suggested a role for hydrophobic interactions which may arise due to the non polar interactions between DNA and polyamines.

Conclusion/Significance

From a thermodynamic analysis, the AT base specificity of polyamines to DNAs has been elucidated for the first time and supplemented by structural studies.     

Systematic Pharmacogenomics Analysis of a Malay Whole Genome: Proof of Concept for Personalized Medicine

Background

With a higher throughput and lower cost in sequencing, second generation sequencing technology has immense potential for translation into clinical practice and in the realization of pharmacogenomics based patient care. The systematic analysis of whole genome sequences to assess patient to patient variability in pharmacokinetics and pharmacodynamics responses towards drugs would be the next step in future medicine in line with the vision of personalizing medicine.

Methods

Genomic DNA obtained from a 55 years old, self-declared healthy, anonymous male of Malay descent was sequenced. The subject''s mother died of lung cancer and the father had a history of schizophrenia and deceased at the age of 65 years old. A systematic, intuitive computational workflow/pipeline integrating custom algorithm in tandem with large datasets of variant annotations and gene functions for genetic variations with pharmacogenomics impact was developed. A comprehensive pathway map of drug transport, metabolism and action was used as a template to map non-synonymous variations with potential functional consequences.

Principal Findings

Over 3 million known variations and 100,898 novel variations in the Malay genome were identified. Further in-depth pharmacogenetics analysis revealed a total of 607 unique variants in 563 proteins, with the eventual identification of 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harboring deleterious SNVs involved in pharmacological pathways, which could have a potential role in clinical settings.

Conclusions

The current study successfully unravels the potential of personal genome sequencing in understanding the functionally relevant variations with potential influence on drug transport, metabolism and differential therapeutic outcomes. These will be essential for realizing personalized medicine through the use of comprehensive computational pipeline for systematic data mining and analysis.     

Multi-strain Inoculation with PGPR Producing ACC Deaminase is More Effective Than Single-strain Inoculation to Improve Wheat (<i>Triticum aestivum</i>) Growth and Yield

Rhizosphere bacteria that colonize plant roots and confer beneficial effects are referred as plant growth promoting rhizobacteria (PGPR). Among all PGPR, some rhizobacteria have an ability to produce ACC deaminase enzyme. This enzyme catalyzes stress ACC into a-ketobutyrate and ammonia instead of letting it to be converted to ethylene. Ethylene level rises in plants under stress conditions i.e., drought, salinity, poor soil fertility etc. As poor soil fertility is a big hurdle to achieve the optimum yield of crops, inoculation of ACC deaminase PGPR can overcome this problem to some extent. The aim of the current study was to examine the influence of multi-strain and single-strain inoculation of different ACC deaminase producing PGPR on wheat growth and yield. There were three PGPR strains, Enterobacter cloacae, Serratia ficaria and Burkholderia phytofirmans which were used as consortia and single-strain inoculations. The results showed that inoculation of E. cloacae + S. ficaria + B. phytofirmans significantly increased plant height (63%), spike length (61%), number of spikelets spike^-1 (61%), number of grains spike-1 (131%), 1000 grains weight (33%), grains yield (71%), straw yield (71%) and biological yield (68%) of wheat as compared to control. A significant improvement in N (37 and 200%), P (46 and 166%) and K (39 and 61%) of seeds and shoot respectively, validated the efficacious and more effective role of multi-strain (E. cloacae + S. ficaria + B. phytofirmans) inoculation over control. It is obviously concluded that multi-strain ACC deaminase producing PGPR inoculation is a better approach as compared to singlestrain inoculation for the improvement in growth and yield of wheat.     

Spinal cord injury regeneration using autologous bone marrow-derived neurocytes and rat embryonic stem cells: A comparative study in rats

BACKGROUNDSpinal cord injury (SCI) is an important cause of traumatic paralysis and is mainly due to motor vehicle accidents. However, there is no definite treatment for spinal cord damage.AIMTo assess the outcome of rat embryonic stem cells (rESC) and autologous bone marrow-derived neurocytes (ABMDN) treatment in iatrogenic SCI created in rats, and to compare the efficacy of the two different cell types.METHODSThe study comprised 45 male Wistar rats weighing between 250 and 300 g, which were divided into three groups, the control, rESC and ABMDN groups. The anesthetized animals underwent exposure of the thoracic 8^th to lumbar 1^st vertebrae. A T10-thoracic 12^th vertebrae laminectomy was performed to expose the spinal cord. A drop-weight injury using a 10 g weight from a height of 25 cm onto the exposed spinal cord was conducted. The wound was closed in layers. The urinary bladder was manually evacuated twice daily and after each evacuation Ringer lactate 5 mL/100 g was administered, twice daily after each bladder evacuation for the first 7 postoperative days. On the 10^th day, the rats underwent nerve conduction studies and behavioral assessment [Basso, Beattie, Brenham (BBB)] to confirm paraplegia. Rat embryonic stem cells, ABMDN and saline were injected on the 10^th day. The animals were euthanized after 8 wk and the spinal cord was isolated, removed and placed in 2% formalin for histopathological analysis to assess the healing of neural tissues at the axonal level.RESULTSAll the animals tolerated the procedure well. The BBB scale scoring showed that at the end of the first week no recovery was observed in the groups. Post-injection, there was a strong and significant improvement in rats receiving rESC and ABMDN as compared to the control group based on the BBB scale, and the Train-of-four-Watch SX acceleromyography device exhibited statistically significant (P < 0.0001) regeneration of neural tissue after SCI. Histological evaluation of the spinal cord showed maximum vacuolization and least gliosis in the control group compared to the rESC and ABMDN treated animals. In the ABMDN group, limited vacuolization and more prominent gliosis were observed in all specimens as compared to the control and rESC groups.CONCLUSIONThis study provided strong evidence to support that transplantation of rESC and ABMDN can improve functional recovery after iatrogenic SCI. The transplanted cells showed a beneficial therapeutic effect when compared to the control group.     

GSK-3beta activity is increased in skeletal muscle after burn injury in rats

Previous reports suggest that burn-induced muscle proteolysis can be inhibited by treatment with GSK-3beta inhibitors, suggesting that burn injury may be associated with increased GSK-3beta activity. The influence of burn injury on muscle GSK-3beta activity, however, is not known. We determined the effect of a 30% total body surface full-thickness burn injury in rats on muscle GSK-3beta activity by measuring GSK-3beta activity and tissue levels of serine 9 phosphorylated GSK-3beta, p(Ser9)-GSK-3beta, by Western blot analysis and immunohistochemistry. Because burn-induced muscle wasting is, at least in part, mediated by glucocorticoids, we used dexamethasone-treated cultured muscle cells in which GSK-3beta expression was reduced with small interfering RNA (siRNA) to further assess the role of GSK-3beta in muscle atrophy. Burn injury resulted in a seven-fold increase in GSK-3beta activity in skeletal muscle. This effect of burn was accompanied by reduced tissue levels of p(Ser9)-GSK-3beta, suggesting that burn injury stimulates GSK-3beta in skeletal muscle secondary to inhibited phosphorylation of the enzyme. In addition, burn injury resulted in inhibited phosphorylation and activation of Akt, an upstream regulatory mechanism of GSK-3beta activity. Reducing the expression of GSK-3beta in cultured muscle cells with siRNA inhibited dexamethasone-induced protein degradation by approximately 50%. The results suggest that burn injury stimulates GSK-3beta activity in skeletal muscle and that GSK-3beta may, at least in part, regulate glucocorticoid-mediated muscle wasting.     

1,25(OH)2-vitamin D3 actions on cell proliferation, size, gene expression, and receptor localization, in the HL-1 cardiac myocyte

The steroid hormone 1,25(OH)₂-vitamin D₃ [1,25D] has been shown to affect the growth and proliferation of primary cultures of ventricular myocytes isolated from neonatal rat hearts. The research presented here shows that the vitamin D receptor [VDR] is present in murine cardiac myocytes (HL-1 cells), and that 1,25D affects the growth, proliferation and morphology of these cells. In addition we show that 1,25D effects expression of ANP, myotrophin, and c-myc. Furthermore, 1,25D effects expression and localization of the VDR within the cell. Murine HL-1 cardiac myocytes were grown and treated with 1,25D in culture, and growth and morphology were assessed with microscopic analysis. Cells were counted and protein levels were evaluated through Western blot analysis. Subcellular localization of the VDR was determined using immunofluorescence and confocal microscopy. 1,25D was found to decrease proliferation and alter cellular morphology of the HL-1 cells. Treatment with 1,25D increased expression of myotrophin while decreasing expression of atrial natriuretic peptide [ANP] and c-myc. 1,25D treatment also increased expression and nuclear localization of the VDR in these cardiac myocytes. Thus 1,25D is an important hormone involved in modulating and maintaining heart cell structure and function.     

1,25(OH)2-vitamin D3 actions on cell proliferation, size, gene expression, and receptor localization, in the HL-1 cardiac myocyte

The steroid hormone 1,25(OH)₂-vitamin D₃ [1,25D] has been shown to affect the growth and proliferation of primary cultures of ventricular myocytes isolated from neonatal rat hearts. The research presented here shows that the vitamin D receptor [VDR] is present in murine cardiac myocytes (HL-1 cells), and that 1,25D affects the growth, proliferation and morphology of these cells. In addition we show that 1,25D effects expression of ANP, myotrophin, and c-myc. Furthermore, 1,25D effects expression and localization of the VDR within the cell. Murine HL-1 cardiac myocytes were grown and treated with 1,25D in culture, and growth and morphology were assessed with microscopic analysis. Cells were counted and protein levels were evaluated through Western blot analysis. Subcellular localization of the VDR was determined using immunofluorescence and confocal microscopy. 1,25D was found to decrease proliferation and alter cellular morphology of the HL-1 cells. Treatment with 1,25D increased expression of myotrophin while decreasing expression of atrial natriuretic peptide [ANP] and c-myc. 1,25D treatment also increased expression and nuclear localization of the VDR in these cardiac myocytes. Thus 1,25D is an important hormone involved in modulating and maintaining heart cell structure and function.     

Cyclin A1-deficient mice lack histone H3 serine 10 phosphorylation and exhibit altered aurora B dynamics in late prophase of male meiosis

Male mice lacking cyclin A1 protein are sterile. Their sterility results from an arrest in the meiotic cell cycle of spermatocytes, which we now identify as occurring at late diplotene, immediately before diakinesis. The stage of arrest in cyclin A1-deficient mice is distinct from the arrest seen in spermatocytes that are deficient in its putative catalytic partner Cdk2, which occurs much earlier in pachytene. The arrest in cyclin A1-deficient spermatocytes is also accompanied by an unusual clustering of centromeric heterochromatin. Consistent with a possible defect in the centromeric region, immunofluorescent staining of cyclin A1 protein shows localization in the region of the centromere. Phosphorylation of histone H3 at serine 10 in pericentromeric heterochromatin, which normally occurs in late diplotene, is reduced in spermatocytes from heterozygous Ccna1(+/-) testes and completely absent in spermatocytes with no cyclin A1 protein. Concomitantly, the levels of pericentromeric aurora B kinase, known to phosphorylate histone H3 during meiosis, are partially reduced in spermatocytes from testes of heterozygous mice and further reduced in homozygous null spermatocytes. These data suggest a critical and concentration-dependent function for cyclin A1 in the pericentromeric region in late diplotene of meiosis, perhaps in assembly or function of the passenger protein complex.