Mitochondrial permeability transition pore: a promising target for the treatment of Parkinson’s disease

Among the neurodegenerative diseases (ND), Parkinson’s disease affects 6.3 million people worldwide characterized by the progressive loss of dopaminergic neurons in substantia nigra. The mitochondrial permeability transition pore (mtPTP) is a non-selective voltage-dependent mitochondrial channel whose opening modifies the permeability properties of the mitochondrial inner membrane. It is recognized as a potent pharmacological target for diseases associated with mitochondrial dysfunction and excessive cell death including ND such as Parkinson’s disease (PD). Imbalance in Ca²⁺ concentration, change in mitochondrial membrane potential, overproduction of reactive oxygen species (ROS), or mutation in mitochondrial genome has been implicated in the pathophysiology of the opening of the mtPTP. Different proteins are released by permeability transition including cytochrome c which is responsible for apoptosis. This review aims to discuss the importance of PTP in the pathophysiology of PD and puts together different positive as well as negative aspects of drugs such as pramipexole, ropinirole, minocyclin, rasagilin, and safinamide which act as a blocker or modifier for mtPTP. Some of them may be detrimental in their neuroprotective nature.     

Cloning of endoglucanase genes fromCellulomonas biazotea intoE. coli andS. cerevisiae using shuttle vector YEp24

We constructed aSmaI genomic library ofCellulomonas biazotea DNA inE. coli and in theS. cerevisiae shuttle vector, YEP 24. Three clone were identified that conferred the ability forE. coli orS. cerevisiae transformants to produce carboxymethylcellulase (CMCase). Cells transformed with these clones were compared with one another and with nontransformed cells for hyper-production of CMCase.In vivo andin vitro studies indicated that the CMCase genes were fully expressed and the enzyme activity was located extracellularly. The optimum pH and temperature for the CMCase thus cloned were pH 7 and 50°C, respectively, as was the case for the donor.     

Stabilizing proteins to prevent conformational changes required for amyloid fibril formation

Amyloid fibrillation is associated with several human maladies, such as Alzheimer’s, Parkinson’s, Huntington’s diseases, prions, amyotrophic lateral sclerosis, and type 2 diabetes diseases. Gaining insights into the mechanism of amyloid fibril formation and exploring novel approaches to fibrillation inhibition are crucial for preventing amyloid diseases. Here, we hypothesized that ligands capable of stabilizing the native state of query proteins might prevent protein unfolding, which, in turn, may reduce the propensity of proteins to form amyloid fibrils. We demonstrated the efficient inhibition of amyloid formation of the human serum albumin (HSA) (up to 85%) and human insulin (up to 80%) by a nonsteroidal anti-inflammatory drug, ibuprofen (IBFN). IBFN significantly increases the conformational stability of both HSA and insulin, as confirmed by differential scanning calorimetry (DSC). Moreover, increasing concentration of IBFN boosts its amyloid inhibitory propensity in a linear fashion by influencing the nucleation phase as assayed by thioflavin T fluorescence, transmission electron microscopy, and dynamic light scattering. Furthermore, circular dichroism analysis supported the DSC results, showing that IBFN binds to the native state of proteins and almost completely prevents their tendency to lose secondary and tertiary structures. Cell toxicity assay confirms that species formed in the presence of IBFN are less toxic to neuronal cells (SH-SY5Y). These results demonstrate the feasibility of using a small molecule to stabilize the native state of proteins, thereby preventing the amyloidogenic conformational changes, which appear to be the common link in several human amyloid diseases.     

Mathematical modelling the systemic regulation of blood glucose: 'a top-down' systems biology approach

The objective of this article is to review the mechanisms which the body uses to regulate its function. The author considers, in particular, the nature and structure of the physiological systems with a specific focus upon the systemic regulation of blood glucose and highlights an innovative technology, based upon the top-down cognitive approach, which incorporates a unique mathematical model of the physiological systems and autonomic nervous system. Most systems biology is a development of the prevailing reductionist biomedical paradigm. It adopts a bottom-up approach seeking systemic justification for biochemical and biophysical research findings. By contrast the 'top-down' approach considers the neural regulation of the physiological systems and the neurological, cognitive and biochemical consequences of systemic dysfunction i.e. the consequences of sensory input upon the neural regulation of the body's systems, organs, and its cellular and molecular biochemistry. In conclusion, the evidence suggests that the onset and progression of Diabetes Mellitus cannot be accurately assessed by individual biomedical indices but instead that the regulation of blood glucose is one of a number of inter-related physiological systems which act in a coordinated manner in order to maintain the body's physiological stability.     

Blood glutathione redox status and global methylation of peripheral blood mononuclear cell DNA in Bangladeshi adults

Oxidative stress and DNA methylation are metabolically linked through the relationship between one-carbon metabolism and the transsulfuration pathway, but possible modulating effects of oxidative stress on DNA methylation have not been extensively studied in humans. Enzymes involved in DNA methylation, including DNA methyltransferases and histone deacetylases, may show altered activity under oxidized cellular conditions. Additionally, in vitro studies suggest that glutathione (GSH) depletion leads to global DNA hypomethylation, possibly through the depletion of S-adenosylmethionine (SAM). We tested the hypothesis that a more oxidized blood GSH redox status is associated with decreased global peripheral blood mononuclear cell (PBMC) DNA methylation in a sample of Bangladeshi adults. Global PBMC DNA methylation and whole blood GSH, glutathione disulfide (GSSG), and SAM concentrations were measured in 320 adults. DNA methylation was measured by using the [³H]-methyl incorporation assay; values are inversely related to global DNA methylation. Whole blood GSH redox status (E_h) was calculated using the Nernst equation. We found that a more oxidized blood GSH E_h was associated with decreased global DNA methylation (B ± SE, 271 ± 103, p = 0.009). Blood SAM and blood GSH were associated with global DNA methylation, but these relationships did not achieve statistical significance. Our findings support the hypothesis that a more oxidized blood GSH redox status is associated with decreased global methylation of PBMC DNA. Furthermore, blood SAM does not appear to mediate this association. Future research should explore mechanisms through which cellular redox might influence global DNA methylation.     

Total Water,Phosphorus Relaxation and Inter-Atomic Organic to Inorganic Interface Are New Determinants of Trabecular Bone Integrity

Bone is the living composite biomaterial having unique structural property. Presently, there is a considerable gap in our understanding of bone structure and composition in the native state, particularly with respect to the trabecular bone, which is metabolically more active than cortical bones, and is readily lost in post-menopausal osteoporosis. We used solid-state nuclear magnetic resonance (NMR) to compare trabecular bone structure and composition in the native state between normal, bone loss and bone restoration conditions in rat. Trabecular osteopenia was induced by lactation as well as prolonged estrogen deficiency (bilateral ovariectomy, Ovx). Ovx rats with established osteopenia were administered with PTH (parathyroid hormone, trabecular restoration group), and restoration was allowed to become comparable to sham Ovx (control) group using bone mineral density (BMD) and µCT determinants. We used a technique combining ¹H NMR spectroscopy with ³¹P and ¹³C to measure various NMR parameters described below. Our results revealed that trabecular bones had diminished total water content, inorganic phosphorus NMR relaxation time (T₁) and space between the collagen and inorganic phosphorus in the osteopenic groups compared to control, and these changes were significantly reversed in the bone restoration group. Remarkably, bound water was decreased in both osteopenic and bone restoration groups compared to control. Total water and T₁ correlated strongly with trabecular bone density, volume, thickness, connectivity, spacing and resistance to compression. Bound water did not correlate with any of the microarchitectural and compression parameters. We conclude that total water, T₁ and atomic space between the crystal and organic surface are altered in the trabecular bones of osteopenic rats, and PTH reverses these parameters. Furthermore, from these data, it appears that total water and T₁ could serve as trabecular surrogates of micro-architecture and compression strength.     

High-Level Production of Plasmid DNA by Escherichia coli DH5α ΩsacB by Introducing inc Mutations

For small-copy-number pUC-type plasmids, the inc1 and inc2 mutations, which deregulate replication, were previously found to increase the plasmid copy number 6- to 7-fold. Because plasmids can exert a growth burden, it was not clear if further amplification of copy number would occur due to inc mutations when the starting point for plasmid copy number was orders of magnitude higher. To investigate further the effects of the inc mutations and the possible limits of plasmid synthesis, the parent plasmid pNTC8485 was used as a starting point. It lacks an antibiotic resistance gene and has a copy number of ∼1,200 per chromosome. During early stationary-phase growth in LB broth at 37°C, inc2 mutants of pNTC8485 exhibited a copy number of ∼7,000 per chromosome. In minimal medium at late log growth, the copy number was found to be significantly increased, to approximately 15,000. In an attempt to further increase the plasmid titer (plasmid mass/culture volume), enzymatic hydrolysis of the selection agent, sucrose, at late log growth extended growth and tripled the total plasmid amount such that an approximately 80-fold gain in total plasmid was obtained compared to the value for typical pUC-type vectors. Finally, when grown in minimal medium, no detectable impact on the exponential growth rate or the fidelity of genomic or plasmid DNA replication was found in cells with deregulated plasmid replication. The use of inc mutations and the sucrose degradation method presents a simplified way for attaining high titers of plasmid DNA for various applications.     

Genome-Wide Association Studies and Heritability Estimates of Body Mass Index Related Phenotypes in Bangladeshi Adults

Many health outcomes are influenced by a person''s body mass index, as well as by the trajectory of body mass index through a lifetime. Although previous research has established that body mass index related traits are influenced by genetics, the relationship between these traits and genetics has not been well characterized in people of South Asian ancestry. To begin to characterize this relationship, we analyzed the association between common genetic variation and five phenotypes related to body mass index in a population-based sample of 5,354 Bangladeshi adults. We discovered a significant association between SNV rs347313 (intron of NOS1AP) and change in body mass index in women over two years. In a linear mixed-model, the G allele was associated with an increase of 0.25 kg/m² in body mass index over two years (p-value of 2.3·10⁻⁸). We also estimated the heritability of these phenotypes from our genotype data. We found significant estimates of heritability for all of the body mass index-related phenotypes. Our study evaluated the genetic determinants of body mass index related phenotypes for the first time in South Asians. The results suggest that these phenotypes are heritable and some of this heritability is driven by variation that differs from those previously reported. We also provide evidence that the genetic etiology of body mass index related traits may differ by ancestry, sex, and environment, and consequently that these factors should be considered when assessing the genetic determinants of the risk of body mass index-related disease.     

Genome-Wide Association Study of Parity in Bangladeshi Women

Human fertility is a complex trait determined by gene-environment interactions in which genetic factors represent a significant component. To better understand inter-individual variability in fertility, we performed one of the first genome-wide association studies (GWAS) of common fertility phenotypes, lifetime number of pregnancies and number of children in a developing country population. The fertility phenotype data and DNA samples were obtained at baseline recruitment from individuals participating in a large prospective cohort study in Bangladesh. GWAS analyses of fertility phenotypes were conducted among 1,686 married women. One SNP on chromosome 4 was non-significantly associated with number of children at P <10^-7 and number of pregnancies at P <10^-6. This SNP is located in a region without a gene within 1 Mb. One SNP on chromosome 6 was non-significantly associated with extreme number of children at P <10^-6. The closest gene to this SNP is HDGFL1, a hepatoma-derived growth factor. When we excluded hormonal contraceptive users, a SNP on chromosome 5 was non-significantly associated at P <10^-5 for number of children and number of pregnancies. This SNP is located near C5orf64, an open reading frame, and ZSWIM6, a zinc ion binding gene. We also estimated the heritability of these phenotypes from our genotype data using GCTA (Genome-wide Complex Trait Analysis) for number of children (h_g ² = 0.149, SE = 0.24, p-value = 0.265) and number of pregnancies (h_g ² = 0.007, SE = 0.22, p-value = 0.487). Our genome-wide association study and heritability estimates of number of pregnancies and number of children in Bangladesh did not confer strong evidence of common variants for parity variation. However, our results suggest that future studies may want to consider the role of 3 notable SNPs in their analysis.     

Potentiality of Different Seed Priming Agents to Mitigate Cold Stress of Winter Rice Seedling

Seed priming has proved to be an effective pre-germination seed invigoration technique for different crops to improve seed and seedling performance under different abiotic stresses. In Bangladesh, winter rice is very often exposed to cold waves just after sowing in the nursery bed resulting in poor seed germination and seedling emergence, yellowish and thin seedlings production, and a very low survival rate. Seed priming may mitigate the cold stress during seed germination and seedling emergence and helps in the quality seedling production of winter rice. To evaluate the efficacy of different seed priming techniques in increasing seedling emergence, growth, vigor and survivability of winter rice cultivars under cold stress, a pot experiment was conducted at the Department of Agronomy, Bangladesh Agricultural University during December 2018 to January 2019. The experiment comprised two factors, (A) Winter rice variety namely, i) BRRI dhan29 and ii) BRRI dhan36; (B) Seed priming agent namely i) Control (no priming), ii) 20000 ppm NaCl, iii) 30000 ppm NaCl, iv) 20000 ppm KCl, v) 30000 ppm KCl, vi) 20000 ppm CaCl₂, vii) 30000 ppm CaCl₂, viii) 50 ppm CuSO₄, ix) 75 ppm CuSO₄, x) 10000 ppm ZnSO₄, xi) 15000 ppm ZnSO₄, xii) 2 ppm Na₂MoO₄, xiii) 3 ppm Na₂MoO₄, xiv) 100 ppm PEG (Polyethylene glycol 4000) and xv) 150 ppm PEG. Seeds were sown on two different dates viz., 1st December and 1st January so that seedlings are exposed to cold stress at different stages. The experiment was laid out in a completely randomized design (CRD) with three replications. Results indicated that (in most of the cases) seed priming has a positive impact on seedling emergence rate (%), root length, shoot length, root shoot ratio, root dry weight, shoot dry weight, seedling dry weight and survival rate (%). Among the priming agents, KCl and CaCl₂ performed best; while priming with NaCl and PEG showed no advantages over no priming for both the sowing dates. In general, BRRI dhan36 performed better than BRRI dhan29 in terms of seedling growth because of its higher tolerance to cold stress. But, both the varieties performed similarly in terms of emergence rate and survival rate. Thus, priming is an effective tool to increase seed germination, better seedling growth, and higher seedling survivability of winter rice under cold stress, and KCl (20000 ppm) or CaCl₂ (20000 ppm) can be considered as a viable priming agent.