Respiration induces variable porosity to polyols in the mitochondrial inner membrane

The osmotic basis of low and high amplitude swelling in mitochondria was investigated in detail using sucrose and mannitol as external osmolytes. Osmotic behaviour of mitochondria in various respiratory states was consistent with significant changes in the porosity of the inner membrane corresponding to the rate of respiration. The stoichiometry of oxidative phosphorylation was confirmed to be dependent on the physical state (i.e., osmotic stretch) of the inner membrane regardless of the external polyol used. High amplitude swelling in polyol media was shown to arise from a sequential disruption of the outer and inner mitochondrial membranes, due to a dynamic instability induced by a combination of respiration, unscreened (fixed) surface charge density and the consequent variable porosity of the inner membrane. These novel experimental findings based on the physical theory of osmosis emphasize the need to define the fine structural changes of the inner membrane associated with oxidative phosphorylation to arrive at a comprehensive mechanism.     

Designing and Testing of Novel Taxanes to Probe the Highly Complex Mechanisms by Which Taxanes Bind to Microtubules and Cause Cytotoxicity to Cancer Cells

Our previous work identified an intermediate binding site for taxanes in the microtubule nanopore. The goal of this study was to test derivatives of paclitaxel designed to bind to this intermediate site differentially depending on the isotype of β-tubulin. Since β-tubulin isotypes have tissue-dependent expression—specifically, the βIII isotype is very abundant in aggressive tumors and much less common in normal tissues—this is expected to lead to tubulin targeted drugs that are more efficacious and have less side effects. Seven derivatives of paclitaxel were designed and four of these were amenable for synthesis in sufficient purity and yield for further testing in breast cancer model cell lines. None of the derivatives studied were superior to currently used taxanes, however computer simulations provided insights into the activity of the derivatives. Our results suggest that neither binding to the intermediate binding site nor the final binding site is sufficient to explain the activities of the derivative taxanes studied. These findings highlight the need to iteratively improve on the design of taxanes based on their activity in model systems. Knowledge gained on the ability of the engineered drugs to bind to targets and bring about activity in a predictable manner is a step towards personalizing therapies.     

Assessing SNP-SNP Interactions among DNA Repair,Modification and Metabolism Related Pathway Genes in Breast Cancer Susceptibility

Genome-wide association studies (GWASs) have identified low-penetrance common variants (i.e., single nucleotide polymorphisms, SNPs) associated with breast cancer susceptibility. Although GWASs are primarily focused on single-locus effects, gene-gene interactions (i.e., epistasis) are also assumed to contribute to the genetic risks for complex diseases including breast cancer. While it has been hypothesized that moderately ranked (P value based) weak single-locus effects in GWASs could potentially harbor valuable information for evaluating epistasis, we lack systematic efforts to investigate SNPs showing consistent associations with weak statistical significance across independent discovery and replication stages. The objectives of this study were i) to select SNPs showing single-locus effects with weak statistical significance for breast cancer in a GWAS and/or candidate-gene studies; ii) to replicate these SNPs in an independent set of breast cancer cases and controls; and iii) to explore their potential SNP-SNP interactions contributing to breast cancer susceptibility. A total of 17 SNPs related to DNA repair, modification and metabolism pathway genes were selected since these pathways offer a priori knowledge for potential epistatic interactions and an overall role in breast carcinogenesis. The study design included predominantly Caucasian women (2,795 cases and 4,505 controls) from Alberta, Canada. We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 and MDM2-rs769412) in logistic regression that conferred elevated risks for breast cancer (P _interaction<7.3×10⁻³). Logic regression identified an interaction involving four SNPs (MBD2-rs4041245, MLH1-rs1799977, MDM2-rs769412, BRCA2-rs1799943) (P _permutation = 2.4×10⁻³). SNPs involved in SNP-SNP interactions also showed single-locus effects with weak statistical significance, while BRCA2-rs1799943 showed stronger statistical significance (P _{correlation/trend} = 3.2×10⁻⁴) than the others. These single-locus effects were independent of body mass index. Our results provide a framework for evaluating SNPs showing statistically weak but reproducible single-locus effects for epistatic effects contributing to disease susceptibility.     

The organisational structure of protein networks: revisiting the centrality–lethality hypothesis

Protein networks, describing physical interactions as well as functional associations between proteins, have been unravelled for many organisms in the recent past. Databases such as the STRING provide excellent resources for the analysis of such networks. In this contribution, we revisit the organisation of protein networks, particularly the centrality–lethality hypothesis, which hypothesises that nodes with higher centrality in a network are more likely to produce lethal phenotypes on removal, compared to nodes with lower centrality. We consider the protein networks of a diverse set of 20 organisms, with essentiality information available in the Database of Essential Genes and assess the relationship between centrality measures and lethality. For each of these organisms, we obtained networks of high-confidence interactions from the STRING database, and computed network parameters such as degree, betweenness centrality, closeness centrality and pairwise disconnectivity indices. We observe that the networks considered here are predominantly disassortative. Further, we observe that essential nodes in a network have a significantly higher average degree and betweenness centrality, compared to the network average. Most previous studies have evaluated the centrality–lethality hypothesis for Saccharomyces cerevisiae and Escherichia coli; we here observe that the centrality–lethality hypothesis hold goods for a large number of organisms, with certain limitations. Betweenness centrality may also be a useful measure to identify essential nodes, but measures like closeness centrality and pairwise disconnectivity are not significantly higher for essential nodes.     

Enantioselective synthesis of (+)-4-demethoxy-1,4-dimethyldaunomycinone

(+)-4-Demethoxy-1,4-dimethyldaunomycinone 1 was synthesized using a convergent approach. Here, the key tetracyclic compound 10 was assembled by way of a Diels-Alder reaction using the sugar-based diene 8 and the quinizarin-related dienophile 7.     

Studies on the non-linear osmotic pressure-volume relationship in mitochondria and entry of sucrose into the matrix space during centrifugation

The two-compartment sucrose-space hypothesis was refuted recently (Sitaramam, V. and Sarma, M.K.J. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 3441-3445), using the novel technique of enzyme osmometry of matrix enzymes based on the following premise: a shift in the discontinuity (break-point) of the activity profile of an occluded enzyme as a function of external osmolarity (i.e., osmotic profiles) would imply a shift in the internal solute content of the same compartment as that of the enzyme. A systematic re-evaluation of the osmotic profiles of mitochondrial enzyme systems has revealed that the activities of several matrix and inner membrane enzyme systems exhibited break-points larger than those of osmolysis (i.e., actual release of marker enzymes into the medium) of mitochondria. The experimental findings were consistent with (i) entry of sucrose across the inner membrane consequent to enhanced permeability effects by gravitational field, and (ii) dependence of the kinetic constant of several membrane-bound enzymes/carrier proteins, respiratory coupling and ADP/O ratio on the volume of mitochondria (i.e., osmotic stretch of the inner membrane).     

Evidence for copurification of micronuclei in sucrose density gradient-enriched plasma membranes from cell lines

Sucrose density gradient-enriched membrane preparations and membrane fraction enrichment through affinity purification techniques are commonly used in proteomic analysis. However, published proteomic profiles characterized by the above methods show the presence of nuclear proteins in addition to membrane proteins. While shuttling of nuclear proteins across cellular compartments and their transient residency at membrane interfaces could explain some of these observations, the presence of nuclear proteins in proteomic profiles generated with crude and enriched membranes could be the result of nonspecific contamination of nuclear debris during cell fractionation procedures. We hypothesized that micronuclei arising from the genomic instability inherent to cancer cells may copurify with plasma membrane fractions on sucrose gradients. Using sucrose gradient-enriched plasma membranes from breast cancer cell lines derived from the MCF-7 cell line, we provide experimental evidence to indicate that micronuclei are present in fresh preparations of plasma membranes. The origin of these micronuclei was traced to budding of nuclei in intact cells. Furthermore, mass spectrometric analysis confirmed the presence of nuclear proteins as well as membrane and associated signaling proteins in sucrose gradient-enriched preparations.     

Role of calcium in synaptosomal substrate oxidation

The effect of veratridine-mediated depolarization on rat brain synaptosomal respiration in the presence and absence of calcium was investigated. Studies on respiration were performed employing three different pretreatments of the synaptosomes which attempted to deplete endogenous substrates. First, synaptosomes were preincubated for 10 min in the absence of any substrates in medium either containing or devoid of calcium. Second, synaptosomes were preincubated for either 15 or 60-min periods in the presence and absence of calcium, and the incubation medium was changed by centrifugation and resuspension of synaptosomes in their respective media. Irrespective of the prior treatment, maximal stimulation of respiration (400-600%) during veratridine (100 microM) elicited depolarization was observed only when calcium was present in the incubation media. In incubations performed in the absence of calcium, veratridine addition either modestly stimulated (10- and 15-min preincubated synaptosomes) or did not affect (60-min preincubated synaptosomes) the rate of respiration. However, when calcium was added back to these incubations the rate of respiration in the presence of veratridine was stimulated by five- to six-fold. Similarly, the rates of 14CO2 production from [1-14C]- and [2-14C]pyruvate were increased by veratridine only when synaptosomes were incubated in calcium-replete medium. These data indicate that calcium plays an obligatory role in depolarization-elicited stimulation of synaptosomal oxidative processes.     

Fractional Plans to Estimate Main Effects and Two Factor Interactions Inclusive of a Specific Factor

Balanced incomplete block designs are used to construct non‐geometric 2ⁿ fractional factorial plans to estimate all n main effects and n – 1, 2 factor interactions with a specific factor included in each interaction. When the balanced incomplete block design is of Family (A), the resulting fractional factorial plan has the same number of runs as a fold‐over Hadamard matrix giving same variances for the estimates; however, some new designs are shown to be non‐isomorphic to the fold‐over Hadamard matrix plans.     

Learning to predict cancer-associated skeletal muscle wasting from 1H-NMR profiles of urinary metabolites

Cancer-associated muscle wasting is associated with reduction in functional status, in response to treatment and in life expectancy. Methods currently used to assess muscle loss involve diagnostic imaging techniques such as computed tomography (CT), which are costly, inconvenient, invasive, time consuming and have limited ability to detect early or slowly evolving wasting. We present a novel approach using single time-point urinary metabolite profiles to determine whether a patient is experiencing muscle wasting. We analyzed 93 random urine samples from patients with cancer using ¹H-NMR. Using two successive CT images we assessed their lumbar skeletal muscle area (cm²) to estimate the rate of muscle change (% loss or gain over time) for each patient. The average muscle change over time was −4.71%/100 days in the muscle-losing group and +3.91%/100 days in the comparator group. Bivariate statistics identified metabolites related with muscle loss, including constituents and metabolites of muscle (creatine, creatinine, 3-OH-isovalerate), amino acids (Leu, Ile, Val, Ala, Thr, Tyr, Gln, Ser) and intermediary metabolites. We also applied machine-learning techniques to identify patterns of urinary metabolites that identify which patients are likely to lose muscle mass. We evaluated the predictive performance of 8 machine-learning approaches using fivefold cross validation and permutation testing, and found that SVM provided the best generalization accuracy (82.2%). These results suggest that ¹H-NMR analysis of a single random urine sample may be a fast, cheap, safe and inexpensive tool to screen and monitor muscle loss, and that useful classifiers for predicting related metabolic conditions are possible with the methodology presented.