An omics-based machine learning approach to predict diabetes progression: a RHAPSODY study.

AIMS/HYPOTHESIS: People with type 2 diabetes are heterogeneous in their disease trajectory, with some progressing more quickly to insulin initiation than others. Although classical biomarkers such as age, HbA1c and diabetes duration are associated with glycaemic progression, it is unclear how well such variables predict insulin initiation or requirement and whether newly identified markers have added predictive value. METHODS: In two prospective cohort studies as part of IMI-RHAPSODY, we investigated whether clinical variables and three types of molecular markers (metabolites, lipids, proteins) can predict time to insulin requirement using different machine learning approaches (lasso, ridge, GRridge, random forest). Clinical variables included age, sex, HbA1c, HDL-cholesterol and C-peptide. Models were run with unpenalised clinical variables (i.e. always included in the model without weights) or penalised clinical variables, or without clinical variables. Model development was performed in one cohort and the model was applied in a second cohort. Model performance was evaluated using Harrel's C statistic. RESULTS: Of the 585 individuals from the Hoorn Diabetes Care System (DCS) cohort, 69 required insulin during follow-up (1.0-11.4 years); of the 571 individuals in the Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS) cohort, 175 required insulin during follow-up (0.3-11.8 years). Overall, the clinical variables and proteins were selected in the different models most often, followed by the metabolites. The most frequently selected clinical variables were HbA1c (18 of the 36 models, 50%), age (15 models, 41.2%) and C-peptide (15 models, 41.2%). Base models (age, sex, BMI, HbA1c) including only clinical variables performed moderately in both the DCS discovery cohort (C statistic 0.71 [95% CI 0.64, 0.79]) and the GoDARTS replication cohort (C 0.71 [95% CI 0.69, 0.75]). A more extensive model including HDL-cholesterol and C-peptide performed better in both cohorts (DCS, C 0.74 [95% CI 0.67, 0.81]; GoDARTS, C 0.73 [95% CI 0.69, 0.77]). Two proteins, lactadherin and proto-oncogene tyrosine-protein kinase receptor, were most consistently selected and slightly improved model performance. CONCLUSIONS/INTERPRETATION: Using machine learning approaches, we show that insulin requirement risk can be modestly well predicted by predominantly clinical variables. Inclusion of molecular markers improves the prognostic performance beyond that of clinical variables by up to 5%. Such prognostic models could be useful for identifying people with diabetes at high risk of progressing quickly to treatment intensification. DATA AVAILABILITY: Summary statistics of lipidomic, proteomic and metabolomic data are available from a Shiny dashboard at https://rhapdata-app.vital-it.ch .

Anti-cancer activity of ultra-short single-stranded polydeoxyribonucleotides.

One of the features that differentiate cancer cells is their increased proliferation rate, which creates an opportunity for general anti-tumor therapy directed against the elevated activity of replicative apparatus in tumor cells. Besides DNA synthesis, successful genome replication requires the reparation of the newly synthesized DNA. Malfunctions in reparation can cause fatal injuries in the genome and cell death. Recently we have found that the ultra-short single-stranded deoxyribose polynucleotides of random sequence (ssDNA) effectively inhibit the catalytic activity of DNA polymerase [Formula: see text]. This effect allowed considering these substances as potential anti-tumor drugs, which was confirmed experimentally both in vitro (using cancer cell cultures) and in vivo (using cancer models in mice). According to the obtained results, ssDNA significantly suppresses cancer development and tumor growth, allowing consideration of them as novel candidates for anti-cancer drugs.

Optimal control analysis of Taenia saginata bovine cysticercosis and human taeniasis.

Bovine cysticercosis and human taeniasis are neglected food-borne diseases that pose challenge to food safety, human health and livelihood of rural livestock farmers. In this paper, we have formulated and analyzed a deterministic model for transmission dynamics and control of taeniasis and cysticercosis in humans and cattle respectively. The analysis shows that both the disease free equilibrium (DFE) and endemic equilibrium (EE) exist. To study the dynamics of the diseases, we derived the basic reproduction number R 0 by next generation matrix method which shows whether the diseases die or persist in humans and cattle. The diseases clear if R 0 < 1 and persist when R 0 > 1. The normalized forward sensitivity index is used to derive sensitive indices of model parameters. Sensitivity analysis results indicate that human's and cattle's recruitment rates, infection rate of cattle from contaminated environment, probability of humans to acquire taeniasis due to consumption of infected meat, defecation rate of humans with taeniasis and the consumption rate of raw or undercooked infected meat are the most positive sensitive parameters whereas the natural death rates for humans, cattle, Taenia saginata eggs and the proportion of unconsumed infected meat are the most negative sensitive parameters in diseases' transmission. These results suggest that control measures such as improving meat cooking, meat inspection and treatment of infected humans will be effective for controlling taeniasis and cysticercosis in humans and cattle respectively. The optimal control theory is applied by considering three time dependent controls which are improved meat cooking, vaccination of cattle, and treatment of humans with taeniasis when they are implemented in combination. The Pontryagin's maximum principle is adopted to find the necessary conditions for existence of the optimal controls. The Runge Kutta order four forward-backward sweep method is implemented in Matlab to solve the optimal control problem. The results indicate that a strategy which focuses on improving meat cooking and treatment of humans with taeniasis is the optimal strategy for diseases' control.

A specific role of magnetic isotopes in biological and ecological systems. Physics and biophysics beyond.

The great diversity of molecular processes in chemistry, physics, and biology exhibits universal property: they are controlled by powerful factor, angular momentum. Conservation of angular momentum (electron spin) is a fundamental and universal principle: all molecular processes are spin selective, they are allowed only for those spin states of reactants whose total spin is identical to that of products. Magnetic catalysis induced by magnetic interactions is a powerful and universal means to overcome spin prohibition and to control physical, chemical and biochemical processes. Contributing almost nothing in total energy, being negligibly small, magnetic interactions are the only ones which are able to change electron spin of reactants and switch over the processes between spin-allowed and spin-forbidden channels, controlling pathways and chemical reactivity in molecular processes. The main source of magnetic and electromagnetic effects in biological systems is now generally accepted and demonstrated in this paper to be radical pair mechanism which implies pairwise generation of radicals in biochemical reactions. This mechanism was convincingly established for enzymatic adenosine triphosphate (ATP) and desoxynucleic acid (DNA) synthesis by using catalyzing metal ions with magnetic nuclei (25Mg, 43Ca, 67Zn) and supported by magnetic field effects on these reactions. The mechanism, is shown to function in medicine as a medical remedy or technology (trans-cranial magnetic stimulation, nuclear magnetic control of the ATP synthesis in heart muscle, the killing of cancer cells by suppression of DNA synthesis). However, the majority of magnetic effects in biology remain to be irreproducible, contradictory, and enigmatic. Three sources of such a state are shown in this paper to be: the presence of paramagnetic metal ions as a component of enzymatic site or as an impurity in an uncontrollable amount; the property of the radical pair mechanism to function at a rather high concentration of catalyzing metal ions, when at least two ions enter into the catalytic site; and the kinetic restrictions, which imply compatibility of chemical and spin dynamics in radical pair. The purpose of the paper is to analyze the reliable sources of magnetic effects, to elucidate the reasons of their inconsistency, to show how and at what conditions magnetic effects exhibit themselves and how they may be controlled, switched on and off, taking into account not only biological and madical but some geophysical and environmental aspects as well.

L-Lysine-modified Fe3O4 nanoparticles for magnetic cell labeling.

The efficiency of magnetic labeling with L-Lys-modified Fe3O4 magnetic nanoparticles (MNPs) and the stability of magnetization of rat adipose-derived mesenchymal stem cells, lineage-negative (Lin(-)) hematopoietic progenitor cells from mouse bone marrow and human leukemia K562 cells were studied. For this purpose, covalent modification of MNPs with 3-aminopropylsilane and N-di-Fmoc-L-lysine followed by removal of N-protecting groups was carried out. Since the degree of hydroxylation of the surface of the starting nanoparticles plays a crucial role in the silanization reaction and the possibility of obtaining stable colloidal solutions. In present work we for the first time performed a comparative qualitative and quantitative evaluation of the number of adsorbed water molecules and hydroxyl groups on the surface of chemically and physically obtained Fe3O4 MNPs using comprehensive FTIR spectroscopy and thermogravimetric analysis. The results obtained can be further used for magnetic labeling of cells in experiments in vitro and in vivo.

Nuclear spin selectivity in enzymatic catalysis: A caution for applied biophysics.

Nuclear magnetic ions 25Mg2+, 43Ca2+, and 67Zn2+ suppress DNA synthesis by 3-5 times with respect to ions with nonmagnetic nuclei. This observation unambiguously evidences that the DNA synthesis occurs by radical pair mechanism, which is well known in chemistry and implies pairwise generation of radicals by electron transfer between reaction partners. This mechanism coexists with generally accepted nucleophilic one; it is switched on, when at least two ions enter into the catalytic site. It is induced by both sorts of ions, magnetic and nonmagnetic but it functions by 3-5 times more efficiently with magnetic ions stimulating radical pair mechanism. Decreasing catalytic activity of polymerases by 3-5 times, nuclear magnetic ions 25Mg2+, 43Ca2+, and 67Zn2+ even more strongly, by 30-50 times, increase mortality of cancer cells. The two reasons of this unique phenomenon are suggested: first, the high concentration of nuclear magnetic ions delivered by specific nano-container into the cancer cells, and, second, generation of short DNA fragments by polymerases loaded with nuclear magnetic ions, which is known to activate protein p53, efficiently stimulating apoptosis of cancer cells.

Ultrashort ssDNA in Retinoblastoma Patients Blood Plasma Detected by a Novel High Resolution HPLC Technique: a Preliminary Report.

A significant population of ultrashort (50-150n) single-stranded DNA fragments were found in exosome-free blood plasma of retinoblastoma patients (6.84 ng mL-1), but not in plasma of healthy donors. An original high resolution HPLC technique has been proposed to reveal and characterize this peculiarity. To solve this task, a novel molecular size exclusion - anion exchange analytical technique was developed. Its applicability to diagnostics and oncogenesis research is quizzed here.

The role of zinc and its compounds in leukemia.

Zinc is one of the most important microelements necessary for normal body functioning. Zinc is marked in numerous diseases and, hence, its properties and behavior in the body have long been a subject of extensive study. This review considers trends in the assessment of the role of zinc and its compounds in the past decade. It becomes evident that redox-inactive zinc is the main supervisor in the conformation of the most important molecules in all body organs and tissues. We placed emphasis on the variety of zinc-binding sites and the role of zinc in the genesis and progress of different forms of leukemia. The importance of some families of transcription factors in the development and prognosis of treatment of various leukemia forms is examined; new directions of these studies are shown.

Retinoblastoma: Magnetic Isotope Effects Might Make a Difference in the Current Anti-Cancer Research Strategy.

Human retinoblastoma cells were proven to possess some very unusual DNApolß species. Being 23.5 kDa monomers, which itself is not common for the DNApolß superfamily members, these chromatin associated proteins manifests most of the DNApolß-specifc functional peculiarities making them legitimate targets for DNA repair cytostatic inhibitors. Particularly, these tumor specific enzymes were found to be very sensitive to 25Mg2+-, 43Ca2+- and 67Zn2+-promoted magnetic isotope effects (MIE) caused a marked DNA sequence growth limitation as well as a formation of the size-invalid, i.e. too short in length, DNA fragments, totally inappropriate for the DNA repair purpose. This MIE-DNApolß match may serve a starting point for further move towards the paramagnetic path in current developments of anti-cancer strategies.

Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis.

The Wnt pathway, which controls crucial steps of the development and differentiation programs, has been proposed to influence lipid storage and homeostasis. In this paper, using an unbiased strategy based on high-content genome-wide RNAi screens that monitored lipid distribution and amounts, we find that Wnt3a regulates cellular cholesterol. We show that Wnt3a stimulates the production of lipid droplets and that this stimulation strictly depends on endocytosed, LDL-derived cholesterol and on functional early and late endosomes. We also show that Wnt signaling itself controls cholesterol endocytosis and flux along the endosomal pathway, which in turn modulates cellular lipid homeostasis. These results underscore the importance of endosome functions for LD formation and reveal a previously unknown regulatory mechanism of the cellular programs controlling lipid storage and endosome transport under the control of Wnt signaling.

An acetyl-methyl switch drives a conformational change in p53.

Individual posttranslational modifications (PTMs) of p53 mediate diverse p53-dependent responses; however, much less is known about the combinatorial action of adjacent modifications. Here, we describe crosstalk between the early DNA damage response mark p53K382me2 and the surrounding PTMs that modulate binding of p53 cofactors, including 53BP1 and p300. The 1.8 Å resolution crystal structure of the tandem Tudor domain (TTD) of 53BP1 in complex with p53 peptide acetylated at K381 and dimethylated at K382 (p53K381acK382me2) reveals that the dual PTM induces a conformational change in p53. The α-helical fold of p53K381acK382me2 positions the side chains of R379, K381ac, and K382me2 to interact with TTD concurrently, reinforcing a modular design of double PTM mimetics. Biochemical and nuclear magnetic resonance analyses show that other surrounding PTMs, including phosphorylation of serine/threonine residues of p53, affect association with TTD. Our findings suggest a novel PTM-driven conformation switch-like mechanism that may regulate p53 interactions with binding partners.

Magnetic isotope and magnetic field effects on the DNA synthesis.

Magnetic isotope and magnetic field effects on the rate of DNA synthesis catalysed by polymerases ß with isotopic ions (24)Mg(2+), (25)Mg(2+) and (26)Mg(2+) in the catalytic sites were detected. No difference in enzymatic activity was found between polymerases ß carrying (24)Mg(2+) and (26)Mg(2+) ions with spinless, non-magnetic nuclei (24)Mg and (26)Mg. However, (25)Mg(2+) ions with magnetic nucleus (25)Mg were shown to suppress enzymatic activity by two to three times with respect to the enzymatic activity of polymerases ß with (24)Mg(2+) and (26)Mg(2+) ions. Such an isotopic dependence directly indicates that in the DNA synthesis magnetic mass-independent isotope effect functions. Similar effect is exhibited by polymerases ß with Zn(2+) ions carrying magnetic (67)Zn and non-magnetic (64)Zn nuclei, respectively. A new, ion-radical mechanism of the DNA synthesis is suggested to explain these effects. Magnetic field dependence of the magnesium-catalysed DNA synthesis is in a perfect agreement with the proposed ion-radical mechanism. It is pointed out that the magnetic isotope and magnetic field effects may be used for medicinal purposes (trans-cranial magnetic treatment of cognitive deceases, cell proliferation, control of the cancer cells, etc).

The tissue-specific "ferromagnetic attack" on hyperactivation of ATP synthesis by magnesium-25 in mitochondria.

A (25)Mg(2+)-operated hyper-activation of ATP synthesis has been investigated in mitochondria (Mt) isolated from iron-rich and iron-poor rat tissues: spleen, liver, skeletal muscle, myocardium, kidneys, brain. Both magnetic ((25)Mg) and non-magnetic ((24)Mg) magnesium isotopes were separately administered to estimate the degree of the ATP production related to the magnetic isotope effect (MIE) of (25)Mg(2+)as a function of the amount of Mt-endogenous iron ions. A strong but negative (r = -0.88) correlation between the (25)Mg-MIE degree and the Mt[Fe(2+)] values was found. The physical and biophysical mechanisms behind these phenomena, as well as the possible impact of these data on further biochemical and pharmacological studies involving (25)Mg-promoted nuclear spin selectivity in mitochondrial function, are under discussion.

Benefit of magnesium-25 carrying porphyrin-fullerene nanoparticles in experimental diabetic neuropathy.

Diabetic neuropathy (DN) is a debilitating disorder occurring in most diabetic patients without a viable treatment yet. The present work examined the protective effect of (25)Mg-PMC(16) nanoparticle (porphyrin adducts of cyclohexil fullerene-C60) in a rat model of streptozotocin (STZ)-induced DN. (25)Mg-PMC(16) (0.5 lethal dose(50) [LD(50)]) was administered intravenously in two consecutive days before intraperitoneal injection of STZ (45 mg/kg). (24)Mg-PMC(16) and MgCl(2) were used as controls. Blood 2,3-diphosphoglycerate (2,3-DPG), oxidative stress biomarkers, adenosine triphosphate (ATP) level in dorsal root ganglion (DRG) neurons were determined as biomarkers of DN. Results indicated that 2,3-DPG and ATP decreased whereas oxidative stress increased by induction of DN which all were improved in (25)Mg-PMC(16)-treated animals. No significant changes were observed by administration of (24)Mg-PMC(16) or MgCl(2) in DN rats. It is concluded that in DN, oxidative stress initiates injuries to DRG neurons that finally results in death of neurons whereas administration of (25)Mg-PMC(16) by release of Mg and increasing ATP acts protectively.

Ion-radical mechanism of enzymatic ATP synthesis: DFT calculations and experimental control.

A new, ion-radical mechanism of enzymatic ATP synthesis was recently discovered by using magnesium isotopes. It functions at a high concentration of MgCl(2) and includes electron transfer from the Mg(H(2)O)(m)(2+)(ADP(3-)) complex (m = 0-4) to the Mg(H(2)O)(n)(2+) complex as a primary reaction of ATP synthesis in catalytic sites of ATP synthase and kinases. Here, the structures and electron transfer reaction energies of magnesium complexes related to ATP synthesis are calculated in terms of DFT. ADP is modeled by pyrophosphate anions, protonated (HP(2)O(7)H(2-), HP(2)O(7)CH(3)(2-)) and deprotonated (HP(2)O(7)(3-), CH(3)P(2)O(7)(3-)). The reaction generates an ion-radical pair, composed of Mg(H(2)O)(n)(+) ion and pyrophosphate anion-radical coordinated to Mg(2+) ion. The addition of the latter to the substrate P=O bond results in ATP formation. Populations of the singlet and triplet states and singlet-triplet spin conversion in the pair are controlled by hyperfine coupling of unpaired electrons with magnetic (25)Mg and (31)P nuclei and by Zeeman interaction. Due to these two interactions, the yield of ATP is a function of nuclear magnetic moment and magnetic field; both of these effects were experimentally detected. Electron transfer reaction does not depend on m but strongly depends on n. It is exoergic and energy allowed at 0 < or = n << infinity for the deprotonated pyrophosphate anions and at 0 < or = n < 4 for the protonated ones; for other values of n, the reaction is energy deficient and forbidden. The boundary between exoergic and endoergic regimes corresponds to the trigger magnitude n* (n* = 4 for protonated anions and 6 < n* << infinity for deprotonated ones). These results explain why ATP synthesis occurs only in special devices, molecular enzymatic machines, but not in water (n = infinity). Biomedical consequences of the ion-radical enzymatic ATP synthesis are also discussed.

The C60-fullerene porphyrin adducts for prevention of the doxorubicin-induced acute cardiotoxicity in rat myocardial cells.

This is a fullerene-based low toxic nanocationite designed for targeted delivery of the paramagnetic stable isotope of magnesium to the doxorubicin (DXR)-induced damaged heart muscle providing a prominent effect close to about 80% recovery of the tissue hypoxia symptoms in less than 24 hrs after a single injection (0.03 - 0.1 LD50). Magnesium magnetic isotope effect selectively stimulates the ATP formation in the oxygen-depleted cells due to a creatine kinase (CK) and mitochondrial respiratory chain-focusing "attack" of 25Mg2+ released by nanoparticles. These "smart nanoparticles" with membranotropic properties release the overactivating cations only in response to the intracellular acidosis. The resulting positive changes in the energy metabolism of heart cell may help to prevent local myocardial hypoxic (ischemic) disorders and, hence, to protect the heart muscle from a serious damage in a vast variety of the hypoxia-induced clinical situations including DXR side effects.

Non-Markovian Population Dynamics: Does it Help to Optimize the Chemotherapeutic Strategy?

A non-Markovian theory of population dynamics is to simulate the anti-cancer drug distribution between malignant and the hosting normal cell pools. The model takes into account both the cell life span and the proliferation rate differences. This new simulation approach looks promising for its potential to optimize a chemotherapeutic strategy by choosing the scheme with a higher degree of the drug-tumor selectivity. The pre-test designed simulation mode fits nicely the experimental data on Porphylleren-MC16 (PMC16) pharmacokinetics patterns including the allometric plots revealed for this novel medicinal nanoparticle possessing some anti-cancer potential and intervening into the oxygen-independent ATP production mechanisms.

Magnetic field affects enzymatic ATP synthesis.

The rate of ATP synthesis by creatine kinase extracted from V. xanthia venom was shown to depend on the magnetic field. The yield of ATP produced by enzymes with 24Mg2+ and 26Mg2+ ions in catalytic sites increases by 7-8% at 55 mT and then decreases at 80 mT. For enzyme with 25Mg2+ ion in a catalytic site, the ATP yield increases by 50% and 70% in the fields 55 and 80 mT, respectively. In the Earth field the rate of ATP synthesis by enzyme, in which Mg2+ ion has magnetic nucleus 25Mg, is 2.5 times higher than that by enzymes, in which Mg2+ ion has nonmagnetic, spinless nuclei 24Mg or 26Mg. Both magnetic field effect and magnetic isotope effect demonstrate that the ATP synthesis is an ion-radical process, affected by Zeeman interaction and hyperfine coupling in the intermediate ion-radical pair.