A catalytically active oscillator made from small organic molecules

Oscillatory systems regulate many biological processes, including key cellular functions such as metabolism and cell division, as well as larger-scale processes such as circadian rhythm and heartbeat1-4. Abiotic chemical oscillations, discovered originally in inorganic systems5,6, inspired the development of various synthetic oscillators for application as autonomous time-keeping systems in analytical chemistry, materials chemistry and the biomedical field7-17. Expanding their role beyond that of a pacemaker by having synthetic chemical oscillators periodically drive a secondary function would turn them into significantly more powerful tools. However, this is not trivial because the participation of components of the oscillator in the secondary function might jeopardize its time-keeping ability. We now report a small molecule oscillator that can catalyse an independent chemical reaction in situ without impairing its oscillating properties. In a flow system, the concentration of the catalytically active product of the oscillator shows sustained oscillations and the catalysed reaction is accelerated only during concentration peaks. Augmentation of synthetic oscillators with periodic catalytic action allows the construction of complex systems that, in the future, may benefit applications in automated synthesis, systems and polymerization chemistry and periodic drug delivery.

History Dependence in a Chemical Reaction Network Enables Dynamic Switching

This work describes an enzymatic autocatalytic network capable of dynamic switching under out-of-equilibrium conditions. The network, wherein a molecular fuel (trypsinogen) and an inhibitor (soybean trypsin inhibitor) compete for a catalyst (trypsin), is kept from reaching equilibria using a continuous flow stirred tank reactor. A so-called 'linear inhibition sweep' is developed (i.e., a molecular analogue of linear sweep voltammetry) to intentionally perturb the competition between autocatalysis and inhibition, and used to demonstrate that a simple molecular system, comprising only three components, is already capable of a variety of essential neuromorphic behaviors (hysteresis, synchronization, resonance, and adaptation). This research provides the first steps in the development of a strategy that uses the principles in systems chemistry to transform chemical reaction networks into platforms capable of neural network computing.

Dynamic Environments as a Tool to Preserve Desired Output in a Chemical Reaction Network

Current efforts to design functional molecular systems have overlooked the importance of coupling out-of-equilibrium behaviour with changes in the environment. Here, the authors use an oscillating reaction network and demonstrate that the application of environmental forcing, in the form of periodic changes in temperature and in the inflow of the concentration of one of the network components, removes the dependency of the periodicity of this network on temperature or flow rates and enforces a stable periodicity across a wide range of conditions. Coupling a system to a dynamic environment can thus be used as a simple tool to regulate the output of a network. In addition, the authors show that coupling can also induce an increase in behavioural complexity to include quasi-periodic oscillations.

Early warning signals in chemical reaction networks

Many natural and man-made complex systems display early warning signals when close to an abrupt shift in behaviour. Here we show that such early warning signals appear in a complex chemical reaction network.

Robustness, Entrainment, and Hybridization in Dissipative Molecular Networks, and the Origin of Life

How simple chemical reactions self-assembled into complex, robust networks at the origin of life is unknown. This general problem-self-assembly of dissipative molecular networks-is also important in understanding the growth of complexity from simplicity in molecular and biomolecular systems. Here, we describe how heterogeneity in the composition of a small network of oscillatory organic reactions can sustain (rather than stop) these oscillations, when homogeneity in their composition does not. Specifically, multiple reactants in an amide-forming network sustain oscillation when the environment (here, the space velocity) changes, while homogeneous networks-those with fewer reactants-do not. Remarkably, a mixture of two reactants of different structure-neither of which produces oscillations individually-oscillates when combined. These results demonstrate that molecular heterogeneity present in mixtures of reactants can promote rather than suppress complex behaviors.

Photochemical Control over Oscillations in Chemical Reaction Networks

Systems chemistry aims to emulate the functional behavior observed in living systems by constructing chemical reaction networks (CRNs) with well-defined dynamic properties. Future expansion of the complexity of these systems would require external control to tune behavior and temporal organization of such CRNs. In this work, we design and implement a photolabile probe, which upon irradiation strengthens the negative feedback loop of a CRN that produces oscillations of trypsin under out-of-equilibrium conditions. By changing the timing and duration of irradiation, we can tailor the temporal response of the network.

Grip on complexity in chemical reaction networks

A new discipline of "systems chemistry" is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior.

Molecular Engineering of Robustness and Resilience in Enzymatic Reaction Networks

Living systems rely on complex networks of chemical reactions to control the concentrations of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. One of the greatest challenges in chemistry is the creation of such functionality from chemical reactions. A key limitation is our lack of understanding of how molecular structure impacts on the dynamics of chemical reaction networks, preventing the design of networks that are robust (i.e., function in a large parameter space) and resilient (i.e., reach their out-of-equilibrium function rapidly). Here we demonstrate that reaction rates of individual reactions in the network can control the dynamics by which the system reaches limit cycle oscillations, thereby gaining information on the key parameters that govern the dynamics of these networks. We envision that these principles will be incorporated into the design of network motifs, enabling chemists to develop "molecular software" to create functional behavior in chemical systems.

Rational design of functional and tunable oscillating enzymatic networks

Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

High frequency of polyoma BK virus shedding in the gastrointestinal tract after hematopoietic stem cell transplantation: a prospective and quantitative analysis

The polyoma BK virus (BKV) remains latent after primary infection and may reactivate during immunosuppression. The uroepithelium is the main latency site defined. This study addressed whether the gastrointestinal tract might be another latency site. To test this hypothesis, we prospectively quantified fecal BKV by quantitative PCR reaction in 40 patients undergoing hematopoietic SCT (HSCT). Urinary BKV was similarly quantified. Fecal BKV excretion was positive in 16/40 patients, of whom 10 were transient (<3 consecutively positive samples), six were persistent (⩾3 consecutively positive samples) and three were persistent with peaking (⩾10³-fold increase in viral load over baseline, reaching 5.11 × 10⁶, 4.68 × 10⁷ and 2.75 × 10⁸ copies/sample at 14, 14 and 21 days post-HSCT, respectively). Urinary BKV excretion was positive in 25/40 patients. Fecal BKV excretion was significantly correlated with that of the urine (P=0.036) and was significantly associated with allogeneic HSCT (P=0.037) and persistent and peaking of urinary BKV excretion (P<0.001). Binary logistic regression showed that BKV viruria was the only significant risk factor for fecal BKV excretion (P=0.021). Fecal BKV excretion occurred in 40% patients undergoing HSCT, implicating the gastrointestinal tract as a BKV latency site.

High frequency of polyoma BK virus shedding in the gastrointestinal tract after hematopoietic stem cell transplantation: a prospective and quantitative analysis

The polyoma BK virus (BKV) remains latent after primary infection and may reactivate during immunosuppression. The uroepithelium is the main latency site defined. This study addressed whether the gastrointestinal tract might be another latency site. To test this hypothesis, we prospectively quantified fecal BKV by quantitative PCR reaction in 40 patients undergoing hematopoietic SCT (HSCT). Urinary BKV was similarly quantified. Fecal BKV excretion was positive in 16/40 patients, of whom 10 were transient (<3 consecutively positive samples), six were persistent (> or =3 consecutively positive samples) and three were persistent with peaking (> or =10(3)-fold increase in viral load over baseline, reaching 5.11 x 10(6), 4.68 x 10(7) and 2.75 x 10(8) copies/sample at 14, 14 and 21 days post-HSCT, respectively). Urinary BKV excretion was positive in 25/40 patients. Fecal BKV excretion was significantly correlated with that of the urine (P=0.036) and was significantly associated with allogeneic HSCT (P=0.037) and persistent and peaking of urinary BKV excretion (P<0.001). Binary logistic regression showed that BKV viruria was the only significant risk factor for fecal BKV excretion (P=0.021). Fecal BKV excretion occurred in 40% patients undergoing HSCT, implicating the gastrointestinal tract as a BKV latency site.

Metabolic studies of turinabol in horses

Turinabol (4-chloro-17alpha-methyl-17beta-hydroxy-1,4-androstadien-3-one) is a synthetic oral anabolic androgenic steroid. As in the case of other anabolic steroids, it is a prohibited substance in equine sports. The metabolism of turinabol in human has been reported previously; however, little is known about its metabolic fate in horses. This paper describes the studies of both the in vitro and in vivo metabolism of turinabol in racehorses with an objective to identify the most appropriate target metabolites for detecting turinabol administration. For the in vitro studies, turinabol was incubated with fresh horse liver microsomes. Metabolites in the incubation mixture were isolated by liquid-liquid extraction and analysed by gas chromatography-mass spectrometry (GC-MS) after trimethylsilylation. The results showed that the major biotransformation of turinabol was hydroxylation at the C6, C16 and C20 sites to give metabolites 6beta-hydroxyturinabol (M1), 20-hydroxyturinabol (M2), two stereoisomers of 6beta,16-dihydroxyturinabol (M3a, M3b) and 6beta,20-dihydroxyturinabol (M4). The metabolite 6beta-hydroxyturinabol was confirmed using an authentic reference standard. The structures of all other turinabol metabolites were tentatively identified by mass spectral interpretation. For the in vivo studies, two horses were administered orally with turinabol. Pre- and post-administration urine samples were collected for analysis. Free and conjugated metabolites were isolated using solid-phase extraction and analysed by GC-MS as described for the in vitro studies. The results revealed that turinabol was extensively metabolised and the parent drug was not detected in urine. Two metabolites detected in the in vitro studies, namely 20-hydroxyturinabol and 6beta,20-dihydroxyturinabol, these were also detected in post-administration urine samples. In addition, 17-epi-turinabol (M5) and six other metabolites (M6a-M6c and M7a-M7c), derived from D-ring hydroxylation and A-ring reduction, were also detected. Except for 17-epi-turinabol, none of these metabolites has ever been reported in any species. All in vivo metabolites were detected within 48 h after administration.

Epigenetic inactivation of the CIP/KIP cell-cycle control pathway in acute leukemias

Dysregulation of the cell cycle is important in oncogenesis. We analyzed the potential inactivation of the CIP/KIP family of the cyclin E/CDK/RB pathway by gene promoter hypermethylation in leukemias. The methylation-specific polymerase chain reaction (MSP) with primers for methylated (M-MSP) and unmethylated (U-MSP) alleles of the p21, p27, and p57 genes was used to study five leukemic cell lines, 50 acute myeloid leukemia (AML) samples, and 25 acute lymphoblastic leukemia (ALL) samples. p21 was hemizygously methylated in Raji and Jurkat but remained unmethylated in U937, HL60, and NB4. p27 was hemizygously methylated in Raji but unmethylated in the other cell lines. p57 was completely methylated in Raji and NB4, hemizygously methylated in U937, and unmethylated in HL60 and Jurkat. At diagnosis, p21 methylation was not detected in any case of AML or ALL. p27 methylation occurred in 2 (4%) AML patients and in 1 (4%) ALL patient. p57 methylation occurred in 1 (2%) AML patient and in 1 (4%) ALL patient. Therefore, methylation inactivation of the INK4/CDK/RB pathway in leukemia is infrequent. A review of the literature showed a marked variation in the frequencies of methylation of these genes, which might be attributable to difference in methodologies used to detect gene methylation.

Absence of p300 gene promoter methylation in acute leukemia

p300 is a widely expressed transcriptional coactivator, and is involved in DNA repair, cell growth, differentiation, and apoptosis. Recent data suggest that it may function as a tumor suppressor. We investigated the frequency of aberrant methylation of p300 promoter in seven leukemic cell lines, as well as in the diagnostic samples of 46 patients with acute myelocytic leukemia (11 with M1, 22 with M2, 3 with M4, and 1 with M5), 24 patients with acute promyelocytic leukemia, and 22 patients with acute lymphoblastic leukemia (3 with T-cell, 1 with pre-B, 2 with Burkitt, 2 with early B-precursors, and 14 with common). None of the cell lines and patient samples showed p300 gene methylation. Therefore, hypermethylation of p300 is not an important mechanism in leukemogenesis.

Supplementary oxygen for elective Caesarean section under spinal anaesthesia: useful in prolonged uterine incision-to-delivery interval? †

BACKGROUND

The benefit of administering supplementary oxygen during elective Caesarean section under regional anaesthesia is controversial. It has been hypothesized that its use would improve fetal oxygenation in the event of a prolonged uterine incision-to-delivery (U-D) interval. Our aim was to test this hypothesis in a prospective, randomized, double-blinded, controlled study.

METHODS

We allocated randomly 204 women having elective Caesarean section under spinal anaesthesia to breathe 21, 40 or 60% oxygen. We recorded the U-D interval, umbilical arterial (UA) and venous (UV) blood gases and oxygen content and Apgar scores. Subgroup analysis was performed according to whether the U-D interval was prolonged (>180 s) or not.

RESULTS

The U-D interval was <180 s in 159 patients and >180 s in 45 patients. There were no differences in UV or UA blood gases, oxygen content or Apgar scores between cases with and without a prolonged U-D interval. In cases without a prolonged U-D interval, administering 60% oxygen increased UV PO(2) (mean 4.3 (SD 1.1) vs 3.7 (1.0) kPa, P=0.003) and oxygen content (14.4 (3.3) vs 12.9 (2.7) ml dl(-1), P=0.007) compared with air. In cases with a prolonged U-D interval, administering 60% oxygen increased UV PO(2) (4.6 (0.6) vs 3.9 (0.8) kPa, P=0.019) compared with air but there was no difference in UV oxygen content. There was no increase in the UV PO(2) or oxygen content when 40% oxygen was administered compared with air.

CONCLUSIONS

Supplementary oxygen did not increase fetal oxygenation in cases where the U-D interval was prolonged. Our data do not support the routine administration of supplementary oxygen during elective Caesarean section for this purpose.

Epigenetic dysregulation of the Jak/STAT pathway by frequent aberrant methylation of SHP1 but not SOCS1 in acute leukaemias

SOCS1 and SHP1 are negative regulators of the Jak/STAT signalling pathway that is implicated in leukaemogenesis. We studied if aberrant methylation of SOCS1 and SHP1 might be involved in the pathogenesis and prognostication of acute leukaemias by methylation-specific polymerase chain reaction (MSP). At diagnosis, methylation of SHP1 occurred more frequently in acute myeloid leukaemia (AML) (n=26, 52%) than acute lymphoblastic leukaemia (ALL) (n=6, 24%) (p=0.02). Methylation of SOCS1 was absent in both AML and ALL patients. SHP1 methylation was not associated with specific clinicopathologic features and had no prognostic impact on AML patients. Frequent methylation of SHP1, but not SOCS1, may be important in the pathogenesis, but not prognosis, of acute leukaemias.

Epigenetic inactivation of INK4/CDK/RB cell cycle pathway in acute leukemias

Dysregulation of cell cycle is important in oncogenesis. We analyzed the inactivation of the INK4 family CKI/CDK/RB pathway by gene promoter hypermethylation in leukemogenesis. The methylation-specific polymerase chain reaction (MSP) with primers for methylated (M-MSP) and unmethylated (U-MSP) alleles of the p15, p16, p18, and RB genes was used to study five leukemic cell lines, 50 acute myeloid leukemia (AML) and 25 acute lymphoblastic leukemia (ALL) samples. None of the leukemic cell lines showed p18 and RB methylation. p15 was methylated in Raji, while p16 was methylated in U937 and Raji. In NB4 and Jurkat, both alleles of p15 and p16 appeared to be deleted. At diagnosis, p15 methylation occurred in 29 (58%) AML patients, and 10 (40.0%) ALL patients. p16 methylation occurred in two (4%) AML and two (8%) ALL patients. Only one each of AML and ALL patients had concurrent p15 and p16 methylation. None of the patients had methylation of p18 or RB. In AML, p15 methylation was associated with M2 subtype ( p=0.018). Patients with and without p15 methylation had similar complete remission (CR) rates and projected 5-year overall survival (OS) or disease-free survival (DFS). Therefore, methylation inactivation of the INK4/CDK/RB pathway in leukemia involved primarily p15 and occasionally p16, but not p18 or RB. In AML, p15 gene methylation was associated with the M2 subtype, but was not prognostic for CR, OS, or DFS.

Infrequent hypermethylation of CEBPA promotor in acute myeloid leukaemia

The gene CEBPA, encoding the transcription factor C/EBPalpha, is crucial for granulocyte differentiation. We investigated the frequency of aberrant CEBPA promotor methylation with the methylation-specific polymerase chain reaction in 70 patients with acute myeloid leukaemia (AML). Two patients, both with M2 morphology, were found to have methylated CEBPA. In one of them, the fusion gene AML1/ETO, reported to cause transcription repression of CEBPA, was also present, suggesting that more than one mechanism might collaborate to suppress CEBPA gene expression. Aberrant CEBPA methylation is infrequent in AML, but may occur preferentially in the M2 phenotype.

Randomized, double-blind comparison of different inspired oxygen fractions during general anaesthesia for Caesarean section

BACKGROUND

The optimal inspired oxygen fraction FI(O(2)) for fetal oxygenation during general anaesthesia for Caesarean section is not known.

METHODS

We randomized patients having elective Caesarean section to receive one of the following: FI(O(2)) 0.3, FI(N(2))(O) 0.7 and end-tidal sevoflurane 0.6% (Group 30, n=20); FI(O(2)) 0.5, FI(N(2))(O) 0.5 and end-tidal sevoflurane 1.0% (Group 50, n=20), or FI(O(2)) 1.0 and end-tidal sevoflurane 2.0% (Group 100, n=20) until delivery. Neonatal outcome was compared biochemically and clinically.

RESULTS

At delivery, for umbilical venous blood, mean PO(2) was greater in Group 100 (7.6 (SD 3.7) kPa) compared with both Group 30 (4.0 (1.1) kPa, P<0.0001) and Group 50 (4.7 (0.9) kPa, P=0.002) and oxygen content was greater in Group 100 (17.2 (1.6) ml dl(-1)) compared with both Group 30 (12.8 (3.6) ml dl(-1), P=0.0001) and Group 50 (13.8 (2.6) ml dl(-1), P=0.0001). For umbilical arterial blood, PO(2) was greater in Group 100 (3.2 (0.4) kPa) compared with Group 30 (2.4 (0.7) kPa, P=0.003), and in Group 50 (2.9 (0.8) kPa) compared with Group 30 (2.4 (0.7) kPa, P=0.04); oxygen content was greater in Group 100 (10.8 (3.5) ml dl(-1)) than in Group 30 (7.0 (3.0) ml dl(-1), P<0.01). Apgar scores, neonatal neurologic and adaptive capacity scores, and maternal arterial plasma concentrations of epinephrine and norepinephrine before induction and at delivery were similar among groups. No patient reported intraoperative awareness.

CONCLUSIONS

Use of FI(O(2)) 1.0 during general anaesthesia for elective Caesarean section increased fetal oxygenation.