Mathematical modeling of a minimal protocell with coordinated growth and division

Self-replication is an essential attribute of life but the molecular-level mechanisms involved are not well understood. Cellular self-replication requires not only duplicating all cellular components and doubling volume and membrane area, but also replicating cellular geometry. A whole-cell modeling framework is presented in which an assumed reaction network determines both concentration changes of cellular components and cell geometry. Cell shape is calculated by minimizing membrane-bending energy. Using this framework, simultaneous doubling of volume, surface area, and all components was found to be insufficient to provide mid-cell “pinching” of the parental cell to form two daughter cells. This prompted the design of a minimal protocell that includes a growing shell, a cell-cycle engine, and a contractile ring to enforce cytokinesis. Kinetic parameters were found such that the system exhibited periodic behavior with fundamental aspects of self-replication. This involved simultaneous doubling of all cellular components during a cell cycle, doubling cell volume and membrane area, achieving periodic changes in surface/volume ratio, and forming daughter cells that were geometrically equivalent to each other and to the “newborn” parental cell. The results presented here impact the design of laboratory protocells and the development of a modular strategy for constructing a comprehensive in silico whole-cell model.     

The combination of transformed and constrained Gibbs energies

Gibbs free energy is the thermodynamic potential representing the fundamental equation at constant temperature, pressure, and molar amounts. Transformed Gibbs energies are important for biochemical systems because the local concentrations within cell compartments cannot yet be determined accurately. The method of Constrained Gibbs Energies adds kinetic reaction extent limitations to the internal constraints of the system thus extending the range of applicability of equilibrium thermodynamics from predefined constraints to dynamic constraints, e.g., adding time-dependent constraints of irreversible chemical change. In this article, the implementation and use of Transformed Gibbs Energies in the Gibbs energy minimization framework is demonstrated with educational examples. The combined method has the advantage of being able to calculate transient thermodynamic properties during dynamic simulation.     

On the estimation of robustness and filtering ability of dynamic biochemical networks under process delays, internal parametric perturbations and external disturbances

Inherently, biochemical regulatory networks suffer from process delays, internal parametrical perturbations as well as external disturbances. Robustness is the property to maintain the functions of intracellular biochemical regulatory networks despite these perturbations. In this study, system and signal processing theories are employed for measurement of robust stability and filtering ability of linear and nonlinear time-delay biochemical regulatory networks. First, based on Lyapunov stability theory, the robust stability of biochemical network is measured for the tolerance of additional process delays and additive internal parameter fluctuations. Then the filtering ability of attenuating additive external disturbances is estimated for time-delay biochemical regulatory networks. In order to overcome the difficulty of solving the Hamilton Jacobi inequality (HJI), the global linearization technique is employed to simplify the measurement procedure by a simple linear matrix inequality (LMI) method. Finally, an example is given in silico to illustrate how to measure the robust stability and filtering ability of a nonlinear time-delay perturbative biochemical network. This robust stability and filtering ability measurement for biochemical network has potential application to synthetic biology, gene therapy and drug design.     

An apoptosis-inducing serine protease secreted by the entomopathogenic nematode Steinernema carpocapsae

Steinernema carpocapsae is an insect parasitic nematode able to parasitise and kill the host within 48 h. Secreted products (ESP) of the parasitic stage of a virulent strain contain higher amounts of proteolytic activity than a low virulence strain, suggesting proteases are involved in virulence. From the ESP we purified a protein (Sc-SP-3) with a M_r of 30 kDa and a pI of 7 that cleaved the synthetic substrate N-succinyl-Ala-Ala-Pro-Phe-pNA and was inhibited by phenylmethanesulfonyl fluoride, benzamidine and chymostatin, thus indicating that it belongs to the chymotrypsin-like serine protease family. Sc-SP-3 has a V_max of 0.3 mM min⁻¹ ml⁻¹ and K_m of 6.6 × 10⁻⁴ M, with maximum activity at pH 8 and 40 °C. The full-length cDNA was obtained using degenerate oligonucleotides for serine proteases. This open reading frame encodes a preproprotein containing a putative signal peptide composed of 16 amino acid residues, a prodomain of 40 residues and a mature protease domain of 261 residues, including the catalytic triad His/Asp/Ser characteristic of trypsin-like serine proteases. The N-terminal sequence and the peptide masses fingerprint obtained by MALDI-TOF–MS for the purified protein matched the cDNA. Gene expression analysis by quantitative real-time-PCR showed that this gene is expressed only during the parasitic stage and that pre-invasive nematodes inside the mid-gut expressed higher amounts of Sc-SP-3 than those that already enter the haemocoel. Sc-SP-3 caused histolysis in the insect mid-gut. In vitro assays demonstrated that Sc-SP-3 digested extracellular proteins and induced apoptosis in Sf9 insect cells, thus suggesting Sc-SP-3 is a multifunctional chymotrypsin-like protease involved in pathogenesis.     

An evaluation of the Oxoid Biochemical Identification System Campy rapid screening test for Campylobacteraceae and Helicobacter spp.

Aims:  To evaluate the Oxoid Biochemical Identification System (OBIS) Campy test (ID0800M) against Campylobacter ; Arcobacter ; and other micro-organisms, with similar colonial morphology, for the detection of l -alanine aminopeptidase ( l -ALA).
Methods and Results:  The KOH and l -ALA (OBIS and Fluka) tests were carried out on every isolate. The procedures were followed as indicated in the OBIS and Fluka kit instructions. A total of 146 strains of 19 species of Campylobacter , seven strains of Arcobacter butzleri , four Arcobacter butzleri -like strains, 42 strains of 10 species of Helicobacter , 96 Gram-negative and 49 Gram-positive clinical isolates were tested. As expected, Campylobacter and Arcobacter strains were negative, while other Gram-negative bacteria were positive for the l -ALA test. An unexpected finding was that Helicobacter strains, although Gram-negative, were all negative for the l -ALA tests suggesting the absence of l -ALA within this genus. This is a novel finding. The absence of l -ALA was confirmed upon comparison with the available full genomic sequences of Helicobacter on the NCBI database.
Conclusions:  The OBIS Campy (ID0800M) test kit proved to be rapid and accurate for the presumptive characterization of Campylobacter and Arcobacter . A novel finding was that Helicobacter species also did not have the l -ALA enzyme.
Significance and Impact of the Study:  The OBIS kit will be useful in diagnostic laboratories for the presumptive diagnosis of Campylobacter , Arcobacter and Helicobacter strains.     

Timing matters

Cells are entities in space and time. Systems biology strives to understand their composition, structural organization as well as dynamic behavior under different conditions. Here, measures for dynamic properties such as characteristic times, time hierarchy and time-dependent response are reviewed. Using a number of examples from yeast and micro-organism systems biology, the importance of considering the timing in experimental and theoretical research is discussed.     

封闭群斑马鱼的遗传生化标记研究

目的通过对AB、LF、ST（short tail,本地短尾群）三个封闭群斑马鱼的研究比较,建立封闭群斑马鱼的遗传生化标记。方法依照国标GB／T14927.1-2008的遗传操作规程优化实验条件,对三种群斑马鱼的7个遗传生化位点进行研究,以得到其遗传生化图谱。结果6-磷酸葡萄糖脱氢酶（Gpd）、过氧化氢酶（Ce）、苹果酸脱氢酶（Mod）、葡萄糖磷酸异构酶（Gpi）、酯酶（ES）位点表现出多态性。对三种群多态性位点进行卡方分析,Gpd、Gpi位点群间差异显著（P〈0.01）,Ce、Mod有群间差异（P〈0.05）。碱性磷酸酶（AKP）、乳酸脱氢酶（LDH）位点,各品系谱带较一致,未见同工酶多态性。结论Gpd、Ce、Mod、Gpi、ES可作为3种封闭群斑马鱼群间评价的生化标记,通过进一步研究,可建立封闭群斑马鱼的遗传标准。     

Headspace analyses of acetone: A rapid method for measuring the H-labeling of water

Measurements of a ²H-labeling of water in biological fluids are required for determining the rates of biochemical flux and for estimating body composition. We have been using the method which relies on the base-catalyzed exchange of hydrogen (deuterium) between water and acetone. ²H-labeling of acetone is then determined using GCMS. Although not noted in the original paper, when chloroform is used to extract the acetone there is slow but substantial backexchange between [²H]acetone and solvent (unpublished observations). We report herein on a refinement of the assay that utilizes headspace analysis, which minimizes the number of transfers and decreases sample preparation time and instrument run time.     

Patients with Leber hereditary optic neuropathy fail to compensate impaired oxidative phosphorylation

Ninety-five percent of Leber hereditary optic neuropathy (LHON) patients carry a mutation in one out of three mtDNA-encoded ND subunits of complex I. Penetrance is reduced and more male than female carriers are affected. To assess if a consistent biochemical phenotype is associated with LHON expression, complex I- and complex II-dependent adenosine triphosphate synthesis rates (CI-ATP, CII-ATP) were determined in digitonin-permeabilized peripheral blood mononuclear cells (PBMCs) of thirteen healthy controls and for each primary mutation of a minimum of three unrelated patients and of three unrelated carriers with normal vision and were normalized per mitochondrion (citrate synthase activity) or per cell (protein content). We found that in mitochondria, CI-ATP and CII-ATP were impaired irrespective of the primary LHON mutation and clinical expression. An increase in mitochondrial density per cell compensated for the dysfunctional mitochondria in LHON carriers but was insufficient to result in a normal biochemical phenotype in early-onset LHON patients.     

Isolation and biochemical characterization of laccase and tyrosinase activities in a novel melanogenic soil bacterium

Bacterial polyphenol oxidases (PPOs) with a high oxidizing capacity for a wide range of substrates could make their applications in phenolic biotransformation, food processing, cosmetics, and textile industry. We have isolated a melanogenic soil bacterium by differential screening of a number of strains which were isolated from the Iranian microflora. The taxonomic characterization of this strain indicates that it belongs to the genus Bacillus (HR03), and has the ability to produce all types of PPOs; cresolase (EC 1.14.18.1), cathecolase (EC.1.10.3.1), and laccase (EC 1.10.3.2). We studied the tyrosinase activity using l-tyrosine and l-dopa as substrates and the laccase activity with specific substrates such as syringaldazine and 2,6-dimethoxyphenol. The optimum pH and temperature, obtained for all types of polyphenol oxidases, were at about pH 5.5 and 55 °C, respectively. Tyrosinase-like enzyme of this strain shows a lag period in its tyrosine hydroxylase activity that could be avoided by the addition of small amounts of l-dopa and sodium dodecyl sulfate (SDS). In addition, tyrosinase and laccase were activated by SDS below the critical micelle concentration and were inhibited by 1 mM EDTA. We tested the resistance of melanized-cells against UVA, UVC and H₂O₂. Results show that melanin protects strain HR03 against UV lights and the oxidant.