Computer‐aided biochemical programming of synthetic microreactors as diagnostic devices

Biological systems have evolved efficient sensing and decision‐making mechanisms to maximize fitness in changing molecular environments. Synthetic biologists have exploited these capabilities to engineer control on information and energy processing in living cells. While engineered organisms pose important technological and ethical challenges, de novo assembly of non‐living biomolecular devices could offer promising avenues toward various real‐world applications. However, assembling biochemical parts into functional information processing systems has remained challenging due to extensive multidimensional parameter spaces that must be sampled comprehensively in order to identify robust, specification compliant molecular implementations. We introduce a systematic methodology based on automated computational design and microfluidics enabling the programming of synthetic cell‐like microreactors embedding biochemical logic circuits, or protosensors, to perform accurate biosensing and biocomputing operations in vitro according to temporal logic specifications. We show that proof‐of‐concept protosensors integrating diagnostic algorithms detect specific patterns of biomarkers in human clinical samples. Protosensors may enable novel approaches to medicine and represent a step toward autonomous micromachines capable of precise interfacing of human physiology or other complex biological environments, ecosystems, or industrial bioprocesses.     

Optimization in integrated biochemical systems

As of yet, steady-state optimization in biochemical systems has been limited to a few studies in which networks of fluxes were optimized. These networks of fluxes are represented by linear (stoichiometric) equations that are used as constraints in a linear program, and a flux or a sum of weighted fluxes is used as the objective function. In contrast to networks of fluxes, systems of metabolic processes have not been optimized in a comparable manner. The primary reason is that these types of integrated biochemical systems are full of synergisms, antagonisms, and regulatory mechanisms that can only be captured appropriately with nonlinear models. These models are mathematically complex and difficult to analyze. In most cases it is not even possible to compute, let alone optimize, steady-state solutions analytically. Rare exceptions are S-system representations. These are nonlinear and able to represent virtually all types of dynamic behaviors, but their steady states are characterized by linear equations that can be evaluated both analytically and numerically. The steady-state equations are expressed in terms of the logarithms of the original variables, and because a function and its logarithms of the original variables, and because a function and its logarithm assume their maxima for the same argument, yields or fluxes can be optimized with linear programs expressed in terms of the logarithms of the original variables. (c) 1992 John Wiley & Sons, Inc.     

Indole alkaloids as systematic markers of the Apocynaceae

Indole alkaloids can be characterized by skeletal specialization (S), determined upon consideration of their relative position on a biogenetic map and the number of their naturally occurring substitutional derivatives, as well as by oxidation level (O). The mean (S) and (O) for contained alkaloids of a given plant taxon are taken to represent evolutionary advancement parameters, respectively EA_s and EA_o.A correlation of these EA_s/EA_o values for tribes of the Apocynaceae-Plumerioideae reveals a chemical gradient, given by gradually increasing EA_s and EA_o values, to link Carisseae-Alstonieae-Rauvolfieae-Tabernaemontaneae.     

TDZ研究进展(综述)

TDZ在组培中应用广泛,植物中许多生理生化现象受TDZ影响。近年来研究初步表明,TDZ是通过调节内源激素起作用,或是诱导胁迫的结果。本文综述TDZ作用机理的研究进展。     

Quinolizidine alkaloids as systematic markers of the papilionoideae

The structural characteristics of quinolizidine alkaloids have been quantified on the basis of their biogenetic origins. Such data have been used to determine evolutionary advancement parameters for genera of the Papilionoideae. These analyses indicate a correlation of the structural characters of alkaloids with ecogeography and morphology of the genera, suggesting an adaptive radiation of the taxa from tropical Africa in three major directions along a southern temperate “pre-cytisine” route, a northern temperatre “pre-cytisine-cytisine” route and a tropical “ormosanine” route with a temperate cytisine branch. The data also suggest the division of the Sophoreae into three chemical groups giving rise to Liparieae, Genisteae, Thermopsideae and Bossiaeeae. These concepts are embodied in a tentative phyletic classification of all genera of the Papilionoideae which contain quinolizidine alkaloids.     

Inactivation of bacterial opportunistic skin pathogens by nonthermal DC-operated afterglow atmospheric plasma

Aims: Multidrug‐resistant opportunistic pathogens are clinically significant and require the development of new antimicrobial methods. In this study, Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus cells were exposed to atmospheric plasma on agar plates and in vitro on porcine skin for the purpose of testing bacterial inactivation. Methods and Results: Microbial inactivation at varying exposure durations was tested using a nonthermal plasma jet generated with a DC voltage from ambient air. The observed reduction in colony forming units was quantified as log₁₀ reductions. Conclusions: Direct plasma exposure significantly inactivated seeded bacterial cells by approx. 6 log₁₀ on agar plates and 2–3 log₁₀ on porcine skin. On agar plates, an indirect ‘bystander’ inactivation outside the plasma delivery area was also observed. The reduced inactivation observed on the skin surface was most likely due to cell protection by the variable surface architecture. Significance and Impact of Study: Atmospheric plasma has potential for clinical application as a disinfectant of patient skin and medically relevant surfaces.     

Genetic regulation of flavonoid content in seeds and seedlings of Melilotus alba

Chemical analysis of seeds and seedlings of the CC and cc genotypes in Melilotus alba indicated that these alleles affect flavonoid biosynthesis. The CC seed coats contained orientin and iso-orientin, which were absent in the cc seed coats. The pigment responsible for the red pigmentation of young seedlings of CC genotypes was a cyanidin glycoside. The embryos of seeds of both the CC and cc genotypes contained a flavonoid tentatively identified as a 6,8-di-C-pentosylapigenin. The observation that 3′,4′-dihydroxyflavonoids were absent in the cc genotype and that 4′-hydroxyflavonoids were present in both genotypes indicated that the C/c alleles controlled the 3′-hydroxylation of flavonoids. The C/c alleles did not, however, control 3′-hydroxylation of cinnamic acids since caffeic acid was detected in both genotypes.     

Biochemical markers of three strains derived from Japanese wild mouse (Mus musculus molossinus)

Twenty-eight biochemical markers were examined in three strains (Mol-A, Mol-N and Mol-T) derived from the Japanese wild mouse, Mus musculus molossinus, as well as five laboratory strains, Mus musculus musculus. The Mol strains showed specific alleles at as many as 12 loci. These findings emphasize that the Mol strains have significance in future genetic and developmental studies.     

Different exposure methods to neonicotinoids influenced biochemical characteristics in cotton aphid,Aphis gossypii Glover (Hemiptera:Aphididae)

We measured lipid, carbohydrate and protein content in three strains of cotton aphid, Aphis gossypii (Hemiptera: Aphididae) from very resistant to neonicotinoids up to semi sensitive and sensitive strains in different exposure method of spraying to neonicotinoids. We observed changes in energy source rates at which each substrate was metabolised under starvation, selection and residue stress method spraying that assist in metabolisation of their biochemical parameters. These particular exposure methods influenced some of biochemical parameters in cotton aphid. Results indicated that Sugar, glycogen, total protein and lipid in aphids have significant changes. Studies showed that among three strains called Ag-R, Ag-M and Ag-D which have different susceptibilities to neonicotinoids, strain Ag-R was the most tolerated aphids in counter of imidacloprid and thiametoxam, strain Ag-D was somewhat more tolerated to these insecticides and strain Ag-M was the most sensitive strain which has the resistance factor of nearly 890 in starvation method and was different depending on the method of exposure. Among energy sources, the total lipid in susceptible strain were decreasing more than resistant strain, whereas total proteins were increasing in resistant strain compared with sensitive strain. Total Glycogen was affected significantly in the stress condition which caused an increase and was the most resistant strain.     

Age-specific reference intervals for routine biochemical parameters in healthy neonates,infants, and young children in Iran

Age and sex need to be considered in the establishment of reference intervals (RIs), especially in early life when there are dynamic physiological changes. Since data for important biomarkers in healthy neonates and infants are limited, particularly in Iranian populations, we have determined age-specific RIs for 7 laboratory biochemical parameters. This cross-sectional study comprised a total of 344 paediatric participants (males: 158, females: 186) between the ages of 3 days and 30 months (mean age: 12.91 ± 7.15 months). Serum levels of creatinine, urea, uric acid, calcium, phosphate, vitamin D and high-sensitivity C-reactive protein (hs-CRP) were measured using an Alpha classic-AT plus auto-analyser. We determined age-specific RIs using CLSI Ep28-A3 and C28-A3 guidelines. No sex partitioning was required for any of the biomarkers. Age partitioning was required for kidney function tests and phosphate. The serum concentration of urea and creatinine increased with age, while phosphate and uric acid decreased with age. Age partitioning was not required for serum calcium, vitamin D, and hs-CRP, which remained relatively constant throughout the age range. Age-specific RIs for 7 routine biochemical markers were determined to address critical gaps in RIs in early life to help improve clinical interpretation of blood test results in young children, including neonates. Established age partitions demonstrate the biochemical changes that take place during child growth and development. These novel data will ultimately better disease management in the Iranian paediatric population and can be of value to clinical and hospital laboratories with similar populations.     

Linkage between amylase-1 locus and a major gene for milk fat content in cattle

Summary
Linkage between the amylase-1 ( Am-1 ) locus and a quantitative trait locus influencing fat content in milk was studied in offspring from heterozygous sires of the Swedish Red and White dairy breed. The effect on bull breeding values for fat content was estimated as interactions between sire and paternal Am-1 allele using a model eliminating the direct effects of sire and Am-1 allele. There were strong indications of linkage, confirming results of previous studies. The interaction was caused by strong associations in 7 out of 14 sire families. A test for within-family variance heterogeneity performed on the whole population of breeding bulls also supported the presence of a major gene for fat content in milk. The results indicate that there is genetic linkage between the Am-1 locus and a locus with large effect on milk fat content.     

Characterization of 1,4-benzoquinone reductase from bovine liver

1,4-Benzoquinone reductase was purified to electrophoretic homogeneity from bovine liver, and the purified enzyme found to have a molecular mass of 29 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme exhibited pH optimum between 8.0 and 8.5. The apparentK _m for 1,4-benzoquinone was 1.643 mM, and the apparent Km for NADH was 1.837 mM. Various divalent cations, such as Hg²⁺, Cu²⁺, and Zn²⁺, exhibited strong inhibitory effects. The enzyme activity was also strongly inhibited by quercetin, dicumarol, and benzoic acid. Incubation of the enzyme withN-bromosuccinimide and pyridoxal 5′-phosphate led to inhibitions of 100% and 99%, respectively. Accordingly, these results suggest that tryptophan and lysine residues are involved at or near the active sites of the enzyme.     

昆虫耐寒性研究

昆虫是变温动物,气候变化是造成种群季节消长的基本原因之一。尤其在不良的低温环境中,昆虫耐寒力的高低是其种群存在与发展的种要前提,昆虫对低温的适应能力及其机理也因而成为昆虫生态学和生物进化研究中的一个深受重视的问题,本文论述了与耐寒性直接相关的过冷却点昆虫的抗寒对策,明确了昆虫耐寒性的一些基本概念,一方面从环境影响昆虫的角度对耐寒性的一般规律,如季节性变化,地理变异快速冷驯化的作用等做了简要的概念括,另一方面阐述了昆虫适应环境的生理生化机制,包括低分子量的抗冻物质的产生,冰核剂的作用及抗冻蛋白的功能等做了简要的概括,另一方面简单述了昆虫适应环境的生理生化机制,包括低分子量的抗冻物质的产生,冰核剂的作用及抗冻蛋白的功能等。强调昆虫与环境相互作用过程中的生态生理适应,并指出昆虫耐寒性应当与生活史中别的因素联系起来,这样才能对耐寒性有一个更加全面的理解。     

Age‐specific reference intervals for routine biochemical parameters in healthy neonates,infants, and young children in Iran

Age and sex need to be considered in the establishment of reference intervals (RIs), especially in early life when there are dynamic physiological changes. Since data for important biomarkers in healthy neonates and infants are limited, particularly in Iranian populations, we have determined age‐specific RIs for 7 laboratory biochemical parameters. This cross‐sectional study comprised a total of 344 paediatric participants (males: 158, females: 186) between the ages of 3 days and 30 months (mean age: 12.91 ± 7.15 months). Serum levels of creatinine, urea, uric acid, calcium, phosphate, vitamin D and high‐sensitivity C‐reactive protein (hs‐CRP) were measured using an Alpha classic‐AT plus auto‐analyser. We determined age‐specific RIs using CLSI Ep28‐A3 and C28‐A3 guidelines. No sex partitioning was required for any of the biomarkers. Age partitioning was required for kidney function tests and phosphate. The serum concentration of urea and creatinine increased with age, while phosphate and uric acid decreased with age. Age partitioning was not required for serum calcium, vitamin D, and hs‐CRP, which remained relatively constant throughout the age range. Age‐specific RIs for 7 routine biochemical markers were determined to address critical gaps in RIs in early life to help improve clinical interpretation of blood test results in young children, including neonates. Established age partitions demonstrate the biochemical changes that take place during child growth and development. These novel data will ultimately better disease management in the Iranian paediatric population and can be of value to clinical and hospital laboratories with similar populations.     

Biochemical properties of a thermostable phytase from Neurospora crassa

A gene (Ncphy) encoding a putative phytase in Neurospora crassa was cloned and expressed in Pichia pastoris, and the biochemical properties of the recombinant protein were examined in relation to the phytic acid hydrolysis in animal feed. The recombinant phytase (rNcPhy) hydrolyzed phytic acid with a specific activity of 125 U mg-1, Km of 228 micromol L-1, Vmax of 0.31 nmol (phosphate) s-1 mg-1, a temperature optimum of 60 degrees C and a pH optimum of 5.5 and a second pH optimum of 3.5. The enzyme displayed pH stability around pH 3.5-9.5 and showed satisfactory thermostability at 80 degrees C. The phytase from N. crassa has potential for improving animal feed processing at higher temperatures.     

Dynamics of a biochemical system with multiple oscillatory domains as a clue for multiple modes of neuronal oscillations

We analyze the behavior of a two-variable biochemical model in conditions where it admits multiple oscillatory domains in parameter space. The model represents an autocatalytic enzyme reaction with input of substrate both from a constant source and from non-linear recycling of product into substrate. This system was previously studied for birhythmicity, i.e. the coexistence between two stable periodic regimes (Moran and Goldbeter 1984), and for multithreshold excitability (Moran and Goldbeter 1985). When two distinct oscillatory domains obtain as a function of the substrate injection rate, the system is capable of exhibiting two markedly different modes of oscillations for slightly different values of this control parameter. Phase plane analysis shows how the multiplicity of oscillatory domains depends on the parameters that govern the underlying biochemical mechanism of product recycling. We analyze the response of the model to various kinds of transient perturbations and to periodic changes in the substrate input that bring the system through the two ranges of oscillatory behavior. The results provide a qualitative explanation for experimental observations (Jahnsen and Llinas 1984b) related to the occurrence of two different modes of oscillations in thalamic neurones.     

Enhanced sampling of chemical and biochemical reactions with metadynamics

Metadynamics (MetaD) is a method that augments molecular dynamics (MD) calculations of all types (classical and quantum) to help systems overcome energy barriers and explore regions of phase space that would otherwise not be seen during a simulation. The method has seen wide ranging uses, and it has proven especially useful for the study of reactions in which bonds break and form. In such cases, the timescale challenges of MD are profoundly limiting, and the advent of this new paradigm for biasing simulations has proven to be incredibly useful. In this review, we set out to summarise the large body of work that uses MetaD for studying reactions so that others can more easily implement this method in their own work. After a brief introduction of the method, we provide detailed summaries of the method applied in various contexts including condensed phase and biological reactions.     

超声强化生化分离技术应用进展

将超声波的空化作用、热效应、机械作用应用于生化分离技术中,可提高分离效率、缩短时间、简化操作过程。综述了超声波在生化分离如天然成分提取、沉淀、萃取、结晶等各种分离方法中的应用现状,并探讨了超声波与分离方法结合的发展前景。     

小菜蛾酪氨酸酶生物化学性质研究

采用时间动力学法对小菜蛾Plutella xylostella酪氨酸酶的最适反应条件、对抑制剂的敏感度以及发育期变化规律进行了研究。结果表明：小菜蛾酪氨酸酶反应的最适pH值为6.4,反应线性时间为0～2 min,在22℃和4℃下其活性分别可保持12 h 和72 h,在-20℃下至少可保持7 天。不同发育阶段小菜蛾酪氨酸酶活性的大小依次为预蛹＞4龄幼虫＞蛹＞1龄、2龄、3龄幼虫＞成虫。苯基硫脲（phenyl thiourea,PTU）对小菜蛾阿维菌素抗性品系和敏感品系酪氨酸酶活性的抑制中浓度（I₅₀）值分别为1.1796 μmol/L和1.2795 μmol/L,二者无明显差异。