CONSTRICTOR: Constraint Modification Provides Insight into Design of Biochemical Networks

Advances in computational methods that allow for exploration of the combinatorial mutation space are needed to realize the potential of synthetic biology based strain engineering efforts. Here, we present Constrictor, a computational framework that uses flux balance analysis (FBA) to analyze inhibitory effects of genetic mutations on the performance of biochemical networks. Constrictor identifies engineering interventions by classifying the reactions in the metabolic model depending on the extent to which their flux must be decreased to achieve the overproduction target. The optimal inhibition of various reaction pathways is determined by restricting the flux through targeted reactions below the steady state levels of a baseline strain. Constrictor generates unique in silico strains, each representing an “expression state”, or a combination of gene expression levels required to achieve the overproduction target. The Constrictor framework is demonstrated by studying overproduction of ethylene in Escherichia coli network models iAF1260 and iJO1366 through the addition of the heterologous ethylene-forming enzyme from Pseudomonas syringae. Targeting individual reactions as well as combinations of reactions reveals in silico mutants that are predicted to have as high as 25% greater theoretical ethylene yields than the baseline strain during simulated exponential growth. Altering the degree of restriction reveals a large distribution of ethylene yields, while analysis of the expression states that return lower yields provides insight into system bottlenecks. Finally, we demonstrate the ability of Constrictor to scan networks and provide targets for a range of possible products. Constrictor is an adaptable technique that can be used to generate and analyze disparate populations of in silico mutants, select gene expression levels and provide non-intuitive strategies for metabolic engineering.     

皮肤组织显微共聚焦拉曼光谱成像研究

显微共聚焦拉曼光谱成像技术(Confocal Raman Microspectroscopy Imaging,CRMI)能够对样品微区进行精确无损的拉曼光谱分析和光谱图像扫描,提供生物样品的无损高分辨光学信息。本项研究工作,利用CRMI技术实验获取了正常人体离体皮肤组织的拉曼光谱特征,并结合典型特征峰的扫描图像,探讨了脂类、蛋白质等成分在皮肤真皮层的分布特点。实验发现皮肤组织真皮层内胶原蛋白的拉曼特征峰1 248 cm-1强度及其空间分布尤为突出,这一实验结果与组织学中胶原纤维占真皮结缔组织95%的事实相符。实验结果显示,CRMI技术能够全面诠释生物组织内部生化组成与分布信息,在实验描述皮肤组织病理变化的分子生物学机制方面具有广阔的应用前景。     

Effect of Chemical Thymectomy on Skin Homografts: A Preliminary Report

In an attempt to combine the results obtained by Miller (mice thymectomized at birth accepted homograft at six weeks of age) and those obtained by Selye (selective calcification of the cortex of the thymus with calciphylaxis), calcification of the thymus was produced by the combined injection of dihydrotachysterol and triamcinolone, in non-inbred Sprague-Dawley and hooded, eight-week-old rats. Six days after the beginning of treatment, full-thickness skin homografts were performed on the rats.Homografts exchanged between two rats with complete calcification of the thymus cortex were accepted for an extended period of time, which in the oldest rats at the time of writing was seven months. Homografts exchanged between rats with incomplete calcification of the thymus resulted in a prolonged homograft survival with final rejection within a period of three weeks. Homografts exchanged between rats that were not treated, surgically thymectomized at the same age as the treated animals, or treated with only one of the two substances used for thymus calcification, resulted in rejection in the average time of eight days.     

Bleomycin A2 and B2 Purification by Flash Chromatography for Chemical and Biochemical Studies

Abstract

The clinically used formulation of the anticancer antibiotic, Blenoxane, is a mixture of bleomycin congeners. A new approach to separating the major A₂ and B₂ congeners has been developed utilizing the flash chromatography technique. A 5–6-inch column of fine mesh silica gel with a solvent system of 1% ammonium formate:methanol (2:3) was used. Low air pressure was applied to the column to increase the flow rate such that separation was complete in ～20 min. Reverse phase size exclusion gravity chromatography with Sephadex G-15 column bedding was an effective, rapid procedure for removal of the 1% ammonium formate, the lowest percentage practical for separating the bleomycins. This separation approach does not damage the antibiotics, as demonstrated by NMR spectroscopy, thin layer chromatography, and DNA cleaving activity. Although not as useful for detection of trace amounts of the drug in biological systems as some of the known HPLC methods, this method is excellent for separating large quantities of the drug (8–32 mg) in order to obtain congeners pure enough for synthetic, biochemical, and biophysical studies.     

Localization of Chemical Stimulation: Capsaicin on Hairy Skin

The ability to localize a chemical stimulus applied to the skin of the forearm was compared to the ability to localize a punctate tactile stimulus. The chemical stimulus was a single, 6-μ1 drop of a 1.0% solution of capsaicin in an ethanol vehicle; the tactile stimulus was a polyester monofilament that exerted 7.5 g of force. Subjects attempted to localize the stimuli at 30-sec intervals for a period of 13.5 min, and rated the perceived intensity and quality of the chemogenic sensations. To avoid generating potentially confounding tactile sensations, localization attempts were made by pointing to the area of sensation with a focused light beam. The results showed that overall, chemical localization was inferior to tactile localization: The absolute error of localization averaged 2.5 cm for capsaicin compared to 1.4 cm for the monofilament. The experiment also revealed that chemical localization (1) varied significantly across arms, (2) exhibited a relatively strong bias toward the elbow, and (3) appeared to be unaffected by the perceived intensity of the sensation. The dominant sensation quality reported was itch. The results are discussed in the context of cutaneous localization in general and localization in the nociceptive system in particular.     

Biochemical and Enzymatic Study of Rice BADH Wild-Type and Mutants: An Insight into Fragrance in Rice

Betaine aldehyde dehydrogenase 2 (BADH2) is believed to be involved in the accumulation of 2-acetyl-1-pyrroline (2AP), one of the major aromatic compounds in fragrant rice. The enzyme can oxidize ω-aminoaldehydes to the corresponding ω-amino acids. This study was carried out to investigate the function of wild-type BADHs and four BADH2 mutants: BADH2_Y420, containing a Y420 insertion similar to BADH2.8 in Myanmar fragrance rice, BADH2_C294A, BADH2_E260A and BADH2_N162A, consisting of a single catalytic-residue mutation. Our results showed that the BADH2_Y420 mutant exhibited less catalytic efficiency towards γ-aminobutyraldehyde but greater efficiency towards betaine aldehyde than wild-type. We hypothesized that this point mutation may account for the accumulation of γ-aminobutyraldehyde/Δ¹-pyrroline prior to conversion to 2AP, generating fragrance in Myanmar rice. In addition, the three catalytic-residue mutants confirmed that residues C294, E260 and N162 were involved in the catalytic activity of BADH2 similar to those of other BADHs.     

The Chemical and Biochemical Properties of Methylphosphotriester DNA

Methylphosphotriester DNA shows a number of interesting bio‐organic properties. Its behavior is quite different from selected modified DNAs as the related methylphosphonate oligonucleotides.     

Production of a Novel Marine Pseudomonas aeruginosa Recombinant L-Asparaginase: Insight on the Structure and Biochemical Characterization

Marine Biotechnology - The present study focused on the cloning, expression, and characterization of L-asparaginase of marine Pseudomonas aeruginosa HR03 isolated from fish intestine. Thus, a gene...     

Further Insight into Substrate Recognition by USP7: Structural and Biochemical Analysis of the HdmX and Hdm2 Interactions with USP7

Ubiquitin-specific protease 7 (USP7) catalyzes the deubiquitination of several substrate proteins including p53 and Hdm2. We have previously shown that USP7, and more specifically its amino-terminal domain (USP7-NTD), interacts with distinct regions on p53 and Hdm2 containing P/AxxS motifs. The ability of USP7 to also deubiquitinate and control the turnover of HdmX was recently demonstrated. We utilized a combination of biochemistry and structural biology to identify which domain of USP7 interacts with HdmX as well as to identify regions of HdmX that interact with USP7. We showed that USP7-NTD recognized two of six P/AxxS motifs of HdmX (⁸AQCS¹¹ and ³⁹⁸AHSS⁴⁰¹). The crystal structure of the USP7-NTD:HdmX^AHSS complex was determined providing the molecular basis of complex formation between USP7-NTD and the HdmX^AHSS peptide. The HdmX peptide interacted within the same residues of USP7-NTD as previously demonstrated with p53, Hdm2, and EBNA1 peptides. We also identified an additional site on Hdm2 (³⁹⁷PSTS⁴⁰⁰) that interacts with USP7-NTD and determined the crystal structure of this complex. Finally, analysis of USP7-interacting peptides on filter arrays confirmed the importance of the serine residue at the fourth position for the USP7-NTD interaction and showed that phosphorylation of serines within the binding sequence prevents this interaction. These results lead to a better understanding of the mechanism of substrate recognition by USP7-NTD.     

Insight on Propolis from Mediterranean Countries: Chemical Composition,Biological Activities and Application Fields

This review updates the information upon the chemical composition of propolis from all Mediterranean countries as well as their biological properties and applications. The non‐volatile fraction of propolis was characterized by the presence of phenolic acids and their esters and flavonoids. Nevertheless, in some countries, diterpenes were also present: Sicily (Italy), Croatia, Malta, Creta (Greece), Turkey, Cyprus, Egypt, Libya, Algeria and Morocco. The volatile fraction of propolis was characterized by the presence of benzoic acid and its esters, mono‐ and sesquiterpenes, being the oxygenated sesquiterpene β‐eudesmol characteristic of poplar propolis, whereas the hydrocarbon monoterpene α‐pinene has been related with the presence of conifers. Regardless the chemical composition, there are common biological properties attributed to propolis. Owing to these attributes, propolis has been target of study for applications in diverse areas, such as food, medicine and livestock.     

Hydroxylation of Phenol to Hydroquinone Catalyzed by A Human Myeloperoxidase-Superoxide Complex: Possible Implications In Benzene-Induced Myelotoxicity

Benzene, a known human rnyelotoxin and leukemogen is metabolized by liver cytochrome P-450 mono-oxygenase to phenol. Further hydroxylation of phenol by cytochrome P-450 monooxygenase results in the formation of mainly hydroquinone, which accumulates in the bone marrow. Bone marrow contains high levels of myeloperoxidase. Here we report that phenol hydroxylation to hydroquinone is also catalyzed by human myeloperoxidase in the presence of a superoxide anion radical generating system, hypoxanthine and xanthine oxidase. No hydroquinone formation was detected in the absence of myeloperoxidase. At low concentrations superoxide disniutase stimulated, but at high concentrations inhibited, the conversion of phenol to hydroquinone. The inhibitory effect at high superoxide dismutase concentrations indicates that the active hydroxylating species of myeloperoxidase is not derived from its interaction with hydrogen peroxide. Furthermore, catalase a hydrogen peroxide scavenger, was found to have no significant effect on hydroxylation of phenol to hydroquinone, supporting the lack of hydrogen peroxide involvement. Mannitol (a hydroxyl radical scavenger) was found to have no inhibitory effect, but histidine (a singlet oxygen scavenger) inhibited hydroquinone formation. Based on these results we postulate that a myeloperoxidase-superoxide complex spontaneously rearranges to generate singlet oxygen and that this singlet oxygen is responsible for phenol hydroxylation to hydroquinone. These results also suggest that myeloperoxidase dependent hydroquinone formation could play a role in the production and accumulation of hydroquinone in bone marrow, the target organ of benzene-induced myelotoxicity.     

Hydroxylation of Phenol to Hydroquinone Catalyzed by A Human Myeloperoxidase-Superoxide Complex: Possible Implications In Benzene-Induced Myelotoxicity

Benzene, a known human rnyelotoxin and leukemogen is metabolized by liver cytochrome P-450 mono-oxygenase to phenol. Further hydroxylation of phenol by cytochrome P-450 monooxygenase results in the formation of mainly hydroquinone, which accumulates in the bone marrow. Bone marrow contains high levels of myeloperoxidase. Here we report that phenol hydroxylation to hydroquinone is also catalyzed by human myeloperoxidase in the presence of a superoxide anion radical generating system, hypoxanthine and xanthine oxidase. No hydroquinone formation was detected in the absence of myeloperoxidase. At low concentrations superoxide disniutase stimulated, but at high concentrations inhibited, the conversion of phenol to hydroquinone. The inhibitory effect at high superoxide dismutase concentrations indicates that the active hydroxylating species of myeloperoxidase is not derived from its interaction with hydrogen peroxide. Furthermore, catalase a hydrogen peroxide scavenger, was found to have no significant effect on hydroxylation of phenol to hydroquinone, supporting the lack of hydrogen peroxide involvement. Mannitol (a hydroxyl radical scavenger) was found to have no inhibitory effect, but histidine (a singlet oxygen scavenger) inhibited hydroquinone formation. Based on these results we postulate that a myeloperoxidase-superoxide complex spontaneously rearranges to generate singlet oxygen and that this singlet oxygen is responsible for phenol hydroxylation to hydroquinone. These results also suggest that myeloperoxidase dependent hydroquinone formation could play a role in the production and accumulation of hydroquinone in bone marrow, the target organ of benzene-induced myelotoxicity.     

Histological,Biochemical, and Ultrastructural Studies on Hyperpigmented Human Skin Xenografts

The mechanisms for hyperpigmentation observed in human cutaneous xenografts placed on athymic nude mice was investigated. Histologic, biochemical, histochemical, and ultrastructural examinations were performed on human skin prior to grafting and at various times ranging from 2 weeks to 30 weeks post-grafting (PG). Hyperpigmentation was macroscopically visible on the graft as early as 4–6 weeks. The number of Dopa-positive melanocytes per unit area was increased at 2 weeks PG and remained elevated until 20 weeks PG. The surface area of the melanocytes, a measure of the activity of the cells, also increased significantly and remained above the pre-grafting size throughout the study. Western blot analysis using tyrosinase specific antibody (αTy-SP) revealed the presence of tyrosinase exclusively in the grafted skin from 2 weeks to 12 weeks PG tested. Histological and ultrastructural observations revealed the presence of numerous dendritic melanocytes, indeterminant clear cells suggestive of Langerhans cells, and dermal melanophages. The results of this study suggest that the observed hyperpigmentation in grafted tissue is caused by an increase in the number of Dopa-positive melanocytes and probably from enhanced melanin production. Extracts of proteins from the xenografts exhibited prominent differences in low and high molecular proteins between pre- and post-grafted skin. Among them, the exclusive appearance of a protein doublet with apparent mw ～14 kDa was found in grafted skin, and subsequent studies indicate it has potent effects on melanocyte function.     

MicroRNAs: A New Insight into Cancer Genome

Cancer is a disease involving multi-step dynamic changes in the genome. However, studies on cancer genome so far have focused most heavily on protein-coding genes, and our knowledge on alterations of the functional non-coding sequences in cancer is largely absent. MicroRNAs (miRNA) are ~22 nt non-coding RNAs, which regulate gene expression in a sequence-specific manner via translational inhibition or mRNA degradation. Mounting evidence is showing that miRNAs may play important roles in tumor development, and a better understanding of their alteration in cancer genome and oncogenic property should contribute to the diagnosis and treatment of cancer.     

Chlorophenol Production by Anaerobic Microorganisms: Transformation of a Biogenic Chlorinated Hydroquinone Metabolite

Chlorinated hydroquinones of biological origin are fully dechlorinated to 1,4-dihydroquinone by anaerobic bacteria such as Desulfitobacterium spp. (C. E. Milliken, G. P. Meier, J. E. M. Watts, K. R. Sowers, and H. D. May, Appl. Environ. Microbiol. 70:385-392, 2004). In the present study, mixed microbial communities from Baltimore Harbor sediment and a pure culture of Desulfitobacterium sp. strain PCE1 were discovered to demethylate, reductively dehydroxylate, and dechlorinate chlorinated hydroquinones into chlorophenols. Mixed microbial cultures from a freshwater source and several other desulfitobacteria in pure culture did not perform these reactions. Desulfitobacterium sp. strain PCE1 degraded 2,3,5,6-tetrachloro-4-methoxyphenol, a metabolite of basidiomycete fungi, to 2,3,5,6-tetrachlorophenol and 2,3,5-trichlorophenol, recalcitrant compounds that are primarily synthesized anthropogenically.