A multiplex single nucleotide polymorphism genotyping method using ligase‐based mismatch discrimination and CE‐SSCP

Accuracy, simplicity, and cost‐effectiveness are the most important criteria for a genotyping method for SNPs compatible with clinical use. One method developed for SNP genotyping, ligase‐based discrimination, is considered the simplest for clinical diagnosis. However, multiplex assays using this method are limited by the detection method. Although CE has been introduced as an alternative to error prone microarray‐based detection, the design process and multiplex assay procedure are complicated because of the DNA size‐dependent separation principle. In this study, we developed a simple and accurate multiplex genotyping method using reaction condition‐optimized ligation and high‐resolution CE‐based SSCP. With this high‐resolution CE‐SSCP system, we are able to use similar‐sized probes, thereby eliminating the complex probe design step and simplifying the optimization process. We found that this method could accurately discriminate single‐base mismatches in SNPs of the tp53 gene, used as targets for multiplex detection.     

Non‐hybridization single nucleotide polymorphism detection and genotyping assay through direct discrimination of single base mutation by capillary electrophoretic separation of single‐stranded DNA

The significant demands for single nucleotide polymorphism detection and genotyping assays have grown. Most common assays are based on the recognition of the target sequence by the hybridization with its specific probe having the complementary sequence of the target. Herein, a simple, label‐free, and economical non‐hybridization assay was developed for single nucleotide polymorphism detection and genotyping, based on the direct discrimination of single base mutation by simple capillary electrophoresis separation for single‐stranded DNA in an acidic electrophoretic buffer solution containing urea. Capillary electrophoresis separation of single‐base sequential isomers of DNA was achieved due to charge differences resulting from the different protonation properties of the DNA bases. Single nucleotide polymorphism detection and genotyping were achieved by discriminating the electropherogram pattern change, that is, peak number in the electropherogram, obtained by the proposed method. The successful practical application of the proposed method was demonstrated through single nucleotide polymorphism detection and genotyping on a known gene region of 84‐mer, in which guanine to adenine single‐base mutation is commonly observed, using a human hair sample in combination with genomic DNA extraction, polymerase chain reaction amplification, DNA purification from polymerase chain reaction products, and capillary electrophoresis separation.     

Toward the synthesis and biological evaluation of hirsutide

Abstract  

The present investigation deals with the synthesis of a N-methylated cyclotetrapeptide, hirsutide (2), by coupling of the dipeptide units Boc-l-phenylalanyl-l-N-methylphenylalanine-OH and l-valyl-l-N-methylphenylalanine-OMe followed by cyclization of the linear tetrapeptide fragment. The chemical structure was established on the basis of analytical as well as spectroscopic data. The newly synthesized cyclic peptide was subjected to pharmacological screening and found to be highly potent against the gram-negative bacteria Pseudomonas aeruginosa and Klebsiella pneumoniae at 6 μg cm⁻³. In addition, potent antihelmintic activity against the earthworms Megascoplex konkanensis and Pontoscotex corethruses at 1 and 2 mg cm⁻³, and potent cytotoxic activity against Dalton’s lymphoma ascites and Ehrlich’s ascites carcinoma cell lines with IC₅₀ values of 14 and 22 μM were also observed. Studies revealed that the pentafluorophenyl ester method employing a catalytic amount of N-methylmorpholine proved to be better for cyclization of the linear tetrapeptide unit.     

Toward the synthesis and biological evaluation of hirsutide

Abstract  The present investigation deals with the synthesis of a N-methylated cyclotetrapeptide, hirsutide (2), by coupling of the dipeptide units Boc-l-phenylalanyl-l-N-methylphenylalanine-OH and l-valyl-l-N-methylphenylalanine-OMe followed by cyclization of the linear tetrapeptide fragment. The chemical structure was established on the basis of analytical as well as spectroscopic data. The newly synthesized cyclic peptide was subjected to pharmacological screening and found to be highly potent against the gram-negative bacteria Pseudomonas aeruginosa and Klebsiella pneumoniae at 6 μg cm⁻³. In addition, potent antihelmintic activity against the earthworms Megascoplex konkanensis and Pontoscotex corethruses at 1 and 2 mg cm⁻³, and potent cytotoxic activity against Dalton’s lymphoma ascites and Ehrlich’s ascites carcinoma cell lines with IC₅₀ values of 14 and 22 μM were also observed. Studies revealed that the pentafluorophenyl ester method employing a catalytic amount of N-methylmorpholine proved to be better for cyclization of the linear tetrapeptide unit. Graphical abstract        

Kinetics of Growth and Enhanced Sophorolipids Production by Candida bombicola Using a Low-Cost Fermentative Medium

In this study, effect of various parameters on sophorolipid (SL) production by the yeast Candida bombicola was investigated for the enhancing of its production by employing L18 orthogonal array design of experiments. At optimum conditions of sugarcane molasses 50 g l⁻¹, soybean oil 50 g l⁻¹, inoculum size 5% (v/v), temperature 30 °C, inoculum age 2 days, and agitation 200 rpm, the yeast produced almost equal amounts of the product in batch shake flasks and in a 3-l fermentor without any pH control (45 and 47 g l⁻¹, respectively). However, the yield increased to 60 g l⁻¹ in the fermentor under controlled pH environment. Time course of SL production, yeast biomass growth, and utilization of sugarcane molasses and soybean oil at these optimized conditions were fitted to existing kinetic models reported in the literature. Estimated kinetic parameters from these models suggested that conventional medium containing glucose can very well be replaced with the present low-cost fermentative medium.     

Long range interaction energies using Gaussian basis sets and a one center method

A one center method, based on the work of Karplus and Kolker, is discussed and used to calculate the induction energy, through O(R^?8), for the H(ls) – H⁺ interaction employing two types of Gaussian basis sets constructed from functions of the form {r^je^?αr2}. The effective hydrogen atom excitation energies and transition multipole moment matrix elements generated in these calculations are used to calculate the dispersion energy for the H(ls) – H(ls) interaction, through O(R^?10), and the R^?9 triple dipole energy corresponding to the interaction of three H(ls) atoms. The results indicate that Gaussian functions can form good basis sets for obtaining long range forces for a variety of multipole interaction energies.     

A new method for the determination of free L-carnitine in serum samples based on high field single quantum coherence filtering 1H-NMR spectroscopy

The rapid and accurate determination of specific metabolites present in biofluids is a very demanding task which is essential in both medicine and chemistry. l-carnitine (3-hydroxy-4-N-trimethylammonium butyrate) is an important metabolite which participates in a series of biological paths and therefore its determination is of diagnostic importance. A single quantum coherence filtering ¹H NMR methodology was used for the accurate and rapid determination of l-carnitine in human serum samples. The methodology is based on spectral simplification, and specifically on the distinction of the N-methyl proton signal of l-carnitine that is greatly overlapped in the ¹H-NMR spectrum of serum. The quantitative results provided by the proposed method are in excellent agreement with those obtained by the enzymatic method, which is widely used. The proposed method is rapid (~20 min of experimental time), selective, sensitive, and has good analytical characteristics (accuracy, reproducibility). Selected protein precipitation methods were also investigated and sample pretreatment with EtOH is suggested.     

Production of Lipids Containing High Levels of Docosahexaenoic Acid by a Newly Isolated Microalga, <Emphasis Type="Italic">Aurantiochytrium</Emphasis> sp. KRS101

In the present study, a novel oleaginous Thraustochytrid containing a high content of docosahexaenoic acid (DHA) was isolated from a mangrove ecosystem in Malaysia. The strain identified as an Aurantiochytrium sp. by 18S rRNA sequencing and named KRS101 used various carbon and nitrogen sources, indicating metabolic versatility. Optimal culture conditions, thus maximizing cell growth, and high levels of lipid and DHA production, were attained using glucose (60 g l⁻¹) as carbon source, corn steep solid (10 g l⁻¹) as nitrogen source, and sea salt (15 g l⁻¹). The highest biomass, lipid, and DHA production of KRS101 upon fed-batch fermentation were 50.2 g l⁻¹ (16.7 g l⁻¹ day⁻¹), 21.8 g l⁻¹ (44% DCW), and 8.8 g l⁻¹ (40% TFA), respectively. Similar values were obtained when a cheap substrate like molasses, rather than glucose, was used as the carbon source (DCW of 52.44 g l⁻¹, lipid and DHA levels of 20.2 and 8.83 g l⁻¹, respectively), indicating that production of microbial oils containing high levels of DHA can be produced economically when the novel strain is used.     

Electrochemical study of gallium(III) with <Emphasis Type="SmallCaps">l</Emphasis>-glutamine at the dropping mercury electrode

Abstract  

Gallium complexes of l-glutamine have been studied polarographically in aqueous media. The reduction was found to be irreversible and diffusion controlled in the presence of 0.1 M KNO₃ and 0.002% Triton-x-100. The values of kinetic parameters, transfer coefficient (α _n), and formal rate constant ( k_{\textf,\texth}⁰ k_{{{\text{f}},{\text{h}}}}^{0} ) of the electrode reactions were calculated by Koutecky's method. The stability constants and composition of the gallium(III)-l-glutamine complexes were evaluated with the help of the Deford-Hume method. The values of stability constants of 1:1, 1:2, and 1:3 gallium(III)-l-glutamine complexes are 1.35, 6.5, and 1,350 at 30 °C, respectively. The values of thermodynamic parameters, the free energy of activation, the enthalpy of activation, and the entropy of activation have been determined at 30 °C. The formation of the metal complexes has been found to be non-spontaneous, endothermic in nature, and entropically favorable at higher temperature.     

Detection of the weak-secretor rs1047781 (385A>T) single nucleotide polymorphism using an unlabeled probe high-resolution melting-based method

FUT2 encodes galactoside 2-α-l -fucosyltransferase 2 which determines the secretor status of ABO(H) blood group antigens. Secretors have at least one functional FUT2 allele (Se), while nonsecretors or weak secretors are homozygous for nonfunctional (non- or weak secretor) FUT2 alleles (se or Se^w). The Se^w having the 385A>T missense SNP (rs1047781) is the prevalent nonfunctional allele in East and Southeast Asians. In this study, we developed an unlabeled-probe high-resolution melting (HRM) analysis for genotyping of 385A>T and validated the method by analyzing 72 Japanese whose 385A>T genotypes were confirmed by DNA sequencing. The unlabeled-probe HRM analysis clearly discriminated three genotypes of 385A>T. In addition, the results obtained for the 72 Japanese by this method were fully concordant with previous ones. Estimation of secretor status using this cost-effective method may be useful in East and Southeast Asian populations.     

Design of silica microparticles with oligopeptide brushes and their interaction with proteins

Synthesis of small oligopeptide brushes (oligo(S-benzyl-l-cysteine)) onto polyelectrolyte functionalized silica microparticles was developed. Poly(vinyl amine) (PVAm) adsorbed from salt-free and KCl 10⁻¹ mol L⁻¹ aqueous solution onto silica microparticles was chemically and naturally cross-linked by epichlorohydrin and CO₂, respectively. After the adsorption of PVAm onto microporous silica particles and stabilization by cross-linking, five repeated coupling reactions of Boc-S-benzyl-l-cysteine were performed. To test the protein interactions with the newly designed surface, human serum albumin (HSA) has been selected as a model protein. X-ray photoelectron spectroscopy, total organic carbon, potentiometric and polyelectrolyte titrations, and electrokinetic analysis were employed to obtain information about the polyelectrolyte adsorption and the amount of the amino acid S-benzyl-l-cysteine that was covalently bound to the solid surface and for determination of the protein amount adsorbed onto functionalized surface. The amount of HSA adsorbed onto modified silica microparticles decreased in order: silica/PVAm-cross-linked (silica/PVAm-C) (8.00 mg g⁻¹) > silica/PVAm-C/S-benzyl-l-cysteine (6.34 mg g⁻¹) > silica (4.86 mg g⁻¹) > silica/PVAm-C/(S-benzyl-l-cysteine)₅ (1.86 mg g⁻¹).     

Simultaneous reactive extraction separation of amino acids from water with D2EHPA in hollow fiber contactors

Reactive extraction separation of binary amino acids from water using a microporous hollow fiber has been studied, in which the acidic extractant di(2-ethylhexyl)phosphoric acid (D2EHPA) was selected as an active carrier dissolved in kerosene. l-Phenylalanine (Phe) was extracted from an aqueous solution through the shell side of module to the organic phase through the lumen of fiber in the extraction module, in which l-Phe was then back-extracted to stripping phase in stripping module. Experiments were conducted as a function of the initial feed concentration of equimolar Phe and l-aspartic acid (l-Asp) (5 mol/m³), feed pH (3–5), the carrier concentration (0.1–0.5 mol/dm³), and stripping acidity (0.1–2 mol/dm³). The effect of process variables on the separation factor of Phe/Asp and the possible transport resistances including aqueous-layer diffusion, membrane diffusion, organic-layer, and interfacial chemical reaction were quantitatively studied and discussed. The high separation factor (β) of Phe/Asp was obtained to be 18.5 at feed pH 5 and 2 mol/dm³ of strip solution (HCl). The extraction and stripping processes appear to rely on pH dependence of the distribution coefficient of amino acids in reactive extraction system. The separation factor (β) was enhanced in hollow fiber membrane (HFM) process compared with conventional solvent process, which was a result of the counter transport of hydrogen ions.     

Plantlet Regeneration from Callus Cultures of Selected Genotype of <Emphasis Type="Italic">Aloe vera</Emphasis> L.—An Ancient Plant for Modern Herbal Industries

Aloe vera L., a member of Liliaceae, is a medicinal plant and has a number of curative properties. We describe here the development of tissue culture method for high-frequency plantlet regeneration from inflorescence axis-derived callus cultures of sweet aloe genotype. Competent callus cultures were established on 0.8% agar-gelled Murashige and Skoog’s (MS) basal medium supplemented with 6.0 mg l⁻¹ of 2,4-dichlorophenoxyacetic acid (2,4-D) and 100.0 mg l⁻¹ of activated charcoal and additives (100 mg l⁻¹ of ascorbic acid, 50.0 mg l⁻¹ each of citric acid and polyvinylpyrrolidone, and 25.0 mg l⁻¹ each of l-arginine and adenine sulfate). The callus cultures were cultured on MS medium containing 1.5 mg l⁻¹ of 2,4-D, 0.25 mg l⁻¹ of Kinetin (Kin), and additives with 4% carbohydrate source for multiplication and long-term maintenance of regenerative callus cultures. Callus cultures organized, differentiated, and produced globular embryogenic structures on MS medium with 1.0 mg l⁻¹ of 2,4-D, 0.25 mg l⁻¹ of Kin, and additives (50.0 mg l⁻¹ of ascorbic acid and 25.0 mg l⁻¹ each of citric acid, l-arginine, and adenine sulfate). These globular structures subsequently produced shoot buds and then complete plantlets on MS medium containing 1.0 mg l⁻¹ of 6-benzylaminopurine and additives. A hundred percent regenerated plantlets were hardened in the greenhouse and stored under an agro-net house/nursery. The regeneration system defined could be a useful tool not only for mass-scale propagation of selected genotype of A. vera, but also for genetic improvement of plant species through genetic transformation.     

n-Alkanes, PAHs and surfactants in the sea surface microlayer and sea water samples of the Gerlache Inlet sea (Antarctica)

Sea surface microlayer (SML) and sea water samples (SSW) collected in the Gerlache Inlet Sea (Antarctica) were analysed for n-alkanes and polycyclic aromatic hydrocarbons (PAHs). The SML is a potential enrichment site of hydrophobic organic compounds compared to the underlying water column. Total concentration ranges of n-alkanes and PAHs (dissolved and particulate) in subsurface water (− 0.5 m depth) were 272-553 ng l^− 1 (mean: 448 ng l^− 1) and 5.27-9.43 ng l^− 1 (mean: 7.06 ng l^− 1), respectively. In the SML, the concentration ranges of n-alkanes and PAHs were 353-968 ng l^− 1 (mean: 611 ng l^− 1) and 7.32-23.94 ng l^− 1 (mean: 13.22 ng l^− 1), respectively. To evaluate possible PAH contamination sources, specific PAH ratios were calculated. The ratios reflected a predominant petrogenic input. A characterisation of surface active substances was also performed on SML and SSW samples, both by gas bubble extraction, and by dynamic surface tension measurements. Results showed a good correlation between n-alkanes, PAHs and refractory organic matter.     

Scale up and Application of Biosurfactant from <Emphasis Type="Italic">Bacillus subtilis</Emphasis> in Enhanced Oil Recovery

There is a lack of fundamental knowledge about the scale up of biosurfactant production. In order to develop suitable technology of commercialization, carrying out tests in shake flasks and bioreactors was essential. A reactor with integrated foam collector was designed for biosurfactant production using Bacillus subtilis isolated from agricultural soil. The yield of biosurfactant on biomass (Y _p/x), biosurfactant on sucrose (Y _p/s), and the volumetric production rate (Y) for shake flask were obtained about 0.45 g g⁻¹, 0.18 g g⁻¹, and 0.03 g l⁻¹ h⁻¹, respectively. The best condition for bioreactor was 300 rpm and 1.5 vvm, giving Y _x/s, Y _p/x, Y _p/s, and Y of 0.42 g g⁻¹, 0.595 g g⁻¹, 0.25 g g⁻¹, and 0.057 g l⁻¹ h⁻¹, respectively. The biosurfactant maximum production, 2.5 g l⁻¹, was reached in 44 h of growth, which was 28% better than the shake flask. The obtained volumetric oxygen transfer coefficient (K _L a) values at optimum conditions in the shake flask and the bioreactor were found to be around 0.01 and 0.0117 s⁻¹, respectively. Comparison of K _L a values at optimum conditions shows that biosurfactant production scaling up from shake flask to bioreactor can be done with K _L a as scale up criterion very accurately. Nearly 8% of original oil in place was recovered using this biosurfactant after water flooding in the sand pack.     

Multiple genotyping based on multiplex PCR and microarray

The genetic variability has obtained more and more attention in the process of diagnosis and treatment of tumors.Herein,we have described a multiple genotyping method based on magnetic enrichmentmultiplex PCR (MEM-PCR) and microarray technology.Monodisperse magnetic beads were fabricated and modified with streptavidin.Four loci on two genes (M235T and A-6G loci on AGT gene,A1298C and C677T loci on MTHFR gene) were selected to study single nucleotide polymorphisms (SNP).Target sequences of these SNP loci were amplified using Cy3-labeled primers through multiplex PCR in one tube after the templates were enriched and purified by functional magnetic beads (MB).Four pairs of NH₂-labeled probes,corresponding to each locus,were fixed on CHO-modified glass slide by covalent binding.Hybridization between target sequences and probes was performed under suitable conditions.The spotting locations on microarray and the ratio of fluorescence intensity,produced by different loci,were used to distinguish the SNP genotypes.Finally,three of gastric cancer samples were collected and genotyping analysis for these four SNP loci was carried out successfully simultaneously by this method.     

Enhancing electrochemical preparation of polyaluminum chloride by a magnetic field

A novel effective method for preparing polyaluminum chloride (PAC) with high content of Al₁₃ polymer through conventional electrolysis coupled with rare earth Nd-Fe-B magnetic field was introduced. The content of Al₁₃ polymer in PAC synthesized by this method was highly influenced by the electrobath voltage (E), the magnetic flux density (B), the current density (i) and the distance between the two adjacent electrodes (d_adj). A total aluminum concentration (Al_T) in the PAC solution of 0.8 mol l⁻¹ was obtained when the E, B and i was 2.2 V, 0.4 T and 3.2 A dm⁻², respectively. The optimum d_adj and circulating flow (Q_f) were 20 mm and 23.7 l h⁻¹. With accelerated mass transfer rate by external magnetic field and high Q_f, this process had the advantages of forming more Al(OH)₄⁻ as the precursor of Al₁₃ polymer and inhibiting the concentration polarization more obviously than conventional electrolysis process. Under the optimum conditions, the amount of Al₁₃ polymer in PAC accounted for 82.3% of the Al_T (Al_T = 0.8 M, basicity = 2.2), which was higher than that of PAC prepared by other methods.     

The Ethanol Tolerance of <Emphasis Type="Italic">Pachysolen tannophilus</Emphasis> in Fermentation on Xylose

The influence of ethanol on fermentation by Pachysolen tannophilus was studied. When xylose utilization rate was 80%, ethanol concentration began to decline. Fermentation of P. tannophilus was affected by ethanol addition in the beginning of fermentation; average xylose consumption rate was 0.065 g·l⁻¹·h⁻¹, and maximum specific growth rate was 0.07 h⁻¹ at 28 g·l⁻¹ ethanol, comparing with the average xylose consumption rate of 0.38 g·l⁻¹·h⁻¹ and maximum specific growth rate of 0.14 h⁻¹ in fermentation with no ethanol addition; P. tannophilus stopped growth at 40 g·l⁻¹ ethanol. When the initial ethanol concentration was 30 g·l⁻¹, the addition of glucose in xylose media made the growth of P. tannophilus better, and the most favorable glucose concentration was 15 g·l⁻¹ with the highest biomass of 1.51 g·l⁻¹ as compared with that of 0.95 g·l⁻¹ in pure xylose media.     

Potential energy profiles of the geometric isomerization and the thermal decomposition of diphosphene HP=PH in the ground and excited electronic states

Summary The geometric isomerization and the dehydrogenation of HP=PH in the ground and some low-lying excited states are investigated by theoretical calculations. The reaction paths are traced by either the CASSCF or UHF-SCF calculations using the 6-31G(d,p) basis functions, and the accompanying energy changes are calculated by the MRD-CI method employing the [5s3p1d]/[2s1p] basis functions. The barrier heights for the trans-to-cis isomerization, by the planar inversion and the nonplanar twisting, in the ground state are calculated to be 265 and 144 kJ/mol (with the vibrational zero-point energy corrections), respectively. The latter barrier is noticeably lower than the H-P and the P-P bond dissociation energies oftrans-HP=PH (¹A_g), which are 304 and 271 kJ/mol, respectively. The ground-state HP₂ radical (²A'), which is to be formed by the dehydrogenation of HP=PH, should suffer further decomposition into P₂ (¹ _g ⁺ ) and H with an activation energy of 139 kJ/mol. The lowest excited state of HP₂ is found to be a hydrogen-bridged 3-electron system (²A₂) having an isosceles triangle structure. It has proved to be formed by the dehydrogenation of the lowest excited singlet state (¹B) of HP=PH via a transition state which lies 194 kJ/mol above the¹B state. The excited HP₂ (²A₂) is state-correlated with P₂ (³_u)+H.     

Enhanced Production of <Emphasis Type="SmallCaps">l</Emphasis>-Arginine by Expression of <Emphasis Type="Italic">Vitreoscilla</Emphasis> Hemoglobin Using a Novel Expression System in <Emphasis Type="Italic">Corynebacterium crenatum</Emphasis>

Corynebacterium crenatum SYPA 5-5 is an aerobic and industrial l-arginine producer. It was proved that the Corynebacterium glutamicum/Escherichia coli shuttle vector pJC1 could be extended in C. crenatum efficiently when using the chloramphenicol acetyltransferase gene (cat) as a reporter under the control of promoter tac. The expression system was applied to over-express the gene vgb coding Vitreoscilla hemoglobin (VHb) to further increase the dissolved oxygen in C. crenatum. As a result, the recombinant C. crenatum containing the pJC-tac-vgb plasmid expressed VHb at a level of 3.4 nmol g⁻¹, and the oxygen uptake rates reached 0.25 mg A₅₆₂⁻¹ h⁻¹ which enhanced 38.8% compared to the wild-type strain. Thus, the final l-arginine concentration of the batch fermentation reached a high level of 35.9 g L⁻¹, and the biomass was largely increased to 6.45 g L⁻¹, which were 17.3% and 10.5% higher than those obtained by the wild-type strain, respectively. To our knowledge, this is the first report that the efficient expression system was constructed to introduce vgb gene increasing the oxygen and energy supply for l-arginine production in C. crenatum, which supplies a good strategy for the improvement of amino acid products.