The Gene Construction Kit: a new computer program for manipulating and presenting DNA constructs

The Gene Construction Kit is a new tool for manipulating and displaying DNA sequence information. Constructs can be displayed either graphically or as formatted sequence. Segments of DNA can be cut out with restriction enzymes and pasted into other sites. The program keeps track of staggered ends and notifies the user of incompatibilities and offers a choice of ligation options. Each segment of a construct can have its own defined thickness, pattern, direction and color. The sequence listing can be displayed in any font and style in user defined grouping. Nucleotide positions can be displayed as can restriction sites and protein sequences. The DNA can be displayed as either single- or double-stranded. Restriction sites can be readily marked. Alternative views of the DNA can be maintained and the history of the construct automatically stored. Gel electrophoresis patterns can be generated and can be used in cloning project design. Extensive comments can be stored with the construct and can be searched rapidly for key words. High quality illustrations showing multiple editable constructs with added graphics and text information can be generated for slides, posters or publication.     

Hybridization-based karyotyping of mouse chromosomes: hybridization-bands.

We have developed a method, which we have named hybridization-banding, to identify simultaneously all chromosomes in a mouse metaphase spread. The method uses a combination of hybridization probes labeled with a single fluor to yield a simple, unique, readily identifiable hybridization pattern on each chromosome. The method is superior to Giemsa- or fluorescence-based banding methods for chromosome identification because the hybridization patterns are simpler and easier to identify, and unique patterns can be designed at will for each chromosome. Analysis can be performed with a standard fluorescence microscope, and images can be recorded on film with an ordinary 35-mm camera, making the method useful to many investigators. The method can also be applied to any species for which chromosomes and probes can be prepared.     

Manipulation of galactolipid Fatty Acid composition with substituted pyridazinones

The fatty acid composition of the major lipids of the chloroplast membranes, the mono- and digalactosyl diglycerides, can be definably altered with various substituted pyridazinones. Galactolipid fatty acid composition of wheat (Triticum aestivum L.) can be altered so that there is a decrease in linolenic acid accompanied by an increase in linoleic acid without a shift in the relative proportion of saturated to unsaturated fatty acids; the fatty acid composition can be shifted toward a higher proportion of saturated fatty acids; or the fatty acid composition of the monogalactosyl diglycerides can be altered in preference to the digalactosyl diglycerides. Also, the light-mediated parallel accumulation of chlorophyll and linolenic acid can be separated with a substituted pyridazinone. The substituted pyridazinones may be useful tools in clarifying the role the galactolipids and their component fatty acids play in the structure and function of chloroplast membranes in higher plants.     

Cloning strategy, production and purification of proteins with exopeptidase-cleavable His-tags

Here, we present a cloning strategy for the production of recombinant proteins tagged with a polyhistidine sequence that can be cleaved by the exopeptidase, DAPase. The method can be used with most commonly available vectors and results in the expression of a His-tag protein that can be purified in its native form regardless of its natural sequence. This approach takes advantage of the TAGZyme system for the removal of amino-terminal affinity tags. Tag removal is accomplished either with DAPase (a recombinant dipeptidyl peptidase) alone or in combination with two accessory enzymes, Qcyclase and pGAPase. The system has been used for the production of intracellular proteins in Escherichia coli and can be applied to other expression hosts for the production of secreted proteins or proteins that require post-translational modification. The production of human interleukin 1beta in E. coli is used as an example to illustrate this method. The complete protocol from initial PCR to the production of a detagged protein with its authentic N terminus can be performed within 5 days.     

Analysis of plasmid samples on a microchip

We have developed a LabChip-based plasmid assay that runs on the Agilent 2100 Bioanalyzer. The assay determines the sizes and relative concentrations of the multiple forms of plasmid samples. Twelve samples can be analyzed on each chip in an automated run lasting approximately 30min. By using a supercoiled DNA sizing standard of 2-16kb, the size of the analyzed plasmid can be determined. The resulting MW has a relative standard deviation (CV) <5% and error <5%. Plasmids from 2-8kb can be separated with resolution better than 1kb. Topological isoforms in a plasmid sample can also be separated. However, due to differential staining, the heterogeneity of plasmid samples can only be measured if the signal of each isomer peak can be calibrated with pure standards for every isomer form. For a typical plasmid preparation which predominately is in the supercoiled form, the normalized corrected peak area for the supercoiled form correlates with the plasmid concentration in a broad range of 1-100ng/microl. The measurement is semiquantitative with a CV lower than 20%. A number of applications of this assay on a Labchip will be shown.     

Use of oil bodies and oleosins in recombinant protein production and other biotechnological applications

Oil bodies obtained from oilseeds have been exploited for a variety of applications in biotechnology in the recent past. These applications are based on their non-coalescing nature, ease of extraction and presence of unique membrane proteins—oleosins. In suspension, oil bodies exist as separate entities and, hence, they can serve as emulsifying agent for a wide variety of products, ranging from vaccines, food, cosmetics and personal care products. Oil bodies have found significant uses in the production and purification of recombinant proteins with specific applications. The desired protein can be targeted to oil bodies in oilseeds by affinity tag or by fusing it directly to the N or C terminal of oleosins. Upon targeting, the hydrophobic domain of oleosin embeds into the TAG matrix of oil body, whereas the protein fused with N and/or C termini is exposed on the oil body surface, where it acquires correct confirmation spontaneously. Oil bodies with the attached foreign protein can be separated easily from other cellular components. They can be used directly or the protein can be cleaved from the fusion. The desired protein can be a pharmaceutically important polypeptide (e.g. hirudin, insulin and epidermal growth factor), a neutraceutical polypeptide (somatotropin), a commercially important enzyme (e.g. xylanase), a protein important for improvement of crops (e.g. chitinase) or a multimeric protein. These applications can further be widened as oil bodies can also be made artificially and oleosin gene can be expressed in bacterial systems. Thus, a protein fused to oleosin can be expressed in Escherichia coli and after cell lysis it can be incorporated into artificial oil bodies, thereby facilitating the extraction and purification of the desired protein. Artificial oil bodies can also be used for encapsulation of probiotics. The manipulation of oleosin gene for the expression of polyoleosins has further expanded the arena of the applications of oil bodies in biotechnology.     

Monitoring biotransformations in polyamide fibres

The enzymatic hydrolysis of polyamide fibres yields amino and carboxylic groups. These groups can be found in solution treatments as polyamide monomers and soluble oligomers. The amino groups can also be found at the surface of the fibres as end group chains. In this paper we report two methods to quantify the formation of these groups as a result of the enzymatic action. Soluble amino groups can be quantified with 2,4,6-trinitrobenzenesulfonic acid (TNBS), which yields a coloured complex which can be determined spectrophotometrically. The amino groups on the fibre surface can be quantified by reaction with a wool reactive dye and determination of colour intensities after a dyeing procedure below the glass transition temperature of polyamide.     

Heidenhain's Hematoxylin in Cytological Studies of Penicillium Notatum

The nuclei in the hyphae of Penicillia can be stained with Heidenhain's hematoxylin, which allows their study before and after treatment with different chemicals. Conidia are inoculated on a very thin Czapek-Dox agar film covering a slide. The spores after germinating in a moist chamber can be fixed in Flemming's fluid and stained at various growth stages. The preparations may then be differentiated in 4% iron-alum until the nuclei (2-10 nuclei in normal cells, many more sometimes in induced cells) show full contrast. The preparations can be made permanent by sealing with Canada balsam. For photomicrographical purposes, embedding in glycerol is most suitable.     

VP7/IFNα-2b融合蛋白防治轮状病毒腹泻的可行性

轮状病毒(RV）外壳蛋白VP7可用作抗原;通过构建植物表达载体,将该抗原基因导入植物细胞,最终在植物细胞中获得抗原蛋白的表达;这种蛋白能保持自然免疫特性,口服能诱发粘膜免疫反应,从而达到对RV的预防作用。干扰素作为一种广谱的抗病毒蛋白质,能对RV引起的肠炎起治疗作用。本提出利用干扰素与轮状病毒表面抗原融合蛋白用于防治轮状病毒腹泻的构想,并对其可行性作了探讨。     

Characterization of DNA chips by nanogold staining

DNA microarray is an important tool in biomedical research. Up to now, there are no chips that can allow both quality analysis and hybridization using the same chip. It is risky to draw conclusions from results of different chips if there is no knowledge of the quality of the chips before hybridization. In this article, we report a colorimetric method to do quality control on an array. The quality analysis of probe spots can be obtained by using gold nanoparticles with positive charges to label DNA through electrostatic attraction. The probe spots can also be detected by a simple personal computer scanner. Gold nanoparticles deposited on a glass surface can be dissolved in bromine-bromide solution. The same microarray treated with gold particles staining and destaining can still be used for hybridization with nearly the same efficiency. This approach makes quality control of a microarray chip feasible and should be a valuable tool for biomarker discovery in the future.     

Kinetics of the polymerization of hemoglobin in high and low phosphate buffers

Diluted solutions of deoxyhemoglobin S in concentrated phosphate buffer form aggregates or gels with a clear exhibition of a delay time. The aggregates can be liquified by cooling, bubbling with O2 or CO gas, or the dilution of phosphate buffer with water. These properties can be used as a simple method for studying the mechanism of polymerization and depolymerization of hemoglobins. The advantages of this method are: 1) The amount of hemoglobin sample required is only 1% to 5% of that required for the gelation of deoxy-Hb S in low phosphate buffer. 2) The kinetics can be measured turbidimetrically using an ordinary spectrophotometer. 3) The solubility of hemoglobin can be directly determined by taking the absorption spectrum of the supernatant solution after polymerization. 4) The polymer phase can be easily separated from the solution so that the amount and composition of the polymers can be analyzed. 5) The volume of the polymer phase is so small that excluded volume effect can be neglected. 6) The method can be applied to the study of polymerization of non-sickle hemoglobins and that of mixtures of sickle and non-sickle hemoglobins. The major question is whether the polymerization of hemoglobin in concentrated phosphate buffer is the same as that of deoxy-Hb S in low phosphate buffer. To answer this question, we studied the polymerization of Hb S, Hb A, Hb C Harlem, and Hb C in phosphate buffers of different molarities. We also studied the mechanism of the conversion of gels of these hemoglobins into crystals.     

Rapid acetylation of alcohols at the microgram level using a celite-acetyl methanesulfonate column.

A simple procedure is described in which micro- and submicrogram amounts of primary, secondary, and several tertiary alcohols can be acetylated. The alcohols, dissolved in a nonpolar solvent, contact a column of Celite charged with the mixed anhydride, acetyl methanesulfonate, contained in a melting-point capillary. The resulting acetate is then eluted for analysis. The entire procedure can be executed in less than a minute. Micromole amounts of alcohols can be acetylated in good yield using larger columns.     

GFP-expressing mammalian cells for fast, sensitive, noninvasive cell growth assessment in a kinetic mode.

This study correlates the fluorescent signal from stable recombinant CHO cell lines expressing the green fluorescent protein (GFP) at high levels with biomass or cell number, extending the use of fluorescent proteins to applications and assays where cell growth rates are important. Using a standard fluorometer, growth of these cells can be quantified noninvasively in multiwell plates, and because signals are obtained without preparation, the same culture samples can be measured repeatedly. Even with a small relative change in biomass, the specific growth rate can be determined in a few hours. The dynamics of cell populations can now be studied with high sensitivity, low error rate, and minimum sample preparation.     

在杂交作物分子育种中利用普通核雄性不育的几个可能途径

由一对隐性基因控制的普通核雄性不育性遗传方式能够满足对植物最佳雄性不育系选育的要求,是水稻等作物杂种优势利用的极好遗传工具。如果能解决其不育系繁殖问题,将优于现有的其他杂种优势利用方式。克隆出普通核雄性不育性的可育基因,通过叶绿体转化,将核雄性不育性可育基因向普通核雄性不育株细胞质转移,创造普通核雄性不育株的保持系;通过种子成熟后表达的启动子;和以位点特异性重组技术为基础的基因开关以及化学诱导启动子的利用,都可能繁殖出100％不育株率的普通核雄性不育系,创造普通核雄性不育性利用的新途径,对植物杂种优势利用产业有十分重要的意义。     

Conjugation of DOTA-like chelating agents to peptides and radiolabeling with trivalent metallic isotopes

Peptides can be labeled with various trivalent radiometals for imaging or targeted radionuclide-therapy applications. The peptide is first conjugated to a chelating agent that is able to form stable complexes with the radionuclide of interest. This conjugation step can be carried out as part of the solid-phase peptide synthesis, or it can be undertaken in the solution phase after synthesis and purification of the peptide. The latter route, described here, involves reacting a molar excess of the activated tri-tert-butyl ester-derivatized chelator with a designated free amino group of a peptide analog, in which all other reactive amines are protected, in the presence of a coupling agent. The conjugate molecule is then purified prior to deprotection and further purification by HPLC. The product can be radiolabeled by addition of a suitable metal salt, followed, if necessary, by removal of the unchelated metal. The entire process of conjugation, purification and radiolabeling should take approximately 12.5 h.     

Pharmacokinetics of monoclonal antibodies and Fc-fusion proteins

There are many factors that can influence the pharmacokinetics (PK) of a mAb or Fc-fusion molecule with the primary determinant being FcRn-mediated recycling. Through Fab or Fc engineering, IgG-FcRn interaction can be used to generate a variety of therapeutic antibodies with significantly enhanced half-life or ability to remove unwanted antigen from circulation. Glycosylation of a mAb or Fc-fusion protein can have a significant impact on the PK of these molecules. mAb charge can be important and variants with pI values of 1–2 unit difference are likely to impact PK with lower pI values being favorable for a longer half-life. Most mAbs display target mediated drug disposition (TMDD), which can have significant consequences on the study designs of preclinical and clinical studies. The PK of mAb can also be influenced by anti-drug antibody (ADA) response and off-target binding, which require careful consideration during the discovery stage. mAbs are primarily absorbed through the lymphatics via convection and can be conveniently administered by the subcutaneous (sc) route in large doses/volumes with co-formulation of hyaluronidase. The human PK of a mAb can be reasonably estimated using cynomolgus monkey data and allometric scaling methods.     

Circuit for the electromanipulation of plant protoplasts

An electric circuit for plant protoplast manipulation is described. The circuit used readily available materials and was designed for use in teaching. This integrated circuit can be placed in a single small box with controls for the aligning voltage, the aligning frequency, the pulse voltage, and the pulse timing. The circuit can be supplied by any suitable source of dc power and can be easily altered for individual requirements. The circuit, as presented here, can be assembled for less than $250.     

Protein φ and ψ dihedral restraints determined from multidimensional hypersurface correlations of backbone chemical shifts and their use in the determination of protein tertiary structures

The chemical shifts of the backbone atoms of proteins can be used to obtainrestraints that can be incorporated into structure determination methods. Eachchemical shift can be used to define a restraint and these restraints can besimultaneously used to define the local, secondary structure features. Theglobal fold can be determined by a combined use of the chemical shift basedrestraints along with the long-range information present in the NOEs ofpartially deuterated proteins or the amide–amide NOEs but not from suchlimited NOE data sets alone. This approach has been demonstrated to be capableof determining the overall folding pattern of four proteins. This suggeststhat solution-state NMR methods can be extended to the structure determinationof larger proteins by using the information present in the chemical shifts ofthe backbone atoms along with the data that can be obtained on a small numberof labeled forms.