Prognostic signature and immune efficacy of m1 A-, m5 C- and m6 A-related regulators in cutaneous melanoma

Cutaneous melanoma (CM) is an aggressive cancer; given that initial and specific signs are lacking, diagnosis is often late and the prognosis is poor. RNA modification has been widely studied in tumour progression. Nevertheless, little progress has been made in the signature of N1 -methyladenosine (m1 A), 5-methylcytosine (m5 C), N6 -methyladenosine (m6 A)-related regulators and the tumour microenvironment (TME) cell infiltration in CM. Our study identified the characteristics of m1 A-, m5 C- and m6 A-related regulators based on 468 CM samples from the public database. Using univariate, multivariate and LASSO Cox regression analysis, a risk model of regulators was established and validated by a nomogram on independent prognostic factors. The gene set variation analysis (GSVA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) clarified the involved functional pathways. A combined single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT approach revealed TME of regulator-related prognostic signature. The nine-gene signature stratified the patients into distinct risk subgroups for personalized prognostic assessment. Additionally, functional enrichment, immune infiltration and immunotherapy response analysis indicated that the high-risk group was correlated with T-cell suppression, while the low-risk group was more sensitive to immunotherapy. The findings presented here contribute to our understanding of the TME molecular heterogeneity in CM. Nine m1 A-, m5 C- and m6 A-related regulators may also be promising biomarkers for future research.

[Effect of simulating leg length inequality on spinal and pelvic posture in the elderly]

Objective: To study the effects of simulating leg length inequality on the spine and pelvic posture in standing and walking states and to explore their compensatory laws. Methods: From January to April, a total of 44 healthy volunteers were rasterstereographically examined for spine and pelvis in Institute of Digitized Medicine, Wenzhou Medical University and Department of Orthopaedics, First Affiliated Hospital of Wenzhou Medical University.Volunteers wore uniform shoes, and single 5 mm thick insoles were customized.The simulating leg length inequalities (5-30 mm) were artificially created by increasing insole height.The parameters of 3D body surface parameters and 4D dynamic parameters of the pelvic and spine were measured and statistically analyzed in standing and walking states. Results: In the static standing state, with the increase of the difference of both lower extremities, coronal plane pelvic tilt and sagittal plane pelvic torsion also increased[the maximum value about (10.6±4.3) mm and (3.3±3.5)°], as well as the frontal deviation of the spine [the maximum value about (11.1±17.9) mm]. But the pelvic rotation, vertebral surface rotation angle (rms) and spine sagittal plane deviation were no obvious changes.In the walking state, with the difference between lower extremities increased, the maximum angles of vertebral surface rotation to the left and right and pelvic rotation to the left and right were no obvious changes, but (coronal) spinal maximum offset distance to left and right increased [the maximum value about (9.8±5.1), (10.4±6.9) mm]. Conclusion: The effect of the leg length discrepancy on the pelvic coronal plane and the sagittal plane changes are obvious, but little effect has on the pelvic cross section.The pelvis is compensated by the increase of the inclination of the coronal plane and the sagittal angle at first order.Similarly, the effect on the coronal plane of the spine is more markedly, but the changes of sagittal and cross-section of the spine is less affected, the spine is mainly compensated by the coronal plane bending at second order.

First Report of Meloidogyne enterolobii on Cotton and Soybean in North Carolina, United States

Stunted cotton plants (Gossypium hirsutum L. cvs. PHY 375 WR and PHY 565 WR) from two separate fields near Goldsboro in Wayne County, North Carolina were collected by the NCDA&CS Agronomic Division nematode lab for nematode assay and identification in December 2011. The galls on cotton plants were very large in comparison with those commonly associated with Meloidogyne incognita Kofoid and White (Chitwood) infected cotton. In August 2012, the lab also received heavily galled roots of soybean (Glycine max (L.) Merr. cv. 7732) from Wayne and Johnston counties. Population densities of the 2nd-stage juveniles ranged from 150 to 3,800 per 500 cc soil. Female perineal patterns were similar to M. incognita, but PCR and DNA sequencing matched that of M. enterolobii Yang and Eisenback (4). DNA sequences of ribosomal DNA small subunit, internal transcribed spacer, large subunit domain 2 and 3, intergeneric spacer, RNA polymerase II large subunit, and histone gene H3, were found to be 100% homologous when comparing populations of M. enterolobii from North Carolina and China. Species identification was also confirmed using PCR by a species-specific SCAR primer set MK7-F/MK7-R (2). M. enterolobii Yang & Eisenback was described in 1983 from a population causing severe damage to pacara earpod tree (Enterolobium contortisiliquum (Vell.) Morong) in China (4). In 2004, M. mayaguensis Rammah & Hirschmann, a species described from Puerto Rico, was synonymized with M. enterolobii based on esterase phenotype and mitochondrial DNA sequence (3). M. enterolobii is considered to be a highly pathogenic species and has been reported from vegetables, ornamental plants, guava, and weeds in China, Africa, Central and South America, the Caribbean, and Florida in the United States (1,3,4). Of particular concern is its ability to develop on crop genotypes carrying root-knot-nematode resistance genes (Mi-1, Mh, Mir1, N, Tabasco, and Rk) in tobacco, tomato, soybean, potato, cowpea, sweet potato, and cotton. Consequently, this species was added to the European and Mediterranean Plant Protection Organization A2 Alert list in 2010. Two populations of M. enterolobii one from soybean and one from cotton were reared on tomato (Solanum lycopersicum L. var. lycopersicum) in a greenhouse setting. Eggs were extracted using NaOCl and inoculated, at a rate of 7,000 per 15-cm-diameter clay pot, into a sandy soil mixture (1:1 washed river sand and loamy sand). Tomato, peanut (Arachis hypogaea L.), cotton, watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), pepper (Capsicum annuum L.), and root-knot-susceptible and -resistant tobacco (Nicotiana tabacum L. cvs. K326 and NC 70, respectively) were transplanted immediately into the infested soil with four replications. Root galls on the host differentials were evaluated after 90 days. Reproduction occurred on all hosts except for peanut, which is consistent with reports for M. enterolobii and M. incognita race 4 (4). Adult females from pepper plants used in the host differential test were sequenced on partial 18S and ITS1 region and confirmed to be M. enterlobii. To our knowledge, this is the first report of a natural infection of North Carolina field crops with M. enterolobii. References: (1) J. Brito et al. J. Nematol. 36:324, 2004. (2) M. S. Tigano et al. Plant Pathol. 59:1054, 2010. (3) J. Xu et al. Eur. J. Plant Pathol. 110:309, 2004. (4) B. Yang and J. D. Eisenback. J. Nematol. 15:381, 1983.

Multiplex PCR for the simultaneous identification and detection of Meloidogyne incognita, M. enterolobii, and M. javanica using DNA extracted directly from individual galls

Meloidogyne incognita, M. enterolobii, and M. javanica are the most widespread species of root-knot nematodes in South China, affecting many economically important crops, ornamental plants, and fruit trees. In this study, one pair of Meloidogyne universal primers was designed and three pairs of species-specific primers were employed successfully to rapidly detect and identify M. incognita, M. enterolobii, and M. javanica by multiplex polymerase chain reaction (PCR) using DNA extracted from individual galls. Multiplex PCR from all M. incognita, M. enterolobii, and M. javanica isolates generated two fragments of ≈500 and 1,000, 500 and 200, and 500 and 700 bp, respectively. The 500-bp fragment is the internal positive control fragment of rDNA 28S D2/D3 resulting from the use of the universal primers. Other Meloidogyne spp. included in this study generated only one fragment of ≈500 bp in size. Using this approach, M. incognita, M. enterolobii, and M. javanica were identified and detected using DNA extracted directly from individual galls containing the Meloidogyne spp. at various stages of their life cycle. Moreover, the percentage of positive PCR amplification increased with nematode development and detection was usually easy after the late stage of the second-stage juvenile. The protocol was applied to galls from naturally infested roots and the results were found to be fast, sensitive, robust, and accurate. This present study is the first to provide a definitive diagnostic tool for M. incognita, M. enterolobii, and M. javanica using DNA extracted directly from individual galls using a one-step multiplex PCR technique.

First Report of Meloidogyne enterolobii on Arrowroot in China

The rhizome of arrowroot (Maranta arundinacea L.) is used as a source of edible starch in many tropical/subtropical areas. In July 2009, cultivated arrowroot plants in a field in Haikou, Hainan Province, China were observed to be exhibiting symptoms of decline, including stunting and yellowing. Roots of affected plants were found to have severe root galling similar to that caused by root-knot nematodes. Meloidogyne sp. females were dissected from the galls. Morphological characteristics of the females fit the description of M. enterolobii Yang & Eisenback (4). The perineal patterns were variable, with moderately high to high dorsal arch and mostly lacking lateral lines, but when present, the lines were not conspicuous, similar to those in the original description.(4). For further confirmation of species identity, isoenzyme patterns of malate dehydrogenase (Mdh) and esterase (Est) phenotypes were analyzed and partial sequences of mtDNA were obtained. Enzyme electrophoresis showed that the phenotypes of Mdh and Est were N1a and VS1-S1 respectively, which were consistent with those of M. enterolobii (1). Amplification and sequencing of the mtDNA between COII and the lRNA gene was accomplished with primers C2F3 (5'-GGTCAATGTTCAGAAATTTGTGG-3') and 1108 (5'-TACCTTTGACCAATCACGCT-3') (2). A DNA fragment of 705 bp was obtained and the sequence (GenBank Accession No. GQ870255) was compared with those in GenBank. A BLAST search indicated the sequence was 100% identical to the sequences of M. mayaguensis (GenBank Accession Nos. AY446969 and AY446970), a synonym of M. enterolobii (3). On the basis of these results, the root-knot nematodes isolated from arrowroot in Hainan were confirmed as M. enterolobii. This species has a high reproduction rate and a wide host range; moreover, it can induce severe galling and is able to overcome the resistance gene Mi-1 in tomato and pepper (4). M. enterolobii has become increasingly important because it has been found in many countries on diverse hosts. In China in recent years, the nematode has been reported on approximately 20 plant species belonging to five families, including Fabaceae, Cucurbitaceae, Solanaceae, Myrtaceae, and Annonaceae. To our knowledge, this is the first record of M. enterolobii parasitizing a plant (i.e., arrowroot) in the family Marantaceae in China. References: (1) P. R. Esbenshade and A. C. Triantaphyllou. J. Nematol. 17:6, 1985. (2) T. O. Powers and T. S. Harris. J. Nematol. 25:1, 1993. (3) J. Xu et al. Eur. J. Plant Pathol. 110:309, 2004. (4) B. Yang and J. D. Eisenback. J. Nematol. 15:381, 1983.

Continuous beds for microchromatography: chromatofocusing and anion exchange chromatography

A method was developed for the preparation of continuous beds derivatized with polyethyleneimine (PEI) for chromatofocusing and anion exchange chromatography in the capillary mode. First, a continuous bed activated by epoxy groups was synthesized inside a fused silica capillary and became at the same time covalently attached to the inner wall of the capillary. A PEI solution was then pumped through the continuous bed to allow the imine groups in PEI to react with the epoxy groups in the bed. Efficient immobilization of PEI was indicated by the high-resolution separation of standard proteins (hemoglobins C, S, F, and A) in both chromatofocusing and anion exchange chromatography on a capillary column prepared by this method.

Biochemical separations by continuous-bed chromatography

Innovations in column-packing media for biomolecule purification have progressed from large spherical, porous polysaccharide beads to advanced polymeric supports. Continuous-bed technology is a radical new technology for chromatography based on the polymerization of advanced monomers and ionomers directly in the chromatographic column. The polymer chains form aggregates which coalesce into a dense, homogeneous network of interconnected nodules consisting of microparticles with an average diameter of 3000 A. The voids or channels between the nodules are large enough to permit a high hydrodynamic flow. Due to the high cross-linking of the polymer matrix, the surface of each nodule is nonporous yet the polymeric microparticles provide a very large surface area for high binding capacity. This paper will demonstrate the properties and advantages of using a continuous bed support for high resolution biomolecule separations at high flow-rates without sacrificing capacity.

Continuous beds for microchromatography: detection of proteins by a blotting membrane technique

Continuous beds have been used as matrices for cation- and anion-exchange chromatography of proteins on columns with an i.d. in the range of 0.005-0.015 mm. On-tube uv detection is not feasible at low protein concentrations with these narrow-bore columns. Therefore, a more sensitive detection system has been developed based on blotting technique: as the protein zones leave the microcolumn chromatographically they become adsorbed onto a rotating polyvinylidene difluoride blotting membrane. The protein spots can then be visualized by means of Coomassie brilliant blue, immunomethods, and other standard techniques. By using an immunomethod 0.015 ng of human transferrin can easily be detected. The blotting membrane can be washed with water without loss of adsorbed protein. This is an attractive feature because the presence of salts, etc., diminishes the accuracy in the determination of molecular weights of proteins by mass spectrometry. The microcolumns are easy to prepare. A solution of appropriate monomers is sucked into a piece of fused silica tubing. The rod formed upon polymerization contains channels through which the eluent can pass. No supporting frit is required because the polymer rod is anchored by covalent bonds to the tubing wall.

Continuous beds for microchromatography: reversed-phase chromatography

Simple and cost-effective methods for the preparation of microcolumns (i.d. 0.025-0.32 mm) for reversed-phase chromatography are described. The procedure includes (1) synthesis in the column tube of a continuous bed matrix from a monomer solution (piperazine diacrylamide, methacrylamide) containing allyl glycidyl ether and 2-hydroxyethyl methacrylate and (2) linking of C18 ligands by reacting 1,2-epoxyoctadecane with the epoxy and hydroxy groups in the matrix. The derivatization can be accomplished within 20 min. The columns prepared in this way showed high performance in the separation of proteins and peptides and permitted short analysis times (100 s).

A highly stable methyl cellulose coating for capillary electrophoresis

A highly stable capillary-coating has been created by coupling covalently a hydroxyl group of methyl cellulose to the epoxy group of alpha-glycidoxypropyltrimethoxysilane attached to a piece of fused silica tubing. This coating strongly suppresses electroendosmotic flow (EOF) and minimizes sample adsorption onto the capillary wall for several weeks or months. The stability of the coating has been tested with isoelectric focusing and free zone electrophoresis. The coupling procedure is easy to perform, and the coating withstands at least 135 consecutive runs under extreme pH conditions (2-12). EOF is still reduced after placing the coated capillary in 0.01 M NaOH for 30 days. A detailed description of the coating procedure is provided.

Fast, high-resolution (capillary) electrophoresis in buffers designed for high field strengths

Capillary electrophoresis in conventional buffers and in 50 microns capillaries permits field strengths as high as 300-500 V/cm with acceptably low thermal zone deformation. However, still higher field strengths (up to at least 2000 V/cm) can be applied without a decrease in resolution if the experiments are performed in the buffers described in this paper. Characteristic of these buffers is their low electrical conductivity and yet satisfactory buffering capacity accomplished either (i) by selecting buffer constituents of relatively high molecular weight and small net charge or (ii) by fractionation of carrier ampholytes (originally introduced for isoelectric focusing experiments) into a series of narrow pH range fractions and using these fractions as buffers, or (iii) by selecting an ampholyte with two acidic groups and one basic group (or one acidic group and two basic groups) and with a pI value close to two of its pK values. In such buffers, aromatic carboxylic acids and proteins used as model substances could be analyzed rapidly. For instance, albumin and transferrin were separated at 30,000 V (1.99 microA) in 15 cm long fused silica capillaries (50 microns ID) within 40 s and the carboxylic acids within 25 s. The resolution was similar to that obtained at standard voltage (5000 V; 0.33 microA), but the analysis time was reduced sixfold. Although not verified experimentally we also suggest the use of relatively high-molecular-weight polyoxyethylene derivatized with one acidic group (for instance, boric acid) and one basic group (an amine), both having the same pK value, which should afford both a very high buffering capacity and very low electrical conductivity (at low buffer concentrations).

Continuous beds for microchromatography: cation-exchange chromatography

Microcolumns (i.d. 10-320 microns) for cation-exchange chromatography can be prepared simply by polymerization of an aqueous solution of appropriate monomers, including the desired ligand, directly in the chromatographic tube (fused-silica tubing) in the presence of salt. The beds thus prepared are in the form of rods traversed by channels through which the eluent can pass. The walls of the channels are composed of very small particles and are impermeable to peptides and proteins, which is important for rapid mass transfer and thus for high resolution at high flow rates. The bed becomes attached covalently to the tube wall during synthesis. A complicated column tube design with a supporting frit at the bottom is thus eliminated. The absence of a frit reduces the flow resistance and facilitates interfacing to mass spectrometers. The covalent linkage of the bed to the tube wall also serves to suppress the zone-broadening "wall effect." A homogeneous "packing" of a continuous bed column with an inner diameter as small as 10 microns is easily obtained. The resolution, binding capacity, and flow rate (i.e., run time at a given pressure) can be varied by changing the composition of the monomer solution. One can thus tailor the beds to each separation problem. The chromatographic properties of the microcolumns are demonstrated by separations of model proteins.

Mitogenic properties of two distinct forms of toxic shock syndrome toxin-1 separated on hydroxyapatite by high-performance liquid chromatography

The homogeneity of a purified staphylococcal toxic shock syndrome toxin-1 (TSST-1) was tested by high-performance methods. This preparation was homogenous in ion-exchange chromatography and isoelectric focusing (pI = 7.4), but was resolved into two distinct peaks by high-performance hydroxyapatite chromatography. Both components, TSST-1hA and TSST-1hB had similar molecular weights (22 kD) and amino acid compositions. TSST-1 did not dimerize or polymerize upon heating at 60 degrees C for 30 min or in solutions with pH varying from 4.0 to 8.5. TSST-1hA and TSST-1hB showed similar immunological reactivity to native TSST-1 goat polyclonal antibodies. TSST-1hA and TSST-1hB as well as staphylococcal enterotoxin A and staphylococcal exfoliative toxin were potent mitogens in lymphocyte proliferation assays. The lymphocyte proliferative response to 10 pg of TSST-1hB was comparable to a response elicited by 10 ng of TSST-1hA, suggesting that the former component is a more potent mitogen. Rabbit or goat polyclonal antibodies to native TSST-1 efficiently neutralized both TSST-1 components. Heat treatment at 80 degrees C for 15 min had minimal or no effect on the mitogenic properties of TSST-1hA and TSST-1hB.

High-performance liquid chromatography of proteins on compressed, non-porous agarose beads. II. Anion-exchange chromatography

Macroporous agarose beads were rendered impermeable to proteins by shrinkage and cross-linking in organic solvents. The chromatographic properties of compressed beds of these non-porous beads derivatized for high-performance ion-exchange chromatography were studied, e.g., the resolution as a function of gradient time, flow-rate (at constant gradient volume) and loading capacity. The columns permit high flow-rates and the resolution is about the same at low and high flow-rates. The beads are stable up to pH 14.

High-performance liquid chromatography of proteins on compressed, non-porous agarose beads. I. Hydrophobic-interaction chromatography

Macroporous agarose beads were converted into non-porous beads by shrinkage and cross-linking in organic solvents. These beads could be used for high-performance hydrophobic-interaction chromatography without derivatization with non-polar ligands, because the 1,4-butanediol diglycidyl ether, used as cross-linker, gives relatively hydrophobic bridges. The resolution for compressed columns packed with these beads was determined as a function of gradient time at constant flow-rate, flow-rate at constant gradient volume and flow-rate at constant gradient time and as a function of loading capacity. Interestingly, the resolution is virtually independent of flow-rate at constant gradient volume even when the column is packed with relatively large beads (diameter 30 microns). The beads have the advantage of being stable up to pH 14.

Carrier-free zone electrophoresis, displacement electrophoresis and isoelectric focusing in a high-performance electrophoresis apparatus

A characteristic feature of high-performance electrophoresis (HPE), the electrophoretic counterpart of high-performance liquid chromatography (HPLC), is that the separation chamber is a thin-walled, narrow-bore (0.05-0.3 mm) glass or fused-silica capillary tube for rapid dissipation of the Joule heat in order to minimize thermal zone deformation even at high field strengths. This paper is centered around the usefulness of HPE for separation in a carrier-free medium (i.e., in buffer alone) and deals with both zone electrophoresis, isoelectric focusing and displacement electrophoresis. Examples are given of analytical and micropreparative separations of inorganic and organic ions, proteins, viruses and bacteria. The run times are 5-30 min. Discontinuous buffer systems have up to now been used exclusively for the separation of proteins by electrophoresis in polyacrylamide gels ("disc electrophoresis"). However, the Ornstein and Davis discontinuous buffer system has been modified to adapt it to carrier-free zone electrophoresis in order to achieve automatic sharpening of the starting zone. Very high resolution of serum proteins was obtained when they were subjected to free high-performance disc electrophoresis in such a modified buffer system. To show that the HPE apparatus permits electrophoresis also in a gel medium, a polyacrylamide electrophoresis in SDS is presented. This experiment illustrates the difference between electropherograms obtained in free solution and in a molecular-sieving medium. Detection can be performed both on- and off-tube. The latter technique permits the rapid identification of the solutes by photodiode array spectrophotometry and the collection of fractions for further studies. The former detection method is simpler but mainly useful for analytical purposes. Non-UV-absorbing ions can be monitored with the aid of an on-tube UV detector if the run is performed in a UV-absorbing buffer.

Application of high-performance chromatographic and electrophoretic methods to the purification and characterization of glucose oxidase and catalase from Penicillium chrysogenum

The high resolving power of the preparative and analytical high-performance chromatographic and electrophoretic methods recently developed in this laboratory for the separation of biopolymers has been demonstrated by the purification and characterization of glucose oxidase and catalase from Penicillium chrysogenum. Crude glucose oxidase was purified to homogeneity in one step by high-performance hydrophobic-interaction chromatography (HIC) on a pentylagarose column. Crude catalase was purified by a combination of HIC and high-performance anion-exchange chromatography on 3-diethylamino-2-hydroxypropylagarose. The homogeneity of the enzymes was monitored by high-performance electrophoresis and free zone electrophoresis. The pI values of these two enzymes determined by isoelectric focusing in the high-performance electrophoresis apparatus were 4.2 and 6.5, respectively. Their molecular weights were determined by high-performance molecular sieve chromatography on an agarose column. Glucose oxidase has a molecular weight of 175,000 and probably consists of two identical subunits, as sodium dodecyl sulphate polyacrylamide gel electrophoresis gave a molecular weight of around 72,000. The molecular weight of catalase, which is probably composed of non-identical subunits, as indicated by sodium dodecyl sulphate electrophoresis, is around 320,000. Some other characteristics of these two enzymes were also investigated, e.g., electrophoretic mobility, pH stability and optimum pH.

Theoretical and experimental study of high-performance electrophoretic mobilization of isoelectrically focused protein zones

In an earlier paper we showed that it is possible to mobilize a train of isoelectrically focused proteins and thus detect them on-tube or off-tube. The mobilization was performed in different ways, for instance electrophoretically by exchanging the anolyte for the catholyte or vice versa. In this paper we treat the electrophoretic mobilization theoretically, originating from the conditions of electroneutrality. The information thus gained was used to design anolytes and catholytes of appropriate compositions for mobilization of focused proteins. The usefulness of these electrode solutions is illustrated by focusing-mobilization experiments performed in free solution in a glass tube of length 110 mm. Since the inside diameter of the tube and its wall thickness were only 0.05 mm, the Joule heat was efficiently removed, which allowed the use of high field strengths (270 V/cm). The focusing time was therefore as short as 6 min. The time required for mobilization was about 15 min (360 V/cm). The mobilized protein zones were detected on-tube by absorbance measurements at 280 nm. The glass tube was treated with non-cross-linked polyacrylamide to eliminate electroendosmosis and adsorption of proteins onto the tube wall. The following conclusions drawn from the theoretical studies were experimentally verified: mobilization toward the anode (cathode) can be accomplished by selecting an anolyte (catholyte) containing a cation (anion) other than the proton (hydroxyl ion); the cation (anion) will then electrophoretically migrate into the separation tube and continuously increase (decrease) the pH from the anodic (cathodic) end of the tube. The pH of the electrode solution toward which the mobilization takes place is critical for off-tube, but not for on-tube detection. With the aid of the electroneutrality condition that applies in isoelectric focusing, one can easily explain the generation of the so-called plateau phenomenon.