Cross-platform comparison of microarray-based multiple-class prediction

High-throughput microarray technology has been widely applied in biological and medical decision-making research during the past decade. However, the diversity of platforms has made it a challenge to re-use and/or integrate datasets generated in different experiments or labs for constructing array-based diagnostic models. Using large toxicogenomics datasets generated using both Affymetrix and Agilent microarray platforms, we carried out a benchmark evaluation of cross-platform consistency in multiple-class prediction using three widely-used machine learning algorithms. After an initial assessment of model performance on different platforms, we evaluated whether predictive signature features selected in one platform could be directly used to train a model in the other platform and whether predictive models trained using data from one platform could predict datasets profiled using the other platform with comparable performance. Our results established that it is possible to successfully apply multiple-class prediction models across different commercial microarray platforms, offering a number of important benefits such as accelerating the possible translation of biomarkers identified with microarrays to clinically-validated assays. However, this investigation focuses on a technical platform comparison and is actually only the beginning of exploring cross-platform consistency. Further studies are needed to confirm the feasibility of microarray-based cross-platform prediction, especially using independent datasets.     

Quantitation of methylmalonic acid and other dicarboxylic acids in normal serum and urine using capillary gas chromatography-mass spectrometry

Methylmalonic acid, succinic acid, and other dicarboxylic acids have been extracted and partially purified from serum and urine using ether extraction and high-performance liquid chromatography. The t-butyldimethylsilyl derivatives were prepared and analyzed using capillary gas chromatography-mass spectrometry with selected ion monitoring. The addition of [methyl-2H3]methylmalonic acid and [1,4-13C2]succinic acid to the starting samples made it possible to quantitate these two dicarboxylic acids. Normal ranges for methylmalonic acid and succinic acid were determined in human and rat serum and in human urine. The utilization of other internal standards would make it possible to quantitate malonic, dimethylmalonic, ethylmalonic, methylsuccinic, glutaric, and other dicarboxylic acids.     

Lymphangiogenesis and breast cancer metastasis

Breast cancer is one of the commonest malignancies in women in the western world. It spreads predominantly via the lymphatic system. However, the understanding of the formation of lymphatics, lymphangiogenesis, has been limited. This has been largely due to the previous lack of lymphatic specific markers. The most specific marker used in humans has been the vascular endothelial growth factor receptor 3 (VEGFR-3). However, this is also found on blood vessel endothelium. The other vascular endothelial factor receptors (VEGFR-1 and -2) are primarily blood vessel receptors. More recently, novel, specific markers for lymphatics have been discovered, such as LYVE-1, prox I and podoplanin, enabling further research into this new field. Each of these new markers is described in detail. The article also outlines the current understanding in breast cancer metastasis, with an emphasis on the more recent research into lymphangiogenesis. Since these specific markers are now available, quantitation of lymphangiogenesis is now possible by using either immunohistochemistry or quantitative PCR approaches. In addition, to breast cancer, research into many other cancers is now possible using these methods and new markers. With this in mind, possible therapeutic strategies for the future are discussed.     

Sentinel lymph node in esophageal cancer before neoadjuvant therapy

The technique of sentinel lymph node identification and biopsy has become a new popular technique for surgeon to improve staging of malignant diseases. It may also reduce the risk of complication related to standard lymphadenectomy. The method is still in experimental phase in case of esophageal cancer. A possible complication for employment of the method in this tumor is neoadjuvant therapy. The authors developed the technique for identifying and obtaining the sentinel lymph node in esophageal cancer using minimally invasive surgical technique before neoadjuvant therapy. The sentinel lymph node is detected using 99mTc-labelled nanocolloid. The authors report and discuss possible difficulties of the method in the case of a patient with detected sentinel lymph node in this way. Conclusion: It is possible to identify and obtain a sentinel lymph node before neoadjuvant therapy in esophageal cancer. On the other hand, the clinical significance and applicability of the method of sentinel lymph node still remains controversial in this kind of a tumor.     

Use of Microautoradiography to Study in situ Physiology of Bacteria in Biofilms

Microautoradiography is a technique that enables direct detection of active bacteria in complex microbial systems on a single cell level. When combined with fluorescence in situ hybridization using oligonucleotide probes for identification of the microorganisms, it is possible to link key physiological features to the identity of microorganism. In this way information can be obtained about the physiology of cultured as well as not-yet cultured microorganism in biofilms and other complex ecosystems in a way that presently cannot be provided by other methods. In this small review we describe the basic procedure, the type of information that can be obtained, the most important limitations by using this approach, and some recent examples from biofilms and other complex microbial communities.     

Self‐report of physical symptoms associated with using mobile phones and other electrical devices

The aim of our work was to study the working‐age population's self‐reported physical symptoms associated with using mobile phones and other electrical devices. A qualitative method was applied using an open‐ended question in a questionnaire, which included questions about the possible influence of new technical equipment on health. We then created subgroups of respondents for different self‐reported symptoms associated with mobile phones and other electrical devices. The research questions were: (1) how the respondents described physical symptoms associated with using mobile phones and other electrical devices and (2) how the answers can be classified into subgroups based on symptoms or devices. We identified the following categories: (1) respondents with different self‐reported symptoms which they associated with using mobile phones (headache, earache, or warmth sensations), (2) respondents who had skin symptoms when they stayed in front of a computer screen, (3) respondents who mentioned physical symptoms associated with using mobile phones and other electrical devices. Total prevalence of self‐reported physical symptoms associated with using mobile phones and other electrical devices (categories 1 and 2) was 0.7%. In the future it will be possible to obtain new knowledge of these topics by using qualitative methods. Bioelectromagnetics 30:431–437, 2009. © 2009 Wiley‐Liss, Inc.     

Rational design of carbonitrile-carboxaldehyde cation receptor models: probing the nature of the heteroatom–metal interaction

Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.     

DNA fingerprinting of Mycobacterium xenopi strains

Mycobacterium xenopi is an environmental bacterium that occasionally causes disease in humans. A method is described for DNA fingerprinting strains of this species. Seven of 10 strains from humans were clearly distinguishable from each other using DNA fingerprinting. This method will enable the investigation of possible environmental sources and human spread of disease due to this species.     

Bihelix: Towards de novo structure prediction of an ensemble of G‐protein coupled receptor conformations

G‐Protein Coupled Receptors (GPCRs) play a critical role in cellular signal transduction pathways and are prominent therapeutic targets. Recently there has been major progress in obtaining experimental structures for a few GPCRs. Each GPCR, however, exhibits multiple conformations that play a role in their function and we have been developing methods aimed at predicting structures for all these conformations. Analysis of available structures shows that these conformations differ in relative helix tilts and rotations. The essential issue is, determining how to orient each of the seven helices about its axis since this determines how it interacts with the other six helices. Considering all possible helix rotations to ensure that no important packings are overlooked, and using rotation angle increments of 30° about the helical axis would still lead to 12⁷ or 35 million possible conformations each with optimal residue positions. We show in this paper how to accomplish this. The fundamental idea is to optimize the interactions between each pair of contacting helices while ignoring the other 5 and then to estimate the energies of all 35 million combinations using these pair‐wise interactions. This BiHelix approach dramatically reduces the effort to examine the complete set of conformations and correctly identifies the crystal packing for the experimental structures plus other near‐native packings we believe may play an important role in activation. This approach also enables a detailed structural analysis of functionally distinct conformations using helix‐helix interaction energy landscapes and should be useful for other helical transmembrane proteins as well. Proteins 2012. © 2011 Wiley Periodicals, Inc.     

Effective saccharification of kraft pulp by using a cellulase cocktail prepared from genetically engineered Aspergillus oryzae

Kraft pulp is a promising feedstock for bioproduction. The efficiency of kraft pulp saccharification was improved by using a cellulase cocktail prepared from genetically engineered Aspergillus oryzae. Application of the cellulase cocktail was demonstrated by simultaneous saccharification and fermentation, using kraft pulp and non-cellulolytic yeast. Such application would make possible to do an efficient production of other chemicals from kraft pulp.     

Characterization of envelope proteins from Pasteurella haemolytica and Pasteurella multocida

A method was devised for the reproducible isolation of envelopes from Pasteurella haemolytica serotype A2. It was also possible to prepare envelopes from other serotypes of P. haemolytica and Pasteurella multocida using this methodology. Examination of these preparations by SDS-PAGE showed major differences between strains of P. haemolytica and strains of P. multocida which allowed the clear distinction of isolates of these species. Amongst the P. haemolytica serotypes it was possible to distinguish envelope preparations made from A biotype and T biotype organisms easily, but it was not possible to identify individual serotypes from each other. Envelope profiles were sufficiently different between the individual P. multocida serotypes examined to allow each to be identified by its polypeptide profile. Experiments using radiolabelling, antibody absorption, and susceptibility to protease digestion, together with heat modifiability and detergent solubility characteristics indicated that 13 of the envelope proteins were probably surface-located. A high molecular mass immunogenic envelope protein was shown, by immunoblotting, to be present in all strains of P. haemolytica and P. multocida examined.     

The importance of HLA typing in cases of disputed paternity

In dispute paternity, the biologists must reply to two questions: 1. Is the paternity excluded or possible? 2. If it is possible, what is its probability? Valid answers can be given, using several genetic markers, among which HLA genes are specially interesting. Looking at HLA-A, B, C, DR typing of child, mother and presumed father, we propose a method which allows a direct calculation of paternity probability. Crossing over between HLA genes in presumed father and in mother are also considered in this method. In our experience, adding the date provided by the HLA genes and other genetic markers, we obtained, either formal exclusions, or possible paternities with a probability almost always higher than 90%.     

Urease from a sea urchin Lytechinus variegatus: partial purification and kinetics.

1. Urease from a sea urchin Lytechinus variegatus, was purified 300-fold, using heat precipitation, ethanol precipitation and gel filtration. 2. The pH optimum is 8.0. 3. The apparent Michaelis constant for urea is 0.13 mM at pH 8.0. 4. The inhibitory effects of seven reagents on urease were evaluated. The pattern of inhibition is similar to other invertebrate ureases. 5. L. variegatus urease is compared with that of several other invertebrates, and its possible significance in CaCO3 formation is discussed.     

Protein and enzyme release from human leukocytes: influence of phenothiazine derivatives.

We studied the influence of chlorpromazine on the release of enzymes (beta-glucuronidase, EC 3.2.1.31; lactate dehydrogenase, EC 1.1.1.27; pyruvate kinase, 2.7.1.40) and proteins using human granulocytes isolated and maintained at 37 degrees C. Chlorpromazine had a biphasic effect on enzyme release and the inhibition of the glycolytic pathway could be demonstrated only at high concentrations of chlorpromazine, after one hour's incubation. The NAD+/NADH ratio was significantly perturbed at all the concentrations. This effect is time dependent. The action of 4 other phenothiazine derivatives made it possible to establish a relationship between their physico-chemical properties and protein release. The results are compared with those from other studies using other biological materials.     

Micropreparation of hemopoietic stem cells from the mouse bone marrow suspension by gravitational field-flow fractionation

Gravitational field-flow fractionation is a relatively simple experimental technique. This method was used for the characterization of stem cells from mouse bone marrow. Because these cells are bigger than the other cells in bone marrow, it is possible to separate them from the mixture. The fractions collected after passing through the separation channel were characterized using a Coulter Counter and used for transplantation into irradiated mice.     

Identification of ubiquitin nitration and oxidation using a liquid chromatography/mass selective detector system.

Ubiquitin is a member of the family of low-molecular-weight heat shock proteins that serve a vital role in physiological and pathological protein turnover. It appears to be one of the proteins involved in cell alterations during aging, degenerative disorders, and age-related cognitive decline. It is not known exactly how ubiquitin alterations are related to aging disorders; however, it is possible that ubiquitin is one of the target proteins for free-radical attack. In vivo, the free radical superoxide reacts with nitric oxide to form peroxynitrite, a powerful oxidant. Peroxynitrite may react directly with proteins, lipids, and other molecules to cause damage, with ubiquitin being a possible target. In vitro reaction of peroxynitrite with ubiquitin produces two modified forms of the protein, one oxidized at methionine and the other nitrated at tyrosine, which were characterized by electrospray ionization time-of-flight mass spectrometry. The exact location of the nitrated tyrosine residue was determined by in-source collision-induced dissociation using electrospray ionization time-of-flight mass spectrometry.     

Olive baboon (Papio anubis anubis) as a model for intrauterine research

BACKGROUND: The Olive baboon is a popular animal model for reproductive and surgical research. The Institute of Primate Research, Nairobi, Kenya, has been using the animal for reproductive research for many years. In the baboon, compared with other smaller non-human primates, it is possible to insert uterine probes such as, catheters, curettes and other linear instruments (to cannulate cervix for uterine procedures like flushing, endometrium biopsy, embryo transfer, etc.). METHODS: However we noticed in a few animals this was difficult and problematic, particularly in some stages of the menstrual cycle, in retroverted uteri, in extensive adhesions or in some anatomically unique animals and we have developed a technique called 'Chai technique' for this purpose. RESULTS AND CONCLUSIONS: The Chai technique is unique to the baboon and not possible in human. It does not seem to cause injuries as frequently as uterine perforation and, in our experience, has been surprisingly successful.     

Revisiting the use of Iprodione and Trichoderma in the integrated management of onion white rot

The biocontrol properties of Trichoderma species are well documented, but their effectiveness in antagonism of the problematic Sclerotium cepivorum, the causal agent of white rot in Allium species, appears limited with reports of significant control only relating to deliberately-mutated strains of Trichoderma. Our previous studies have indicated the possibility of using selected naturally-occurring strains of the antagonist in the suppression of other diseases; now in vitro and controlled environment in vivo studies have indicated that a degree of control of Onion White Rot is possible, and that the selected antagonist strains can be used in integrated treatments with Iprodione to good effect. The possible value of such treatments is considered in light of other approaches to the suppression of this continuing problem.