Machine learning approaches in MALDI-MSI: clinical applications

Introduction: Despite the unquestionable advantages of Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging in visualizing the spatial distribution and the relative abundance of biomolecules directly on-tissue, the yielded data is complex and high dimensional. Therefore, analysis and interpretation of this huge amount of information is mathematically, statistically and computationally challenging.

Areas covered: This article reviews some of the challenges in data elaboration with particular emphasis on machine learning techniques employed in clinical applications, and can be useful in general as an entry point for those who want to study the computational aspects. Several characteristics of data processing are described, enlightening advantages and disadvantages. Different approaches for data elaboration focused on clinical applications are also provided. Practical tutorial based upon Orange Canvas and Weka software is included, helping familiarization with the data processing.

Expert commentary: Recently, MALDI-MSI has gained considerable attention and has been employed for research and diagnostic purposes, with successful results. Data dimensionality constitutes an important issue and statistical methods for information-preserving data reduction represent one of the most challenging aspects. The most common data reduction methods are characterized by collecting independent observations into a single table. However, the incorporation of relational information can improve the discriminatory capability of the data.     

Selection for novel metabolic capabilities in Salmonella enterica

Bacteria are known to display extensive metabolic diversity and many studies have shown that they can use an extensive repertoire of small molecules as carbon‐ and energy sources. However, it is less clear to what extent a bacterium can expand its existing metabolic capabilities by acquiring mutations that, for example, rewire its metabolic pathways. To investigate this capability and potential for evolution of novel phenotypes, we sampled large populations of mutagenized Salmonella enterica to select very rare mutants that can grow on minimal media containing 124 low molecular weight compounds as sole carbon sources. We found mutants growing on 18 of these novel carbon sources, and identified the causal mutations that allowed growth for four of them. Mutations that relieve physiological constraints or increase expression of existing pathways were found to be important contributors to the novel phenotypes. For the remaining 14 novel phenotypes, whole genome sequencing of independent mutants and genetic analysis suggested that these novel metabolic phenotypes result from a combination of multiple mutations. This work, by virtue of identifying the genetic and mechanistic basis for new metabolic capabilities, sheds light on the properties of adaptive landscapes underlying the evolution of novel phenotypes.     

Chiral discrimination by ligand-exchange chromatography: A comparison between phenylalaninamide-based stationary and mobile phases

The copper(II) complexes of two new diastereomeric ligands, N²-(R)- and N²-(S)-2′-hydroxypropyl-(S)-phenylalaninamide [(R, S)-1 and (S, S)-1], have been used as additives to the eluent in high-performance liquid chromatography (HPLC) reversed phase for the chiral separation of DNS-amino acids. The aim was that of comparing the separation process obtained by the chiral eluent with that obtained by an analogous bonded stationary phase containing (S)-phenylalaninamide, previously studied [CSP-(S)-Phe-NH₂]. The affinity of the ternary complexes for the C₁₈ column was determined by adsorption experiments in HPLC. It was shown that the two systems (chiral eluent, chiral stationary phase) work according to different mechanisms. Ternary complex formation in solution was studied by fluorescence spectroscopy. It was shown that chiral separation with the Cu(II) complexes added to the eluent was determined by the relative affinities of the ternary complexes for the column-stationary phase rather than by their stabilities in solution. With CSP-(S)-Phe-NH₂ the separation is accounted for by the relative stabilities of the ternary complexes, which depends mainly on the “allowed” geometry of the complex and on the steric repulsion of the amino acid side chain with the spacer. © 1996 Wiley-Liss, Inc.     

Serum total prostate-specific antigen assay in women with Cushing's disease or alcohol-dependent pseudo-Cushing's State

BACKGROUND: The distinction between Cushing's disease (Cushing's syndrome dependent on adrenocorticotropic hormone (ACTH)-secreting tumors of pituitary origin) and pseudo-Cushing's states (Cushingoid features and hypercortisolism sometimes present in alcoholic, depressed or obese subjects) can present a diagnostic challenge in clinical endocrinology. Recently, the availability of a highly sensitive immunofluorometric assay for the measurement of total prostate-specific antigen (PSA) provided the possibility to measure serum PSA levels in women. Interestingly, PSA gene expression and protein production has been found to be upregulated by steroid hormones, such as androgens, glucocorticoids, mineral corticoids and progestins. In fact, serum total PSA concentrations appear to be higher in female patients with Cushing's disease than in normal women. We wondered whether a similar phenomenon also occurs in pseudo-Cushing's state. METHODS: In order to answer this question, we compared the serum total PSA levels measured in 10 female subjects with alcohol-dependent pseudo-Cushing's state with those observed in 8 female patients with Cushing's disease and in 15 age-matched healthy women. Serum testosterone, ACTH and cortisol, and 24-hour urinary cortisol levels were measured; cortisol suppression after dexamethasone was also tested in all subjects. RESULTS: The basal serum levels of ACTH and cortisol were significantly lower in normal subjects than in patients with Cushing's disease or pseudo-Cushing's state; these latter groups showed similar basal hormonal values. Dexamethasone administration was unable to suppress serum cortisol levels in 5 subjects with Cushing's disease and 6 subjects with pseudo-Cushing's state. Serum testosterone values in the group with Cushing's disease were higher than in the other groups. No differences were observed between pseudo-Cushing's and normal subjects. Serum total PSA levels were significantly higher in women with Cushing's disease than in subjects with pseudo-Cushing's state and normal controls; these latter groups showed similar PSA values. When serum total PSA and testosterone levels were considered together, a significant positive correlation was observed in the group with Cushing's disease, but not in the other groups. CONCLUSIONS: These data indicate that the steroid milieu responsible for the elevation in serum PSA in women with Cushing's disease is not present in subjects with alcohol-dependent pseudo-Cushing's state, suggesting the possible use of PSA as a marker of differentiation between these pathological conditions in women.     

Light-induced multistep oxidation of dinuclear manganese complexes for artificial photosynthesis

Two dinuclear manganese complexes, [Mn(2)BPMP(mu-OAc)(2)].ClO(4) (1, where BPMP is the anion of 2,6-bis([N,N-di(2-pyridinemethyl)amino]methyl)-4-methylphenol) and [Mn(2)L(mu-OAc)(2)].ClO(4) (2, where L is the trianion of 2,6-bis([N-(2-hydroxy-3,5-di-tert-butylbenzyl)-N-(2-pyridinemethyl)amino]methyl)-4-methylphenol), undergo several oxidations by laser flash photolysis, using ruthenium(II)-tris-bipyridine (tris(2,2-bipyridyl)dichloro-ruthenium(II) hexahydrate) as photo-sensitizer and penta-amminechlorocobalt(III) chloride as external electron acceptor. In both complexes stepwise electron transfer was observed. In 1, four Mn-valence states from the initial Mn(2)(II,II) to the Mn(2)(III,IV) state are available. In 2, three oxidation steps are possible from the initial Mn(2)(III,III)state. The last step is accomplished in the Mn(2)(IV,IV) state, which results in a phenolate radical. For the first time we provide firm spectral evidence for formation of the first intermediate state, Mn(2)(II,III), in 1 during the stepwise light-induced oxidation. Observation of Mn(2)(II,III) is dependent on conditions that sustain the mu-acetato bridges in the complex, i.e., by forming Mn(2)(II,III) in dry acetonitrile, or by addition of high concentrations of acetate in aqueous solutions. We maintain that the presence of water is necessary for the transition to higher oxidation states, e.g., Mn(2)(III,III) and Mn(2)(III,IV) in 1, due to a bridging ligand exchange reaction which takes place in the Mn(2)(II,III) state in water solution. Water is also found to be necessary for reaching the Mn(2)(IV,IV) state in 2, which explains why this state was not reached by electrolysis in our earlier work (Eur. J. Inorg. Chem (2002) 2965). In 2, the extra coordinating oxygen atoms facilitate the stabilization of higher Mn valence states than in 1, resulting in formation of a stable Mn(2)(IV,IV) without disintegration of 2. In addition, further oxidation of 2, led to the formation of a phenolate radical (g = 2.0046) due to ligand oxidation. Its spectral width (8 mT) and very fast relaxation at 15 K indicates that this radical is magnetically coupled to the Mn(2)(IV,IV) center.     

d-matrix – database exploration,visualization and analysis

Background  

Motivated by a biomedical database set up by our group, we aimed to develop a generic database front-end with embedded knowledge discovery and analysis features. A major focus was the human-oriented representation of the data and the enabling of a closed circle of data query, exploration, visualization and analysis.     

Head development in the onychophoran Euperipatoides kanangrensis with particular reference to the central nervous system

The neuroectoderm of the Euperipatoides kanangrensis embryo becomes distinguishable during germ band formation when the antennal segment is evident externally. During later stages of development, the neuroectoderm proliferates extensively and, at the anterior part of the head, newly-formed neuron precursor cells occupy most of the volume. The antenna forms from the dorsolateral side of the anterior somite. The antenna has no neuroectoderm of its own at the onset of its formation, but instead, neurons migrate out to the appendage from the nearby region of the developing brain. When the antennal tract is formed it is positioned horizontally in the brain, in line with the antennal commissure. Only later, and coincidentally with the anterior repositioning of the antenna, is the tract's distal part bent anteriorly and positioned laterally. The eye starts to develop posteriorly to the antenna and the antennal commissure. This suggests that the segment(s) associated with the onychophoran eye and antenna are not serially homologous with segments carrying equivalent structures within the Euarthropoda. Evidence is presented to further support the presence of a terminal mouth in the ground plan of the Onychophora and, hence, an acron may not exist in the arthropod clade.