Reactive trityl derivatives: stabilised carbocation mass-tags for life sciences applications

The rational design of novel triarylmethyl (trityl)-based mass tags (MT) for mass-spectrometric (MS) applications is described. We propose a "pKR+ rule" to correlate the stability of trityl carbocations with their MS performance: trityls with higher pKR+ values ionise and desorb better. Trityl blocks were synthesised that have high pKR+ values and are stable in conditions of MS analysis; these MTs can be ionised by matrix as well as irradiation with a 337 nm nitrogen laser. 13C-Labelled tags were prepared for MS quantitation applications. Moreover, the tags were equipped with a variety of functional groups allowing conjugation with different functionalities within (bio)molecules to enhance the MS characteristics of the latter. The MS behaviour of model polycationic trityl compounds with and without the matrix was studied to reveal that poly-trityl clusters are always singly charged under the (MA)LDI-TOF conditions. Several peptide-trityl conjugates were prepared and comparisons revealed a beneficial effect of trityl tags on the conjugate detection in MS. Trityl compounds containing para-methoxy- and dimethylamine groups, as well as a xanthene fragment, showed considerable enhancement in MS detection of model peptides; thus they are promising tools for proteomic applications. Dimethoxytrityl derivatives allow one to distinguish between Arg- and Lys-containing peptides. Maleimido trityl derivatives are suitable for the efficient derivatisation of thiol-containing peptides in pyridine

Properties of Graphene: A Theoretical Perspective

In this review, we provide an in-depth description of the physics of monolayer and bilayer graphene from a theorist's perspective. We discuss the physical properties of graphene in an external magnetic field, reflecting the chiral nature of the quasiparticles near the Dirac point with a Landau level at zero energy. We address the unique integer quantum Hall effects, the role of electron correlations, and the recent observation of the fractional quantum Hall effect in the monolayer graphene. The quantum Hall effect in bilayer graphene is fundamentally different from that of a monolayer, reflecting the unique band structure of this system. The theory of transport in the absence of an external magnetic field is discussed in detail, along with the role of disorder studied in various theoretical models. We highlight the differences and similarities between monolayer and bilayer graphene, and focus on thermodynamic properties such as the compressibility, the plasmon spectra, the weak localization correction, quantum Hall effect, and optical properties. Confinement of electrons in graphene is nontrivial due to Klein tunneling. We review various theoretical and experimental studies of quantum confined structures made from graphene. The band structure of graphene nanoribbons and the role of the sublattice symmetry, edge geometry and the size of the nanoribbon on the electronic and magnetic properties are very active areas of research, and a detailed review of these topics is presented. Also, the effects of substrate interactions, adsorbed atoms, lattice defects and doping on the band structure of finite-sized graphene systems are discussed. We also include a brief description of graphane -- gapped material obtained from graphene by attaching hydrogen atoms to each carbon atom in the lattice.Comment: 189 pages. submitted in Advances in Physic

Effects of dietary supplementation with protected sodium butyrate on gut microbiota in growing-finishing pigs

The study assessed changes in the gut microbiota of pigs after dietary supplementation with protected sodium butyrate (PSB) during the growing-fattening period (˜90 days). One gram of colon content from 18 pigs (9 from the treatment group-TG-and 9 from the control group-CG-) was collected. Bacterial DNA was extracted and 16S rRNA high-throughput amplicon sequencing used to assess microbiota changes between groups. The groups shared 75.4% of the 4697 operational taxonomic units identified. No differences in alpha diversity were found, but significant differences for some specific taxa were detected between groups. The low-represented phylum Deinococcus-Thermus, which is associated with the production of carotenoids with antioxidant, anti-apoptotic, and anti-inflammatory properties, was increased in the TG (p = 0.032). Prevotellaceae, Lachnospiraceae, Peptostreptococcaceae, Peptococcaceae and Terrisporobacter were increased in the TG. Members of these families have the ability to ferment complex dietary polysaccharides and produce larger amounts of short chain fatty acids. Regarding species, only Clostridium butyricum was increased in the TG (p = 0.048). Clostridium butyricum is well-known as probiotic in humans, but it has also been associated with overall positive gut effects (increased villus height, improved body weight, reduction of diarrhea, etc.) in weanling pigs. Although the use of PSB did not modify the overall richness of microbiota composition of these slaughter pigs, it may have increased specific taxa associated with better gut health parameters

Identification of Hypoxia-Regulated Proteins Using MALDI-Mass Spectrometry Imaging Combined with Quantitative Proteomics

Hypoxia is present in most solid tumors and is clinically correlated with increased metastasis and poor patient survival. While studies have demonstrated the role of hypoxia and hypoxia-regulated proteins in cancer progression, no attempts have been made to identify hypoxia-regulated proteins using quantitative proteomics combined with MALDI-mass spectrometry imaging (MALDI-MSI). Here we present a comprehensive hypoxic proteome study and are the first to investigate changes in situ using tumor samples. In vitro quantitative mass spectrometry analysis of the hypoxic proteome was performed on breast cancer cells using stable isotope labeling with amino acids in cell culture (SILAC). MS analyses were performed on laser-capture microdissected samples isolated from normoxic and hypoxic regions from tumors derived from the same cells used in vitro. MALDI-MSI was used in combination to investigate hypoxia-regulated protein localization within tumor sections. Here we identified more than 100 proteins, both novel and previously reported, that were associated with hypoxia. Several proteins were localized in hypoxic regions, as identified by MALDI-MSI. Visualization and data extrapolation methods for the in vitro SILAC data were also developed, and computational mapping of MALDI-MSI data to IHC results was applied for data validation. The results and limitations of the methodologies described are discussed. 2014 American Chemical Societ

Ευρετικές προσεγγίσεις του μοναδιάστατου προβλήματος πακετοποίησης

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and non-pleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data

Gene expression profiling and its use in adenocarcinomas of unknown primary origin: A case report

Carcinomas of unknown primary origin account for 3-5% of all malignancies. The current literature suggests that metastatic dissemination is able to occur in the absence of primary tumor growth. In metastatic disease that is difficult to diagnose, the origin usually remains unknown even after an exhaustive evaluation of immunohistochemistry (IHC) markers. In the current study, a 49-year-old male presented with lymph nodes metastases of unknown origin. The exci- sional biopsy of an inguinal node revealed an adenocarcinoma growth pattern, but the IHC could not determine the primary origin. A gene profiling test was performed to complete the diagnosis and a salivary gland adenocarcinoma was diagnosed with 90% probability. Subsequently, the patient underwent appropriate chemotherapy for salivary gland adenocarcinoma, and exhibited an improved partial response. The present case study highlights the importance of an accurate diagnosis of the primary tumor and the use of all the current tools available in order to provide patients with the best treatment possibl

DNA polymerase lambda (Pol λ), a novel eukaryotic DNA polymerase with a potential role in meiosis

A new gene (POLL) encoding a novel DNA polymerase (Pol λ) has been identified at mouse chromosome 19. Murine Pol λ, consisting of 573 amino acid residues, has a 32 % identity to Pol β, involved in nuclear DNA repair in eukaryotic cells. It is interesting that Pol λ contains all the critical residues involved in DNA binding, nucleotide binding and selection, and catalysis of DNA polymerization, that are conserved in Pol β and other DNA polymerases belonging to family X. Murine Pol λ, overproduced in Escherichia coli, displayed intrinsic DNA polymerase activity when assessed by in situ gel analysis. Pol λ also conserves the critical residues of Pol β required for its intrinsic deoxyribose phosphate lyase (dRPase) activity. The first 230 amino acid residues of Pol λ, that have no counterpart in Pol β, contain a BRCT domain, present in a variety of cell-cycle check-point control proteins responsive to DNA damage and proteins involved in DNA repair. Northern blotting, in situ hybridization analysis and immunostaining showed high levels of Pol λ specifically expressed in testis, being developmentally regulated and mainly associated to pachytene spermatocytes. These first evidences, although indirect, suggest a potential role of Pol λ in DNA repair synthesis associated with meiosis.This work has been granted by DGES (PB97-1192) and CAM (08.1/0044/98) to LB; CAM(08.1/0044.2/98) to AB; DGICYT (PB 95-0119), EC PL96-0183 and CAM (07/0022) to JM, and by an institutional grant from Fundación Ramón Areces

Enfermedad ganglionar residual tras quimioradioterapia con intención radical en pacientes con tumores de faringolaringe

Introducción y objetivo: La afectación ganglionar cervical es el principal factor pronóstico en el carcinoma epidermoide de cabeza y cuello. La cirugía de rescate se considera la intervención más curativa para la enfermedad residual o recurrente tras el tratamiento con quimiorradioterapia. Los objetivos del estudio fueron describir los datos epidemiológicos de los pacientes, valorar la utilidad de las pruebas de imagen, analizar la supervivencia y realizar una revisión de la bibliografía actual. Método: Se realizó un estudio retrospectivo en el que se incluyeron pacientes intervenidos de cirugía ganglionar cervical entre enero de 2010 y diciembre de 2015, con sospecha radiológica de enfermedad ganglionar persistente, tras haber recibido tratamiento quimio-radioterápico con intención radical por presentar un carcinoma de faringe o laringe. Resultados: Se incluyeron 30 pacientes. La localización tumoral más común fue la supraglotis (13). El resultado histológico más frecuente fue de carcinoma epidermoide pobremente y moderadamente diferenciado (10 casos en cada uno). El 60% de los pacientes presentaban un estadio IVa. El valor predictivo positivo (VPP) de la TAC fue de 55, 26%. El 87, 5% de las histologías que confirmaron la sospecha diagnóstica radiológica en una primera cirugía ocurrieron en los pacientes a los que se les había realizado una TAC de forma precoz. La supervivencia global fue del 53, 33%, terminando el 40% de los pacientes libres de enfermedad al final del periodo. Conclusiones: El bajo VPP de la TAC hace replantear su utilidad como método para valorar respuesta ganglionar a la quimiorradioterapia. Parece razonable plantear la realización de vaciamientos ganglionares selectivos en pacientes seleccionados. Introduction and objective: Cervical nodal involvement is the main prognostic factor in squamous cell carcinoma of the head and neck. Salvage surgery is considered the most curative intervention for residual or recurrent disease after treatment with chemo-radiotherapy. The objectives of the study were to describe the epidemiological data of the patients, to evaluate the usefulness of the imaging tests, to analyze the survival, and to make a review of the current bibliography. Method: A retrospective study was carried out, including patients undergoing cervical lymph node surgery between January 2010 and December 2015, after radiological suspicion of persistent regional disease was found. All the patients had previously received chemo-radiotherapy treatment with radical intention due to a carcinoma of pharynx or larynx. Results: Thirty patients were included. The most common tumoral site was supraglottis (13). The most frequent histological result was poorly and moderately differentiated epidermoid carcinoma (10 cases in each). Sixty percent of the patients had stage IVa. The positive predictive value (PPV) of the CT scan was 55.26%. Eighty-seven point five percent of the histologies confirming radiological diagnostic suspicion in a first surgery occurred in patients who had an early CT scan. Overall survival was 53.33%; forty percent of the patients were free of disease at the end of the period. Conclusions: The low PPV of the CT scan makes its usefulness questionable as a method to assess nodal response to chemo-radiotherapy. It seems reasonable to propose selective lymph node surgery in selected patients