A rock- and paleomagnetic study of a Holocene lava flow in Central Mexico

Magnetic measurements of the Tres Cruces lava flow (ca. 8500 years BP, Central Mexico) show the presence of two remanence carriers, a Ti-rich titanomagnetite with a Curie temperature between 350 and 400 °C and a Ti-poor magnetite with a Curie temperature close to 580°C. Magnetic changes after heating indicate that the titanomagnetite exsolves into magnetite w and ilmenite when the sample is heated to 580 °C. Paleointensity estimates with the Thellier and Thellier method [Thellier, E., Thellier, O., 1959. Sur l'intensité du champ magnetique terrestre dans le passe historique et geologique. Ann. Geophysique., 15, 285-376] were only successful up to temperatures of 350 to 400 °C. This temperature corresponds with the Curie temperature of the titanomagnetite, which is probably pseudo-single or multi-domain. Therefore, the paleointensities should be interpreted with caution. The magnetic composition changes after 580 °C heating may explain the large w variations in previous paleointensity determinations for the Tres Cruces rocks [Gonzalez, S., Sherwood, G., Bohnel, H., Schnepp, E., 1997. Palaeosecular variation in Central Mexico over the last 30,000 years: the record from lavas. Geophys. J. Int., 130, 201-219] using the [Shaw method Shaw, J., 1974. A new method of determining the magnitude of the palaeomagnetic field: application to five historic lavas and five archaeological samples. Geophys. J. R. Astr. Soc., 39, 133-141]

Surface display of Salmonella epitopes in Escherichia coli and Staphylococcus carnosus

<p>Abstract</p> <p>Background</p> <p><it>Salmonella enterica </it>serotype Enteritidis (SE) is considered to be one of the most potent pathogenic <it>Salmonella </it>serotypes causing food-borne disease in humans. Since a live bacterial vaccine based on surface display of antigens has many advantages over traditional vaccines, we have studied the surface display of the SE antigenic proteins, H:gm and SefA in <it>Escherichia coli </it>by the β-autotransporter system, AIDA. This procedure was compared to protein translocation in <it>Staphylococcus carnosus</it>, using a staphylococci hybrid vector earlier developed for surface display of other vaccine epitopes.</p> <p>Results</p> <p>Both SefA and H:gm were translocated to the outer membrane in <it>Escherichia coli</it>. SefA was expressed to full length but H:gm was shorter than expected, probably due to a proteolytic cleavage of the N-terminal during passage either through the periplasm or over the membrane. FACS analysis confirmed that SefA was facing the extracellular environment, but this could not be conclusively established for H:gm since the N-terminal detection tag (His₆) was cleaved off. Polyclonal salmonella antibodies confirmed the sustained antibody-antigen binding towards both proteins. The surface expression data from <it>Staphylococcus carnosus </it>suggested that the H:gm and SefA proteins were transported to the cell wall since the detection marker was displayed by FACS analysis.</p> <p>Conclusion</p> <p>Apart from the accumulated knowledge and the existence of a wealth of equipment and techniques, the results indicate the selection of <it>E. coli </it>for further studies for surface expression of salmonella antigens. Surface expression of the full length protein facing the cell environment was positively proven by standard analysis, and the FACS signal comparison to expression in <it>Staphylococcus carnosus </it>shows that the distribution of the surface protein on each cell was comparatively very narrow in <it>E. coli</it>, the <it>E. coli </it>outer membrane molecules can serve as an adjuvant for the surface antigenic proteins and multimeric forms of the SefA protein were detected which would probably be positive for the realisation of a strong antigenic property. The detection of specific and similar proteolytic cleavage patterns for both the proteins provides a further starting point for the investigation and development of the <it>Escherichia coli </it>AIDA autotransporter efficiency.</p

Evidencia de una zona triangular en Pampas-Ojo de Consuzo. Ancash, Norte del Perú

Las zonas triangulares son un conjunto de fallas usualmente convergencia opuesta cuya configuración tiene forma de cuña que son típicas del frente de deformación en las Fajas plegadas y corridas (FTBs por sus siglas en inglés) (MacKay et al., 1996). En la Faja plegada y corrida del Marañón, sector del Ojo de Conzuso (Pampas-Provincia de Ancash), se tiene una zona triangular de tipo “Duplex de techo pasivo” (Banks & Warburton, 1986) que se ha determinado en base a un detallado cartografiado geológico-estructural que incluye las relaciones de clivaje con respecto a las capas y otras estructuras de escala mesoscópica (Torres, En prensa). Este trabajo se desarrolló entre los meses de octubre y noviembre del año 2017 y abril del año 2018 como parte de la actualización a escala 1:50,000 de la Hoja Pallasca 17h4 del Proyecto GR40C “Geología de la cuenca sedimentaria peruana occidental del norte entre 7°30’ y 9°30’ S”, de la Dirección de Geología Regional

Minigene-like inhibition of protein synthesis mediated by hungry codons near the start codon

Rare AGA or AGG codons close to the initiation codon inhibit protein synthesis by a tRNA-sequestering mechanism as toxic minigenes do. To further understand this mechanism, a parallel analysis of protein synthesis and peptidyl-tRNA accumulation was performed using both a set of lacZ constructs where AGAAGA codons were moved codon by codon from +2, +3 up to +7, +8 positions and a series of 3–8 codon minigenes containing AGAAGA codons before the stop codon. β-Galactosidase synthesis from the AGAAGA lacZ constructs (in a Pth defective in vitro system without exogenous tRNA) diminished as the AGAAGA codons were closer to AUG codon. Likewise, β-galactosidase expression from the reporter +7 AGA lacZ gene (plus tRNA, 0.25 μg/μl) waned as the AGAAGAUAA minigene shortened. Pth counteracted both the length-dependent minigene effect on the expression of β-galactosidase from the +7 AGA lacZ reporter gene and the positional effect from the AGAAGA lacZ constructs. The +2, +3 AGAAGA lacZ construct and the shortest +2, +3 AGAAGAUAA minigene accumulated the highest percentage of peptidyl-tRNAArg4. These observations lead us to propose that hungry codons at early positions, albeit with less strength, inhibit protein synthesis by a minigene-like mechanism involving accumulation of peptidyl-tRNA

An unstructured 5′-coding region of the prfA mRNA is required for efficient translation

Expression of virulence factors in the human bacterial pathogen Listeria monocytogenes is almost exclusively regulated by the transcriptional activator PrfA. The translation of prfA is controlled by a thermosensor located in the 5′-untranslated RNA (UTR), and is high at 37°C and low at temperatures <30°C. In order to develop a thermoregulated translational expression system, the 5′-UTR and different lengths of the prfA-coding sequences were placed in front of lacZ. When expressed in Escherichia coli, the β-galactosidase expression was directly correlated to the length of the prfA-coding mRNA lying in front of lacZ. A similar effect was detected with gfp as a reporter gene in both L. monocytogenes and E. coli, emphasizing the requirement of the prfA-coding RNA for maximal expression. In vitro transcription/translation and mutational analysis suggests a role for the first 20 codons of the native prfA-mRNA for maximal expression. By toe-print and RNA-probing analysis, a flexible hairpin-loop located immediately downstream of the start-codon was shown to be important for ribosomal binding. The present work determines the importance of an unstructured part of the 5′-coding region of the prfA-mRNA for efficient translation

Nuevos registros paleobotánicos del grupo Chicama (Cordillera Occidental, norte del Perú): implicancias estratigráficas

Se pone en evidencia la presencia de plantas fósiles en niveles estratigráficos correspondientes al Grupo Chicama al noroeste de Sihuas (8°35’S, 77°50’W), cuya asociación de facies permite identificar al Miembro Huaycay de la Formación Tinajones. Se trata de lutitas y areniscas cuarzosas que contienen plantas fósiles constituidas por los géneros Zamites, Pterophyllum y Thuites en excelente estado de preservación, los cuales son reportados por primera vez en la zona. Las características sedimentológicas y morfológicas de su contenido fósil confirman la extensión de las facies del Miembro Huarcay hasta la Cordillera Occidental del norte de Perú, en relación a su estratotipo en el Valle del río Chicama (7°36’S, 78°54’O)

Análisis sedimentológico y paleogeográfico de la Cuenca Condoroma (Arequipa), sur del Perú

Durante el Neógeno, la evolución de los Andes Centrales engendró pequeñas cuencas intramontañosas. Sus evoluciones sedimentarias y tectónicas estuvieron producidas por una deformación continua (Noblet et al, 1985; Marocco et al., 1995; Carlotto, 1998). La cuenca Condoroma es una de estas cuencas, que está limitada por fallas principales y paralelas a las direcciones orográficas de la Cordillera de los Andes. Se encuentra en la Cordillera Occidental, en el límite entre los departamentos de Arequipa y Cusco en el Sur del Perú. Esta cuenca presenta una forma sigmoidal alargada, con dirección NNO-SSE; aproximadamente de 28,8 km de largo y 4 km de ancho, y cubre una superficie aproximada de 150 km2. Está ubicada 40 km al NE de la ciudad de Chivay (Departamento de Arequipa), entre las localidades de Chichas (Represa Condoroma) e Ichocollo. Al relleno sedimentario de la cuenca Condoroma se le ha denominado con el nombre de Formación Condoroma

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

BACKGROUND:Production of proteins as therapeutic agents, research reagents and molecular tools frequently depends on expression in heterologous hosts. Synthetic genes are increasingly used for protein production because sequence information is easier to obtain than the corresponding physical DNA. Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles. PRINCIPAL FINDINGS:To identify sequence features that affect protein expression we synthesized and expressed in E. coli two sets of 40 genes encoding two commercially valuable proteins, a DNA polymerase and a single chain antibody. Genes differing only in synonymous codon usage expressed protein at levels ranging from undetectable to 30% of cellular protein. Using partial least squares regression we tested the correlation of protein production levels with parameters that have been reported to affect expression. We found that the amount of protein produced in E. coli was strongly dependent on the codons used to encode a subset of amino acids. Favorable codons were predominantly those read by tRNAs that are most highly charged during amino acid starvation, not codons that are most abundant in highly expressed E. coli proteins. Finally we confirmed the validity of our models by designing, synthesizing and testing new genes using codon biases predicted to perform well. CONCLUSION:The systematic analysis of gene design parameters shown in this study has allowed us to identify codon usage within a gene as a critical determinant of achievable protein expression levels in E. coli. We propose a biochemical basis for this, as well as design algorithms to ensure high protein production from synthetic genes. Replication of this methodology should allow similar design algorithms to be empirically derived for any expression system

Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses

<p>Abstract</p> <p>Background</p> <p>Recent studies have demonstrated a selection pressure for reduced mRNA secondary-structure stability near the start codon of coding sequences. This selection pressure can be observed in bacteria, archaea, and eukaryotes, and is likely caused by the requirement of efficient translation initiation in cellular organism.</p> <p>Results</p> <p>Here, we surveyed the complete genomes of 650 dsDNA virus strains for signals of reduced stability of mRNA secondary structure near the start codon. Our analysis included viruses infecting eukaryotic, prokaryotic, and archaeic hosts. We found that many viruses showed evidence for reduced mRNA secondary-structure stability near the start codon. The effect was most pronounced in viruses infecting prokaryotes, but was also observed in viruses infecting eukaryotes and archaea. The reduction in stability generally increased with increasing genomic GC content. For bacteriophage, the reduction was correlated with a corresponding reduction of stability in the phage hosts.</p> <p>Conclusions</p> <p>We conclude that reduced stability of the mRNA secondary structure near the start codon is a common feature for dsDNA viruses, likely driven by the same selective pressures that cause it in cellular organisms.</p

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

Catechol-O-methyltransferase (COMT) is a major enzyme controlling catecholamine levels that plays a central role in cognition, affective mood and pain perception. There are three common COMT haplotypes in the human population reported to have functional effects, divergent in two synonymous and one nonsynonymous position. We demonstrate that one of the haplotypes, carrying the non-synonymous variation known to code for a less stable protein, exhibits increased protein expression in vitro. This increased protein expression, which would compensate for lower protein stability, is solely produced by a synonymous variation (C166T) situated within the haplotype and located in the 5′ region of the RNA transcript. Based on mRNA secondary structure predictions, we suggest that structural destabilization near the start codon caused by the T allele could be related to the observed increase in COMT expression. Our folding simulations of the tertiary mRNA structures demonstrate that destabilization by the T allele lowers the folding transition barrier, thus decreasing the probability of occupying its native state. These data suggest a novel structural mechanism whereby functional synonymous variations near the translation initiation codon affect the translation efficiency via entropy-driven changes in mRNA dynamics and present another example of stable compensatory genetic variations in the human population