Geological investigation of a section at Kulyumbe river in Siberia

An integrated, high-resolution chemostratigraphic (C, O and Sr isotopes) and magnetostratigraphic study through the upper Middle Cambrian - lowermost Ordovician shallow-marine carbonates of the northwestern margin of the Siberian Platform is reported. The interval was analysed at the Kulyumbe section, which is exposed along the Kulyumbe River: an eastern tributary of the Enisej River. It comprises the upper Ust'-Brus, Labaz, Orakta, Kulyumbe, Ujgur, and lower Iltyk formations and includes the Steptoean positive carbon isotopic excursion (SPICE) studied here in detail from upper Cambrian carbonates of the Siberian Platform for the first time. The peak of the excursion, showing d13C positive values as high as +4.6? and least-altered 87Sr/86Sr ratios of 0.70909, is reported herein from the Yurakhian Horizon of the Kulyumbe Formation. The stratigraphic position of the SPICE excursion does not support traditional correlation of the boundary between the Orakta and Labaz formations at Kulyumbe River with its supposedly equivalent level in Australia, Laurentia, South China, and Kazakhstan, where the Glyptagnostus stolidotus and G. reticulatus biozones are known to immediately precede the SPICE excursion and span the Middle-Upper Cambrian boundary. The Cambrian-Ordovician boundary is probably situated in the middle Nyajan Horizon of the Iltyk Formation, in which carbon isotope values show a local maximum below a decrease in the upper part of the Nyajan Horizon, attributed herein to the Tremadocian. A refined magnetic polarity sequence shows that the geomagnetic reversal frequency was very high during the Middle Cambrian at 5-10 reversals per Ma, assuming a total duration of ~10 Ma and up to 100 magnetic intervals in the Middle Cambrian. By contrast, the sequence attributed herein to the Upper Cambrian on chemostratigraphic grounds contains only 10-11 magnetic intervals. Preprint in Open Access hdl:10013/epic.30209.d001

(Table 2) Location, age of accompanied sediments, chemical and Sr isotopic compositions of manganese nodules in DSDP/ODP cores

Strontium isotopic compositions of acetic acid (HOAc) leachate fractions of eight manganese oxide deposits from the modern seafloor, and of twenty-one buried manganese nodules from Cretaceous to Recent sediments in DSDP/ODP cores were measured. ratios of HOAc leachates in all modern seafloor manganese oxides of various origins are identical with present seawater. The ratios of the HOAc leachates of buried nodules from DSDP/ODP cores are significantly lower than those of nodules from the modern seafloor and are mostly identical with coeval seawater values estimated from the age of associated sediments. It is suggested that the buried nodules in DSDP/ODP cores are not artifacts transported from the present seafloor during the drilling process, but are in situ fossil deposits from the past deep-sea floor during Cretaceous to Quaternary periods. The formation of deep-sea fossil nodules prior to the formation of Antarctic Bottom Water (AABW) indicates that the circulation of oxygenated deep seawaters have activately deposited manganese oxides since the Eocene Epoch, or earlier.

Isolation and selection of plant growth-promoting bacteria associated with sugarcane

v. 46, n. 2, p. 149-158, apr./jun. 2016.

Aspetti meccanicistici della coordinazione di [(PPh3)3Ru(CO)(H2)] com Timina Acido Acetico

Ruthenium complexes have proved to exhibit antineoplastic activity related to the interaction of metal ion with DNA nucleobases. It is indeed of great interest to provide new insights on theses cutting-edge studies, such as the identification of distinct coordinative modes of DNA binding sites. During the investigation on the reaction between [(PPh3)3Ru(CO)(H)2], 1, and the Thymine Acetic Acid (THA) as model for nucleobases, we identified an unstable monohapto hydride acetate complex 2, which rapidly evolves into elusive intermediates whose nature was evidenced by NMR spectra and DFT calculations. We obtained crystals of [(PPh3)2Ru(CO)(k1-THA)(k2-THA)] 17, and [Ru(CO)(PPh3)2(k2-N,O)-[THA(A)];(k1-O)[THA(B)]2 18, phosphine ligands assuming cis conformation. The thesis deals on the analogue reactions of 1 with acetic acid by varying different parameters and operating conditions. The reaction yields to the hydride dihapto-acetate [(PPh3)2RuH(CO)(k2-Ac)] 8 through the related meridian monohapto, by releasing of phosphine ligand. However, the reaction yields a mixture of compounds, in which the dihapto hydride complex 8 is prevailing in any cases and does not provide any disclosure for the proposed mechanistic aspects. The reaction with two equivalents of acetic acid, affords the complex [(PPh3)2Ru(CO)(k1-Ac)(k2-Ac)] 11, exhibiting mutual trans:cis locations in 2:1 ratio for the phosphine. Such evidence agrees with the results obtained DFT calculations in vacuo, whereas it is in contrast with those obtained with the THA. Therefore we can inferred that the products obtained from the latter reaction is intermolecularly ruled by the hydrogen binding interactions between the functions [-NH•••(O)C-] in the two coordinated thymine ligands.

Salicaceae Endophytes: Growth Promotion Potential in Rice (Oryza sativa L.) and Maize (Zea mays L.) and Bio-Control of Plant Pathogen

Thesis (Ph.D.)--University of Washington, 2016-08

Ruthenibacterium lactatiformans gen. nov., sp.nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces

Two novel strains of Gram-stain-negative, rod-shaped, obligately anaerobic, non-spore-forming, non-motile bacteria were isolated from the faeces of healthy human subjects. The strains, designated as 585-1T and 668, were characterized by mesophilic fermentative metabolism, production of d-lactic acid, succinic acid and acetic acid as end products of d-glucose fermentation, prevalence of C18 : 1 ω9, C18 : 1 ω9 aldehyde, C16 : 0 and C16 : 1 ω7c fatty acids, presence of glycine, glutamic acid, lysine, alanine and aspartic acid in the petidoglycan peptide moiety and lack of respiratory quinones. Whole genome sequencing revealed the DNA G+C content was 56.4–56.6 mol%. The complete 16S rRNA gene sequences of the two strains shared 91.7/91.6 % similarity with Anaerofilum pentosovorans FaeT, 91.3/91.2 % with Gemmiger formicilis ATCC 27749T and 88.9/88.8 % with Faecalibacterium prausnitzii ATCC 27768T. On the basis of chemotaxonomic and genomic properties it was concluded that the strains represent a novel species in a new genus within the family Ruminococcaceae , for which the name Ruthenibacterium lactatiformans gen. nov., sp. nov. is proposed. The type strain of Ruthenibacterium lactatiformans is 585-1T (=DSM 100348T=VKM B-2901T).

Avaliação da interação entre aflatoxina M1 e B1 com a fração proteica do leite

Dissertação composta por 02 artigos.

Xylose from lignocellulosic waste in the production and industrial processing of pinneaple (Ananascomusus)

Lignocellulosicwaste from the pineapple production is a raw material useful for the xylose production by hydrolysis and it can be converted to xylitol. The objective of this work was to study the hydrolysis of pineapple peel with sulfuric acid at variable concentration (2-6%), reaction time (0-350 min) and temperature at 98 ˚C. The concentration of xylose, glucose and degradation products as acetic acid and furfural was determined. Optimal conditions found for hydrolysis were 6% H2SO4 at 98 ˚C for 83 min which yield was 26,9 g xylose/L, 2,61 g glucose/L, 7,71 g acetic acid/L and 0,29 g furfural/L.

CHARACTERIZATION OF TOBACCO MOSAIC VIRUS DIRECTED REPROGRAMMING OF PHLOEM GENE EXPRESSION TO PROMOTE VIRAL PHLOEM LOADING AND SYSTMEIC MOVEMENT

Vascular phloem loading has long been recognized as an essential step in the establishment of a systemic virus infection. Yet little is known about this process and the mechanisms that control it. In this study, an interaction between the replication protein of Tobacco mosaic virus (TMV) and phloem specific auxin/indole acetic acid (Aux/IAA) transcriptional regulators was found to modulate virus phloem loading. Promoter expression studies show TMV 126/183 kDa interacting Aux/IAAs predominantly express and accumulate within the nuclei of phloem companion cells (CC). Furthermore, CC Aux/IAA nuclear localization is disrupted upon infection with an interacting virus but not during infection with a non-interacting virus. In situ analysis of virus spread shows the inability of TMV variants to disrupt Aux/IAA CC nuclear localization correlates with a reduced ability to load into the vascular tissue. Subsequent systemic movement assays also demonstrate that a virus capable of disrupting Aux/IAA localization is significantly more competitive at systemic movement than a non-interacting virus. Similarly, CC expression and over-accumulation of a degradation-resistant-interacting Aux/IAA protein was found to selectively inhibit TMV accumulation and phloem loading. Transcriptional expression studies demonstrate a role for interacting Aux/IAA proteins in the regulation of salicylic acid and jasmonic acid dependent host defense responses as well as virus specific movement factors including pectin methylesterase that are involved in regulating plasmodesmata size exclusion limits and promoting virus cell-to-cell movement. Further characterization of the phloem environment was done using two phloem specific promoters (pSUC2 and pSULTR2;2) to generate epitope-tagged polysomal-RNA complexes. Immuno-purification using the epitope tag allowed us to obtain mRNAs bound to polysomes (the translatome) specifically in phloem tissue. We found the phloem translatome is uniquely altered during TMV infection with 90% and 88% of genes down regulated in the pSUC2 and pSULTR2;2 phloem translatomes, compared to 31% of genes down regulated in the whole plant p35S translatome. Transcripts down regulated in phloem include genes involved in callose deposition at plasmodesmata, host defense responses, and RNA silencing. Combined, these findings indicate TMV reprograms gene expression within the vascular phloem as a means to enhance phloem loading and systemic spread.

Improving the stability of an oxime based electrochemical microsensor for organo-phosphate vapor detection

A micro gas sensor has been developed by our group for the detection of organo-phosphate vapors using an aqueous oxime solution. The analyte diffuses from the high flow rate gas stream through a porous membrane to the low flow rate aqueous phase. It reacts with the oxime PBO (1-Phenyl-1,2,3,-butanetrione 2-oxime) to produce cyanide ions, which are then detected electrochemically from the change in solution potential. Previous work on this oxime based electrochemistry indicated that the optimal buffer pH for the aqueous solution was approximately 10. A basic environment is needed for the oxime anion to form and the detection reaction to take place. At this specific pH, the potential response of the sensor to an analyte (such as acetic anhydride) is maximized. However, sensor response slowly decreases as the aqueous oxime solution ages, by as much as 80% in first 24 hours. The decrease in sensor response is due to cyanide which is produced during the oxime degradation process, as evidenced by the cyanide selective electrode. Solid phase micro-extraction carried out on the oxime solution found several other possible degradation products, including acetic acid, N-hydroxy benzamide, benzoic acid, benzoyl cyanide, 1-Phenyl 1,3-butadione, 2-isonitrosoacetophenone and an imine derived from the oxime. It was concluded that degradation occurred through nucleophilic attack by a hydroxide or oxime anion to produce cyanide, as well as a nitrogen atom rearrangement similar to Beckmann rearrangement. The stability of the oxime in organic solvents is most likely due to the lack of water, and specifically hydroxide ions. The reaction between oxime and organo-phosphate to produce cyanide ions requires hydroxide ions, and therefore pure organic solvents are not compatible with the current micro-sensor electrochemistry. By combining a concentrated organic oxime solution with the basic aqueous buffer just prior to being used in the detection process, oxime degradation can be avoided while preserving the original electrochemical detection scheme. Based on beaker cell experiments with selective cyanide sensitive electrodes, ethanol was chosen as the best organic solvent due to its stabilizing effect on the oxime, minimal interference with the aqueous electrochemistry, and compatibility with the current microsensor material (PMMA). Further studies showed that ethanol had a small effect on micro-sensor performance by reducing the rate of cyanide production and decreasing the overall response time. To avoid incomplete mixing of the aqueous and organic solutions, they were pre-mixed externally at a 10:1 ratio, respectively. To adapt the microsensor design to allow for mixing to take place within the device, a small serpentine channel component was fabricated with the same dimensions and material as the original sensor. This allowed for seamless integration of the microsensor with the serpentine mixing channel. Mixing in the serpentine microchannel takes place via diffusion. Both detector potential response and diffusional mixing improve with increased liquid residence time, and thus decreased liquid flowrate. Micromixer performance was studies at a 10:1 aqueous buffer to organic solution flow rate ratio, for a total rate of 5.5 μL/min. It was found that the sensor response utilizing the integrated micromixer was nearly identical to the response when the solutions were premixed and fed at the same rate.

Recuperação de carotenóides microbianos por diferentes técnicas de ruptura celular

O objetivo deste trabalho foi utilizar diferentes técnicas químicas (dimetilsulfóxido, ácido clorídrico, acético e lático), técnicas mecânicas (banho ultrassônico, abrasão com pérolas de vidro, maceração com terra diatomácea, ruptor ultrassônico e imersão em nitrogênio líquido) e técnica enzimática (preparado enzimático comercial Glucanex®) para a recuperação de carotenoides a partir da ruptura da parede celular das leveduras Sporidiobolus pararoseus e Rhodotorula mucilaginosa isoladas de amostras ambientais. Para isso a obtenção de biomassa foi realizada através de cultivos submersos no meio YM, a 25 °C, 180 rpm por 168 h. Para a ruptura celular, a operação de congelamento da biomassa (-18°C por 48 h) foi estudada. Os métodos de secagem convencional por ar forçado (35°C/48h) e liofilização (-80°C/48h, em ultrafreezer, seguido de liofilizador até alcançar 2% de umidade da amostra) também foram avaliados. Nas técnicas químicas aplicadas, o dimetilsulfóxido apresentou os melhores resultados para as duas leveduras, porém o seu uso é limitado devido a sua toxicidade. Para S. pararoseus, os maiores valores encontrados foram para o ácido clorídrico, seguido do acético e do lático, sendo detectada diferença entre eles quando aplicado o congelamento. Com R. mucilaginosa, os maiores valores foram encontrados para os ácidos acético e lático, seguido do ácido clorídrico, no qual o congelamento da biomassa também não influenciou a recuperação dos carotenoides. Dentre as técnicas mecânicas estudadas, para a levedura S. pararoseus, o banho ultrassônico e a abrasão com pérolas de vidro apresentaram os resultados mais promissores comparados ao DMSO (84,79±2,34 e 76,87±2,06 μg/g respectivamente), onde o processo de congelamento da biomassa não influenciou positivamente no percentual de extratibilidade e na concentração específica dos carotenoides quando utilizada estas técnicas. Com Rhodotorula mucilaginosa, o banho ultrassônico propiciou a recuperação da maior concentração específica de carotenoides (193,5±25,8 μg/g), sendo que o processo de congelamento também não influenciou positivamente no percentual de extratibilidade e na concentração específica dos carotenoides. Através do Delineamento Central Composto Rotacional (DCCR) 23 foi possível avaliar que a levedura S. pararoseus não demonstrou nenhum efeito sob as variáveis pH, temperatura e concentração de enzima. Assim, a melhor condição de trabalho escolhida foi pH 7,4, 30 ºC e concentração de enzima de 1,0 g/gcs, onde apresentou a concentração específica de 42,6 μg/g e volumétrica de 308 μg/L de carotenoides. Para R. mucilaginosa, a condição ótima foi definida como 1,0 g/gcs, pH 5,0 e temperatura de 30 ºC, onde foi encontrado 115,1±8,1 μg/g e 470,1±38,8 μg/L para a concentração específica e volumétrica de carotenoides, respectivamente. A utilização de técnicas combinadas empregando banho ultrassônico e lise enzimática não proporcionou melhorias nos resultados para ambas as leveduras. A liofilização provocou um ganho de 20% e 13,7% na concentração específica dos carotenoides das leveduras S. pararoseus e R. mucilaginosa, respectivamente, onde o congelamento da biomassa não influenciou significativamente (p<0,05) a recuperação de carotenoides provenientes das duas leveduras, podendo ser eliminada do processo. Assim, para S. pararoseus o banho ultrassônico e as pérolas de vidro apresentaram os melhores resultados na recuperação de carotenoides, e para R. mucilaginosa o melhor resultado foi alcançado com o banho ultrassônico.

Amidos crioulos: caracterização fundamental e influência de biopolímeros nas propriedades funcionais do amido

O trabalho apresentado nesta tese focou-se no estudo do amido, nomeadamente na avaliação das características físico-químicas, morfológicas, térmicas e reológicas do amido de seis variedades de milho crioulo, preservadas no estado de Santa Catarina (Brasil), com o intuito de contribuir para a valorização e preservação de variedades locais que são cultivadas em sistemas de produção orgânica, também conhecidas como variedades crioulas. Estas sementes são importantes quer para a preservação da biodiversidade quer para os pequenos produtores que as conservam e as produzem fazendo uso de uma agricultura sustentável e independente comercialmente. Para além da caracterização dos amidos crioulos foram também analisadas as alterações que ocorrem nos processos de gelatinização e retrogradação do amido quando realizados na presença de outros biopolímeros, nomeadamente a quitosana e galactomananas. No Capítulo I é apresentada uma breve revisão do conhecimento científico sobre o amido e sobre a quitosana e galactomananas, os outros biopolímeros utilizados. Igualmente é feita uma sucinta abordagem sobre as principais técnicas analíticas que foram utilizadas: reologia fundamental, calorimetria diferencial de varrimento, microscopia eletrónica de varrimento e espectroscopia de infravermelho médio. No capítulo II apresenta-se o isolamento dos amidos das seis variedades de milho crioulo e a sua caracterização junto com um amido comercial usado como modelo de comparação. Os amidos apresentaram genericamente características físicoquímicas semelhantes e o amido extraído das variedades crioulas MT e MPA 01 apresentaram menor temperatura de gelatinização e maior percentagem de retrogradação, respetivamente. Os efeitos da adição da quitosana e de três galactomananas (goma guar, goma de alfarroba e goma cassia) em sistemas mistos com o amido são analisados nos Capítulos III e IV respetivamente. A adição dos biopolímeros aos amidos resultou no aumento das temperaturas de gelatinização, na alteração da retrogradação do amido pelas galactomananas e na alteração das propriedades viscoeláticas dos géis formados. Os dados de infravermelho esclareceram que nos sistemas com quitosana, o amido formou complexos com o ácido acético usado para dissolver a quitosana e que esta por sua vez formou acetato de quitosana. O comportamento durante a gelatinização do amido comercial quando comparado com o amido do milho crioulo MPA na sua interação com as galactomananas é diferenciado.

Transcriptome, carbohydrate, and phytohormone analysis of Petunia hybrida reveals a complex disturbance of plant functional integrity under mild chilling stress

Cultivation of chilling-tolerant ornamental crops at lower temperature could reduce the energy demands of heated greenhouses. To provide a better understanding of how sub-optimal temperatures (12 degrees C vs. 16 degrees C) affect growth of the sensitive Petunia hybrida cultivar 'SweetSunshine Williams', the transcriptome, carbohydrate metabolism, and phytohormone homeostasis were monitored in aerial plant parts over 4 weeks by use of a microarray, enzymatic assays and GC-MS/MS. The data revealed three consecutive phases of chilling response. The first days were marked by a strong accumulation of sugars, particularly in source leaves, preferential up-regulation of genes in the same tissue and down-regulation of several genes in the shoot apex, especially those involved in the abiotic stress response. The midterm phase featured a partial normalization of carbohydrate levels and gene expression. After 3 weeks of chilling exposure, a new stabilized balance was established. Reduced hexose levels in the shoot apex, reduced ratios of sugar levels between the apex and source leaves and a higher apical sucrose/hexose ratio, associated with decreased activity and expression of cell wall invertase, indicate that prolonged chilling induced sugar accumulation in source leaves at the expense of reduced sugar transport to and reduced sucrose utilization in the shoot. This was associated with reduced levels of indole-3-acetic acid and abscisic acid in the apex and high numbers of differentially, particularly up-regulated genes, especially in the source leaves, including those regulating histones, ethylene action, transcription factors, and a jasmonate-ZIM-domain protein. Transcripts of one Jumonji C domain containing protein and one expansin accumulated in source leaves throughout the chilling period. The results reveal a dynamic and complex disturbance of plant function in response to mild chilling, opening new perspectives for the comparative analysis of differently tolerant cultivars.

A transcriptome approach towards understanding the development of ripening capacity in 'Bartlett' pears (Pyrus communis L.)

Background: The capacity of European pear fruit (Pyrus communis L.) to ripen after harvest develops during the final stages of growth on the tree. The objective of this study was to characterize changes in 'Bartlett' pear fruit physico-chemical properties and transcription profiles during fruit maturation leading to attainment of ripening capacity. Results: The softening response of pear fruit held for 14days at 20°C after harvest depended on their maturity. We identified four maturity stages: S1-failed to soften and S2- displayed partial softening (with or without ET-ethylene treatment); S3 - able to soften following ET; and S4 - able to soften without ET. Illumina sequencing and Trinity assembly generated 68,010 unigenes (mean length of 911bp), of which 32.8% were annotated to the RefSeq plant database. Higher numbers of differentially expressed transcripts were recorded in the S3-S4 and S1-S2 transitions (2805 and 2505 unigenes, respectively) than in the S2-S3 transition (2037 unigenes). High expression of genes putatively encoding pectin degradation enzymes in the S1-S2 transition suggests pectic oligomers may be involved as early signals triggering the transition to responsiveness to ethylene in pear fruit. Moreover, the co-expression of these genes with Exps (Expansins) suggests their collaboration in modifying cell wall polysaccharide networks that are required for fruit growth. K-means cluster analysis revealed that auxin signaling associated transcripts were enriched in cluster K6 that showed the highest gene expression at S3. AP2/EREBP (APETALA 2/ethylene response element binding protein) and bHLH (basic helix-loop-helix) transcripts were enriched in all three transition S1-S2, S2-S3, and S3-S4. Several members of Aux/IAA (Auxin/indole-3-acetic acid), ARF (Auxin response factors), and WRKY appeared to play an important role in orchestrating the S2-S3 transition. Conclusions: We identified maturity stages associated with the development of ripening capacity in 'Bartlett' pear, and described the transcription profile of fruit at these stages. Our findings suggest that auxin is essential in regulating the transition of pear fruit from being ethylene-unresponsive (S2) to ethylene-responsive (S3), resulting in fruit softening. The transcriptome will be helpful for future studies about specific developmental pathways regulating the transition to ripening. © 2015 Nham et al.

A new technique to automatically quantify microstructures of fine grained carbonate mylonites: two-step etching combined with SEM imaging and image analysis

A two-step etching technique for fine-grained calcite mylonites using 0.37% hydrochloric and 0.1% acetic acid produces a topographic relief which reflects the grain boundary geometry. With this technique, calcite grain boundaries become more intensely dissolved than their grain interiors but second phase minerals like dolomite, quartz, feldspars, apatite, hematite and pyrite are not affected by the acid and therefore form topographic peaks. Based on digital backscatter electron images and element distribution maps acquired on a scanning electron microscope, the geometry of calcite and the second phase minerals can be automatically quantified using image analysis software. For research on fine-grained carbonate rocks (e.g. dolomite calcite mixtures), this low-cost approach is an attractive alternative to the generation of manual grain boundary maps based on photographs from ultra-thin sections or orientation contrast images.