Oligodeoxynucleotide Duplexes Containing (5′S)-5′-C-Alkyl-Modified 2′-Deoxynucleosides: Can an Alkyl Zipper across the DNA Minor-Groove Enhance Duplex Stability?

10.1002/hlca.200390311.abs A series of oligonucleotides containing (5′S)-5′-C-butyl- and (5′S)-5′-C-isopentyl-substituted 2′-deoxyribonucleosides were designed, prepared, and characterized with the intention to explore alkyl-zipper formation between opposing alkyl chains across the minor groove of oligonucleotide duplexes as a means to modulate DNA-duplex stability. From four possible arrangements of the alkyl groups that differ in the density of packing of the alkyl chains across the minor groove, three (duplex types I–III, Fig. 2) could experimentally be realized and their duplex-forming properties analyzed by UV-melting curves, CD spectroscopy, and isothermal titration calorimetry (ITC), as well as by molecular modeling. The results show that all arrangements of alkyl residues within the minor groove of DNA are thermally destabilizing by 1.5–3°/modification in Tm. We found that, within the proposed duplexes with more loosely packed alkyl groups (type-III duplexes), accommodation of alkyl residues without extended distorsion of the helical parameters of B-DNA is possible but does not lead to higher thermodynamic stability. The more densely packed and more unevenly distributed arrangement (type-II duplexes) seems to suffer from ecliptic positioning of opposite alkyl groups, which might account for a systematic negative contribution to stability due to steric interactions. The decreased stability in the type-III duplexes described here may be due either to missing hydrophobic interactions of the alkyl groups (not bulky enough to make close contacts), or to an overcompensation of favorable alkyl-zipper formation presumably by loss of structured H2O in the minor groove.

On the Methyl-Transfer Reaction in Crystalline Methyl 2-(Methylthio)benzenesulfonate: a Thermally Induced Non-Topochemical Solid-State Reaction

The rearrangement of methyl 2-(methylthio)benzenesulfonate (1) to the zwitterionic 2-(dimethyl-sulfonium)benzenesulfonate (2) is known to proceed in solution by intermolecular Me transfers. The same rearrangement has been observed to occur in crystalline 1, but the crystal structure shows that the molecular packing is not conducive to intermolecular Me transfer. The reaction has been carried out with mixed crystals composed of 1 and deuteriomethylated (D6)-l. By fast-atom-bombardment mass spectroscopy, it has been shown that the product consists of a 1:2:1 mixture of the non-, tri-, and hexadeuterated species, the mixture expected, if the solid-state reaction proceeds by intermolecular Me transfers. From this result, together with the slower rates of conversion in the single crystal compared with the melt, it can be concluded that the reaction must occur not topochemically but rather at defects such as microcavities, surfaces, and other irregularities in the ordered crystal arrangement.

Explosive speciation rates and unusual species richness in haplochromine cichlid fishes: Effects of sexual selection

Ancient lakes are often unusually species rich, mostly as a result of radiation and species-flock formation having taken place in only one or a few of many taxa present. Understanding why some taxa radiate and others do not is at the heart of understanding biodiversity. In this chapter I discuss possible explanations for disproportionally large species numbers in some cichlid fish lineages in East African Great Lakes: the halochromine cichlid fishes in Lakes Victoria and Malawi. I show that speciation rates in this group are higher than in any other lacustrine fish radiation. Against this background, I review hypotheses put forward to explain diversity in cichlid species flocks. The evolution of species diversity requires three processes: speciation, ecological radiation and anatomical diversification, and it is wrong to consider hypotheses that are relevant to different processes as alternatives to each other. The African cichlid species flocks show unusually high ecological species packing in several phylogenetic groups and unusually high speciation rates in haplochromines. Therefore, it maybe concluded that at least two evolutionary models are required to explain the difference between cichlid diversity and other fish diversity in East African Lakes: one for speciation in haplochromines and one for coexistence. Subsequently I review work on speciation in haplochromines, and in particular studies aimed at testing the hypothesis of speciation by sexual selection. Haplochromines have a polygynous mating system, conducive to sexual selection, but other polygynous cichlids are not particularly species rich. This suggests that more than just strong sexual selection is required to explain haplochromine species richness. Recent palaeoecological evidence undermines the previously popular hypotheses that explained the species richness of Lake Victoria in terms of speciation under varying natural or sexual selection regimes in satellite lakes or in isolated lake basins. I summarize experimental and comparative studies, which provide evidence for two mechanisms of sympatric speciation by disruptive sexual selection on polymorphic coloration. Such modes of speciation may explain (i) the high speciation rates in colour polymorphic lineages of haplochromine cichlids under conditions where colour variation is visible in clear water, and (ii) in combination with factors that affect population survival, the unusual species richness in haplochromine species flocks. I argue that sexual selection, if disruptive, can accelerate the pace of adaptive radiation because the resultant genetic population fragmentation allows a much increased rate of differential response to disruptive natural selection. Hence, the ecological pattern of diversity resembles that produced by disruptive natural selection, with the difference that disruptive sexual selection continues to cause (gross) speciation even after niche space is saturated. This may explain the unusually high numbers of very closely related and ecologically similar species in haplochromine species flocks. The role of disruptive sexual selection is twofold: it not only causes speciation, but also maintains reproductive isolation in sympatry between species that have evolved in sympatry or allopatry. Therefore, the maintenance of diversity in species flocks that originated through sexual selection depends on the persistence of the selection regime within the environmental signal space under which that diversity evolved.

Interaction of the Trinuclear Triangular Secondary Building Unit [Cu 3 (μ 3 -OH)(μ-pz) 3 ] 2+ with 4,4′-Bipyridine. Structural Characterizations of New Coordination Polymers and Hexanuclear Cu II Clusters. 2°

By reacting 4,4′-bipyridine (bpy) with selected trinuclear triangular CuII complexes, [Cu3(μ3-OH)(μ-pz)3(RCOO)2(LL′)] [pz = pyrazolate anion; R = CH3, CH3CH2, CH2═CH, CH2═C(CH3); L, L′ = Hpz, H2O, MeOH] in MeOH, the substitution of monotopic ligands by ditopic bpy was observed. Depending on the stoichiometric reaction ratios, different compounds were isolated and structurally characterized. One- and two-dimensional coordination polymers (CPs), as well as two hexanuclear CuII clusters were identified. One of the hexanuclear clusters self-assembles into a supramolecular three-dimensional structure, and its crystal packing shows the presence of two intersecting channels, one of which is almost completely occupied by guest bpy, while in the second one guest water molecules are present. This compound also shows a reversible, thermally induced, single-crystal-to-single-crystal transition.

Synthesis and Structural Characterizations of New Coordination Polymers Generated by the Interaction Between the Trinuclear Triangular SBU [Cu 3 (μ 3 -OH)(μ-pz) 3 ] 2+ and 4,4′-Bipyridine. 3°

The reactions of 4,4′-bipyridine with selected trinuclear triangular copper(II) complexes, [Cu3(μ3-OH)(μ-pz)3(RCOO)2Lx], [pz = pyrazolate anion, R = CH3(CH2)n (2 ≤ n ≤ 5); L = H2O, MeOH, EtOH] yielded a series of 1D coordination polymers (CPs) based on the repetition of [Cu3(μ3-OH)(μ-pz)3] secondary building units joined by bipyridine. The CPs were characterized by conventional analytical methods (elemental analyses, ESI-MS, IR spectra) and single crystal XRD determinations. An unprecedented 1D CP, generated through the bipyridine bridging hexanuclear copper clusters moieties, two 1D CPs presenting structural analogies, and two monodimensional tapes having almost exactly superimposable structures, were obtained. In one case, the crystal packing makes evident the presence of small, not-connected pores, accounting for ca. 6% of free cell volume.

Modeling the Histidine–Phenylalanine Interaction: The NH···π Hydrogen Bond of Imidazole·Benzene

NH···π hydrogen bonds occur frequently between the amino acid side groups in proteins and peptides. Data-mining studies of protein crystals find that ~80% of the T-shaped histidine···aromatic contacts are CH···π, and only ~20% are NH···π interactions. We investigated the infrared (IR) and ultraviolet (UV) spectra of the supersonic-jet-cooled imidazole·benzene (Im·Bz) complex as a model for the NH···π interaction between histidine and phenylalanine. Ground- and excited-state dispersion-corrected density functional calculations and correlated methods (SCS-MP2 and SCS-CC2) predict that Im·Bz has a Cs-symmetric T-shaped minimum-energy structure with an NH···π hydrogen bond to the Bz ring; the NH bond is tilted 12° away from the Bz C₆ axis. IR depletion spectra support the T-shaped geometry: The NH stretch vibrational fundamental is red shifted by −73 cm⁻¹ relative to that of bare imidazole at 3518 cm⁻¹, indicating a moderately strong NH···π interaction. While the Sₒ(A1g) → S₁(B₂u) origin of benzene at 38 086 cm⁻¹ is forbidden in the gas phase, Im·Bz exhibits a moderately intense Sₒ → S₁ origin, which appears via the D₆h → Cs symmetry lowering of Bz by its interaction with imidazole. The NH···π ground-state hydrogen bond is strong, De=22.7 kJ/mol (1899 cm⁻¹). The combination of gas-phase UV and IR spectra confirms the theoretical predictions that the optimum Im·Bz geometry is T shaped and NH···π hydrogen bonded. We find no experimental evidence for a CH···π hydrogen-bonded ground-state isomer of Im·Bz. The optimum NH···π geometry of the Im·Bz complex is very different from the majority of the histidine·aromatic contact geometries found in protein database analyses, implying that the CH···π contacts observed in these searches do not arise from favorable binding interactions but merely from protein side-chain folding and crystal-packing constraints. The UV and IR spectra of the imidazole·(benzene)₂ cluster are observed via fragmentation into the Im·Bz+ mass channel. The spectra of Im·Bz and Im·Bz₂ are cleanly separable by IR hole burning. The UV spectrum of Im·Bz₂ exhibits two 000 bands corresponding to the Sₒ → S₁ excitations of the two inequivalent benzenes, which are symmetrically shifted by −86/+88 cm⁻¹ relative to the 000 band of benzene.

Retrospective study of prevalence of Community Associated Methicillin Resistant Staphylococcus Aureus (CA-MRSA) seen in Texas MedClinics, San Antonio, TX from April 2006-August 2009

Purpose. To evaluate the presence of Community Associated–Methicillin Resistant Staphylococcus Aureus, CA-MRSA, in abscesses and skin and soft tissue infections presenting at 9 urgent care clinics in San Antonio, TX. ^ Methods. During the 40-month retrospective study (April 2006 to August 2009), wound cultures collected in 9 urgent care centers were evaluated for MRSA growth, antibiotics prescribed, follow up wound care, and antibiotic prescribing habits by physicians for all patients presenting with abscesses and skin/soft tissue infections. ^ Results. Across 9 urgent care centers in San Antonio, TX, 36,797 abscesses and cases of skin and soft tissue infections were treated during 40 months. Of the 36,797 cases, 9290 patients had wound cultures sent with 5,630 cultures sent to Texas MedClinic’s primary lab. Of the 5630 cultures sent to their primary lab, this reflected a prevalence of 4727 (84 %) cultures were positive for MRSA. Of the 9290 patients who had a wound culture sent (April 10th, 2006 to August 31st, 2009), a total of 4,307 antibiotics were prescribed. The top five antibiotics prescribed for CA-MRSA were Bactrim (55.5%), Clindamycin (18.4%), Bactroban (5%), Amoxicillin (3.5%), and Doxycycline (3%) representing 85.4% of the antibiotics prescribed. 8809/9290 (94.8%) of patients required no more than 3 follow up visits. Of the 33 physicians working full time during the entire study period, 29/33 (87.8%) of the physicians were family medicine physicians and represented varied prescribing rates of antibiotics between 11-76% with 26/33 (78.8%) of physicians prescribing antibiotics greater than 40% of the time.^ Conclusions. Abscesses and soft tissue infections are a common presenting complaint to urgent care centers. This study reveals that antibiotic-prescribing practices can be improved with physician education since this high prevalence was not known previously. Also, treating abscesses with limited packing has been shown to be a viable option in this particular circumstance and would be open field for additional clinical research. Due to the high prevalence of CA-MRSA skin and soft tissue infections among patients presenting to urgent care centers presumptive treatment for MRSA is indicated. Increasing levels of resistance to penicillin antibiotics is concerning and warrants alternative antibiotic management strategies.^

Age analysis, aragonite and high magnesium calcite content from different IODP Holes from Exp 310

The widespread occurrence of microbialites in the last deglacial reef frameworks (16-6 Ka BP) implies that the accurate study of their development patterns is of prime importance to unravel the evolution of reef architecture through time and to reconstruct the reef response to sea-level variations and environmental changes. The present study is based on the sedimentological and chronological analysis (14C AMS dating) of drill cores obtained during the IODP Expedition #310 "Tahiti Sea Level" on the successive terraces which typify the modern reef slopes from Tahiti. It provides a comprehensive data base to investigate the microbialite growth patterns (i.e. growth rates and habitats), to analyze their roles in reef frameworks and to reconstruct the evolution of the reef framework architecture during sea-level rise. The last deglacial reefs from Tahiti are composed of two distinctive biological communities: (1) the coralgal communities including seven assemblages characterized by various growth forms (branching, robust branching, massive, tabular and encrusting) that form the initial frameworks and (2) the microbial communities developed in the primary cavities of those frameworks, a few meters (1.5 to 6 m) below the living coral reef surface, where they heavily encrusted the coralgal assemblages to form microbialite crusts. The dating results demonstrate the occurrence of two distinctive generations of microbialites: the "reefal microbialites" which developed a few hundred years after coralgal communities in shallow-water environments, whereas the "slope microbialites" grew a few thousands of years later in significantly deeper water conditions after the demise of coralgal communities. The development of microbialites was controlled by the volume and the shape of the primary cavities of the initial reef frameworks determined by the morphology and the packing of coral colonies. The most widespread microbialite development occurred in frameworks dominated by branching, thin encrusting, tabular and robust branching coral colonies which built loose and open frameworks typified by a high porosity (> 50%). In contrast, their growth was minimal in compact coral frameworks formed by massive and thick encrusting corals where primary cavities yielded a low porosity (~ 30%) and could not host a significant microbialite expansion.

Conservación de dos variedades de arándano alto en condiciones de frío convencional

Se evaluaron dos cultivares de arándano alto por su comportamiento en almacenamiento refrigerado convencional. Frutos completamente azules se seleccionaron, envasaron en "clamshells" y sometieron a almacenamiento refrigerado a 0 °C y 85-90 % HR durante 10, 17, 24 y 31 días. Para cada período de almacenamiento se realizaron muestreos: (1) a salida de frío y (2) después de dos días a temperatura ambiente. Se evaluó la homogeneidad en el empaque, pérdida de peso, firmeza, contenido de sólidos solubles, acidez titulable, pH y relación sólidos solubles:acidez titulable. El peso promedio de los frutos fue de 1.9 g, correspondiéndoles el grado "extralarge". La fruta se mantuvo en buenas condiciones durante 11 días de almacenamiento refrigerado, después perdió calidad como consecuencia de la pérdida de peso. Se encontró que Bluejay superó a Brigitta en firmeza. El contenido de sólidos solubles aumentó proporcionalmente a la duración del período de almacenamiento. En los períodos de 10 y 31 días Brigitta presentó mayor acidez titulable y menor relación sólidos solubles:acidez titulable que Bluejay. En ambos cultivares se observó un aumento significativo del pH al mes de almacenamiento. A partir de la correlación entre las variables evaluadas se infiere que el contenido de sólidos solubles y la firmeza constituyeron buenos índices de la calidad de la fruta en ambas variedades.

Aceite esencial de tomillo como antioxidante y conservador de hamburguesas funcionales

Para determinar el poder antioxidante y conservante del aceite esencial de tomillo mendocino (Acantholippia seriphioides) en hamburguesas funcionales, conservadas a 4 ± 0.5 °C, se elaboraron medallones utilizando: 83 % carne vacuna 5 % grasa vacuna 5 % salvado de avena 5 % texturizado de soja 2 % sustituto graso 0.08 g NaCl/kg aceite esencial de tomillo (AET) 106 ufc/g Se estudió: • tipo de envasado: bolsas de poliamidapolietileno; atmósfera modificada: 70 % N 2 y 30 % CO2, y vacío; • tiempo de almacenamiento: 0, 1, 2, 3 y 4 semanas; • dosis de tomillo: 0 y 150 mg AET/kg Los datos se analizaron de acuerdo con un arreglo factorial 2 (tipo de envasado) x 5 (tiempos de almacenamiento) x 2 (dosis de AET) en un diseño de parcelas subdivididas, con 4 repeticiones. Se evaluaron TBA, pH, NBV, color, olor y carga microbiana. Las tres primeras variables se estudiaron mediante el ANOVA. Para color y olor se recurrió a un análisis sensorial descriptivo. La carga microbiana se representó gráficamente. El AET disminuyó el TBA, independientemente del tipo de envasado utilizado. El pH disminuyó en el tiempo siguiendo un modelo polinomial de 2° grado. El NBV resultó significativo para: envasamiento al vacío y 0 mg/kg AET. El AET mantiene los atributos sensoriales durante las dos primeras semanas pero no disminuye la carga microbiana. Conclusión: el AET tiene efecto antioxidante pero no conservante en hamburguesas funcionales de carne vacuna bajo las condiciones del ensayo.

Duraznos O'Henry : impacto económico por pérdidas de calidad

El durazno O'Henry para consumo en fresco es una variedades apta para la exportación. Consecuentemente se propone un método sencillo para determinar las pérdidas de calidad que impiden obtener mejores precios en los mercados.. Las mismas se relacionan con una mala gestión en todos los niveles: producción, empaque y comercialización, y la deficiente capacitación del personal involucrado. En la temporada 1999/2000 el granizo fue la causa más frecuente en precosecha; sus marcas explican el 70 % de los frutos con falta de calidad. En cambio, el principal factor en cosecha fueron las picaduras de grafolita, dando 80 % de frutos sin calidad exportable. En galpón de empaque, el mal manejo poscosecha -revelado en machucones, marcas de uñas y rajaduras- originó el 30 % de las causas de no calidad; si se le agregan las picaduras de grafolita, el porcentaje se aproxima al 60 %. Ambas causas pueden minimizarse con buena planificación y capacitación. Con simulación económica se detectó -en la precitada temporada- 20 % de pérdida de calidad de una partida lo cual motiva una disminución superior al 13 % en los ingresos. Esta diferencia depende no sólo del peso relativo de las distintas calidades sino también del precio pactado.

Almacenamiento refrigerado de cerezas : efecto de madurez y atmósfera modificada

Se estudió el efecto de cosechar cerezas en dos estados de madurez: rojo pálido y rojo maduro y la utilización de atmósferas modificadas, empleando PBD de 11 y 40 m, sobre la calidad de fruta almacenada a 0 °C y después de 3 días a temperatura ambiente. La calidad fue evaluada en términos de pérdida de peso (%), color (ángulo hue), firmeza, contenido de sólidos solubles, aspecto de los pedicelos y presencia de podredumbres. La fruta cosechada más madura presentó color, sólidos solubles y firmeza adecuados durante 21 días a 0 °C pero el almacenamiento prolongado estuvo limitado por la deshidratación de los pedicelos, que mantuvieron aspecto comercial sólo durante una semana. Para ambos estados de madurez se registró importante pérdida de peso; disminución del valor de °hue y aumentos de sólidos solubles y de firmeza. Durante la simulación comercial la fruta experimentó ablandamiento, pérdida de peso, oscurecimiento de la piel y deshidratación de los pedicelos. Con el uso del PBD no se detectaron cambios significativos para ninguno de los parámetros estudiados, permitiendo además reducir la deshidratación y mantener el aspecto comercial de los pedicelos, independientemente del espesor de la película.

Envases para frutas y hortalizas frescas

La calidad con que llegan las frutas al consumidor depende, en gran medida, del material del envase. Dado las exigencias cada vez mayores, tanto del mercado de exportación como del interno, es importante la adecuada selección del material para envase y embalaje. El envase apropiado es el que soluciona problemas fisiológicos propios de la fruta, la protege prolongando su conservación y, al mismo tiempo, resalta su presentación sin incrementar considerablemente el precio del producto final.

Procesos de innovación agroalimentaria y demanda internacional de alimentos frescos. El sector empaque de cítricos en Entre Ríos

Las firmas agroindustriales exportadoras argentinas de productos en fresco están transitando por un proceso progresivo de modernización e implementación de normativas internacionales sobre calidad agroalimentaria. Desde esta perspectiva, el presente trabajo aporta algunos elementos de análisis que permiten profundizar en el conocimiento del eslabón de acondicionamiento/ empaque del complejo agroindustrial citrícola del noreste de la provincia de Entre Ríos, departamentos de Concordia y Federación, a partir de la segunda mitad de la década de los noventa, centrando la mirada en las empresas exportadoras y en las innovaciones que han implementado para ajustar los estándares de calidad.

Territorios y mercados globales: Las firmas agroexportadoras citrícolas del noreste argentino

El trabajo aborda la problemática de las firmas empacadoras/exportadoras de cítricos dulces del denominado corredor citrícola del río Uruguay -departamentos de Federación y Concordia en la provincia de Entre Ríos y departamento de Monte Caseros en Corrientes-. Específicamente nos preguntamos si la convergencia geográfica de firmas en un mismo espacio regional/local propicia mecanismos de articulación que favorezcan la obtención de sinergias y su participación en el segmento exportador, considerándolas en relación al capital trasnacional que opera en la misma región. En nuestro análisis exploramos algunas de las estrategias que adoptan las firmas para la inserción en los mercados, enfocándonos en los mecanismos de coordinación interempresarial a nivel horizontal y a escala local-regional, prestando particular atención a la sustentabilidad de los mismos. Empleamos un enfoque metodológico que pone énfasis en técnicas de análisis cualitativas, aplicadas a entrevistas semi-estructuradas y en profundidad a los integrantes de la trama, seleccionados en función del rol que cumplen dentro de ella. La información relevada se complementa con datos secundarios y la revisión de bibliografía pertinente para el área de estudio.