Comparing the performances of SSR and SNP markers for population analysis in Theobroma cacao L., as alternative approach to validate a new ddRADseq protocol for cacao genotyping.

Proper cacao (Theobroma cacao L.) plant genotyping is mandatory for the conservation and use of the species genetic resources. A set of 15 international standard SSR markers was assumed as universal cacao genotyping system. Recently, different SNPs and SNP genotyping techniques have been exploited in cacao. However, a consensus on which to use has not been reached yet, driving the search for new approaches. To validate a new ddRADseq protocol for cacao genotyping, we compared the performances for population analysis of a dataset with 7,880 SNPs obtained from ddRADseq and the genotypic data from the aforementioned SSR set, using 158 cacao plants from productive farms and gene bank. Four genetic groups were identified with STRUCTURE and ADMIXTURE softwares using SSR and SNP data, respectively. Similarities of cacao ancestries among these groups allowed the identification of analogous pairs of groups of individuals, referred to as: G1SSR/G1SNP, G2SSR/G2SNP, G3SSR/G3SNP, G4SSR/G4SNP, whether SSRs or SNPs were used. Both marker systems identified Amelonado and Criollo as the most abundant cacao ancestries among all samples. Genetic distance matrices from both data types were significantly similar to each other according to Mantel test (p < 0.0001). PCoA and UPGMA clustering mostly confirmed the identified genetic groups. AMOVA and FST pairwise comparison revealed a moderate to very large genetic differentiation among identified groups from SSR and SNP data. Genetic diversity parameters from SSR (Hobs = 0.616, Hexp = 0.524 and PIC = 0.544) were higher than that from SNP data (0.288, 0.264, 0.230). In both cases, genetic groups carrying the highest Amelonado proportion (G1SSR and G1SNP) had the lowest genetic diversity parameters among the identified groups. The high congruence among population analysis results using both systems validated the ddRADseq protocol employed for cacao SNP genotyping. These results could provide new ways for developing a universal SNP-based genotyping system very much needed for cacao genetic studies.

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes.

The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093-0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.

Structural and Electronic Properties of Iron-Doped Sodium Montmorillonite Clays: A First-Principles DFT Study.

First-principles calculations done via density functional theory were used to study the structural and electronic properties of sodium montmorillonite clay (Mt-Na+) of general formula M x Al3Si8O24H4Na·nH2O (M x : Mg or Fe). The final position of the interlamellar sodium atom is found to be close to the oxygen atoms located on the upper surface of silica. Following Fe-Mt-Na+ system relaxation, with subsequent analysis of magnetic moment and magnetic states, the electroneutrality of the system established that both Fe2+ and Fe3+ oxidation states are possible to occur. The Mg2+-Mt-Na+ material shows a band gap energy greater than that of Fe2+-Mt-Na+ when iron is in the octahedral site. It is found that the valence-band maximum and the conduction-band minimum of iron-doped montmorillonite are both at the Γ-point, while it is at V → Γ for magnesium-doped montmorillonite. The calculated band gap from hybrid functional (HSE06) of Fe2+-Mt-Na+ is equal to 4.3 eV, exhibiting good agreement with experimental results obtained from ultraviolet-visible spectroscopy of the natural Mt-Na+ (Cloisite-Na+).

The environmental and intrinsic yeast diversity of Cuban cocoa bean heap fermentations.

The environmental yeast diversity of spontaneous cocoa bean fermentations in east Cuba was investigated. Seven fermentations, 25 equipment- and handling-related samples, and 115 environmental samples, such as flowers, leaf and cocoa pod surfaces, as well as drosophilid insects, were analysed. The basic fermentation parameters temperature and pH were recorded during five fermentations for at least six days. A total of 435 yeast isolates were identified by a combination of PCR-fingerprinting of genomic DNA with the M13 primer and sequence analysis of DNA from representative isolates, using the internal transcribed spacer region, the D1/D2 region of the large subunit rRNA gene, and an actin gene-encoding fragment, as required. Among 65 yeast species detected, Pichia manshurica and Hanseniaspora opuntiae were the most frequently isolated species, obtained from five and four fermentations, followed in frequency by Pichia kudriavzevii from two fermentations. Saccharomyces cerevisiae was isolated only occasionally. Cocoa fermentation yeast species were also present on processing equipment. The repeated isolation of a preliminarily as Yamadazyma sp. classified species, a group of strains similar to Saccharomycopsis crataegensis from fermentations and equipment, and the isolation of fifteen other potentially novel yeast species in low numbers provides material for further studies. Environmental samples showed higher yeast diversity compared to the fermentations, included the most frequent fermentation species, whereas the most frequently isolated environmental species were Candida carpophila, Candida conglobata, and Candida quercitrusa. Potential selective advantages of the most frequently isolated species were only partly explained by the physiological traits tested. For instance, tolerance to higher ethanol concentrations was more frequent in strains of Pichia spp. and S. cerevisiae compared to Hanseniaspora spp.; the ability to also assimilate ethanol might have conferred a selective advantage to Pichia spp. In contrast, high glucose tolerance was common among strains of Hanseniaspora spp., Torulaspora delbrueckii, and Candida tropicalis, among which only Hanseniaspora spp. were frequently isolated.

Electronic and magnetic properties of SnO2/CrO2 thin superlattices.

In this article, using first-principles electronic structure calculations within the spin density functional theory, alternated magnetic and non-magnetic layers of rutile-CrO2 and rutile-SnO2 respectively, in a (CrO2)n(SnO2)n superlattice (SL) configuration, with n being the number of monolayers which are considered equal to 1, 2, ..., 10 are studied. A half-metallic behavior is observed for the (CrO2)n(SnO2)n SLs for all values of n. The ground state is found to be FM with a magnetic moment of 2 µB per chromium atom, and this result does not depend on the number of monolayers n. As the FM rutile-CrO2 is unstable at ambient temperature, and known to be stabilized when on top of SnO2, the authors suggest that (CrO2)n(SnO2)n SLs may be applied to spintronic technologies since they provide efficient spin-polarized carriers.

Profile of hemodynamic and gasometric parameters in rabbits submitted to controlled hemorrhagic shock / Perfil dos parâmetros hemodinâmicos e gasométricos em coelhos submetidos a choque hemorrágico controlado

Objective: the aim of this study was to assess the values ofhemodynamic, gasometric and electrolytic parameters, in rabbits submitted to controlled hemorrhagic shock, using an experimental model for catheterization of right carotid artery and jugular vein. Methods: fourteen male California rabbits were submitted to intramuscular anesthesia, and medi um cervicotomy was performed for catheterization of right carotid artery and right jugular vein. The animals were bled to a mean arterial pressure of 40mmHg and were maintained at this level, by further blood withdrawal, during 20 minutes, followed by 15 minutes of resuscitation using lactated Ringer's solution and remaining shed blood volume (3:1) to mean arterial pressure equal 80mmHg, and 120 minutes of reperfusion. Arterial blood gas, serum lactate and electrolytes (sodium and potassium)samples were measured at baseline, hemorrhagic shock, at the time of resuscitation, and at the time ofreperfusion (30,60,90 and 120min). Results: the mean ofinitial values ofhemodynamic parameters wereMAP=82.3mmHg, RR=51.4breaths/min, HR=141.5beats/min; gasometric parameters - pH=7.358, PaC02=46.6mmHg, Pa02=271.9mmHg, HCO]-=25.0mmol/L, base deficit=1.5mmol/L, serum lactate=2.6mmo/IL; electrolytic parameters - Na+=131. 7mEq/L and K+=3.4mEq/L. Conclusions: this study presents a reproducible model of hemorrhagic shock in Californian rabbits, which describes the progressive hemodynamic and metabolic changes that reflect the changes seen frequently in the clinical situation, besides offers a model to assess novel therapeutics interventions in a controlled setting.

Objetivo: avaliar os valores dos parâmetros hemodinâmicos, gasométricos e eletrolíticos, em coelhos submetidos a choque hemorrágico controlado, com a utilização de um modelo experimental de cateterização da artéria carótida e veia jugular direitas. Método: catorze coelhos Califórnia, machos, foram submetidos à anestesia intramuscular seguida de cervicotomia mediana e cateterização da artéria carótida direita e da veia jugular direita. Os animais foram sangrados até a pressão arterial média (PAM) de 40mmHg e mantidos neste nível durante 20 minutos, seguidos de 15 minutos de reposição com a utilização de solução de Ringer lactato e sangue (3:1) até a PAM atingir 80mmHg, e 120 minutos de reperfusão. Amostras dos gases arteriais, do lactato sérico e dos eletrólitos (sódio e potássio) foram coletadas no início do experimento, no choque hemorrágico, no período de reposição e na reperfusão (30, 60, 90 e 120 minutos). Resultados: a média dos valores iniciais dos parâmetros hemodinâmicos foram - PAM=82.3mmHg, FR=51.4mov/min, FC=141.5bat/min; parâmetros gasométricos - pH=7.358, PaC02=46.6mmHg, Pa02=271.9mmHg,HC03-=25.0mmol/L, déficit de base=1.5mmol/L, lactato sérico=2.6mmol/L; parâmetros eletrolíticos-Na+=131.7mEq/L and K+=3.4mEq/L. Conclusões: este estudo apresenta um modelo reprodutível de choque hemorrágico controlado em coelhos Califórnia, o qual descreve as progressivas alterações hemodinâmicas e metabólicas que refletem aquelas freqüentemente observadas em situações clínicas, além de oferecer um modelo para avaliar novas terapêuticas em estudos controlados.

Síndrome de Wolf-Hirschhorn (deleção do braço curto do cromossomo 4p): Relato de caso / Wolf-hirschhorn syndrome (terminal deletion of the short arm of chromosome 4p): case report

Objective: to report a case of Wolf-Hirschhorn Syndrome or partial deletion of the short arm of one chromosome 4 and present a brief literature review. Case Report: the authors report a case of a seven years-old child presenting the main findings of the syndrome: hypertelorism, big and large nose, prominent glabella, high arched eyebrows, antimongoloid palpebral fissures, bilateral low implantation of auricles, and microcephaly. Echodopplercardiographic study evidenced interatrial communication type ostium secundum without hemodynamic repercussion. Radiological examination showed clubfeet. The patient presents many cognitive deficits, mainly in functions as interaction and learning. Evident motor dysfunctions compromising gait and also muscle atrophy. The child also presented convulsive crises in the first year of life that are currently controlled by the use of anticonvulsants. Final considerations: the incidence of the Wolf-Hirschhorn Syndrome is rare, with only 100 cases reported until1981. The prognosis is relative, with one third of the patients dying with in the first year, while other children are alive with more than twelve years of age. This case was diagnosed based on clinical, radiological, echodopplercardiographical criteria and confirmed by the karyotype's result 46,XX,del(4)(p15?1).

Objetivo: descrever um caso de síndrome de Wolf-Hirschhorn ou deleção parcial terminal do braço curto de um dos cromossomos 4 e apresentar uma breve revisão da literatura. Relato de Caso: criança de sete anos que apresenta os principais aspectos da síndrome: hipertelorismo, nariz grande e adunco, glabela proeminente, fissuras palpebrais antimongolóides, implantação baixa dos pavilhões auriculares, micrognatia e microcefalia. Radiografias do esqueleto revelaram má formação óssea, causando pés eqüinovaros. A ecodopplercardiografia evidenciou CIA sem repercussão hemodinâmica. A paciente apresenta inúmeros déficits cognitivos, fundamentalmente nas funções de interação e aprendizado, além dos distúrbios motores evidentes, com comprometimento da marcha e atrofia muscular; crises convulsivas no primeiro ano de vida, mas que estão atualmente controladas pelo uso de anticonvulsivante. Considerações Finais: a incidência da Síndrome de Wolh-Hirschhorn é rara, com 100 casos publicados até 1981. O prognóstico é relativo, com 1/3 dos pacientes morrendo no decorrer do primeiro ano, enquanto outras crianças estão vivas com mais de 12 anos. O caso apresentado foi diagnosticado com base em critérios clínicos, radiológicos, ecodopplercardiogáficos e confirmado pelo resultado do cariótipo: 46,XX,del(4)(p15?1).

Moderately and strongly supercooled liquids: a temperature-derivative study of the primary relaxation time scale.

The primary relaxation time scale tau(T) derived from the glass forming supercooled liquids (SCLs) is discussed within ergodic-cluster Gaussian statistics, theoretically justified near and above the glass-transformation temperature T(g). An analysis is given for the temperature-derivative data by Stickel et al. on the steepness and the curvature of tau(T). Near the mode-coupling-theory (MCT) crossover T(c), these derivatives separate by a kink and a jump, respectively, the moderately and strongly SCL states. After accounting for the kink and the jump, the steepness remains a piecewise conitnuous function, a material-independent equation for the three fundamental characteristic temperatures, T(g), T(c), and the Vogel-Fulcher-Tamman (VFT) T(0), is found. Both states are described within the heterostructured model of solidlike clusters parametrized in a self-consistent manner by a minimum set of observable parameters: the fragility index, the MCT slowing-down exponent, and the chemical excess potential of Adam and Gibbs model (AGM). Below the Arrhenius temperature, the dynamically and thermodynamically stabilized clusters emerge with a size of around of seven to nine and two to three molecules above and close to T(g) and T(c), respectively. On cooling, the main transformation of the moderately into the strongly supercooled state is due to rebuilding of the cluster structure, and is attributed to its rigidity, introduced through the cluster compressibility. It is shown that the validity of the dynamic AGM (dynamically equivalent to the standard VFT form) is limited by the strongly supercooled state (T(g) < T < T(c)) where the superrigid cooperative rearranging regions are shown to be well-chosen parametrized solidlike clusters. Extension of the basic parameter set by the observable kinetic and diffusive exponents results in prediction of a subdiffusion relaxation regime in SCLs that is distinct from that established for amorphous polymers.