Assisted-selection of naturally caffeine-free coffee cultivars—characterization of SNPs from a methyltransferase gene

Breeding of caffeine-free coffee cultivars require tools for an early selection of progenies bearing this later trait. Genes from caffeine synthesis and degradation represent major targets for the development of molecular markers for assisted selection. In this study, we characterized SNPs identified on the caffeine synthase gene from AC1 mutant, a naturally caffeine-free arabica coffee plant. Molecular analysis of normal and mutant sequences indicates the occurrence of SNPs in protein domains, potentially associated with caffeine synthesis in coffee. Progenies F₂, F₁BC₁ and BC from crosses of AC mutants and elite cultivars were evaluated regarding caffeine content in grains and genomic segregation profile of selected SNPs. Genotyping analysis allowed the discrimination between homozygous and heterozygous plants. Quantification of caffeine content indicated a significant variability among progenies and a low frequency of caffeine-free plants. Statistical analyses of genotyping and phenotyping results showed significant association between presence of selected SNPs and reduced caffeine content. Moreover, this association occurs through all evaluated genetic backgrounds and generations, indicating an inheritance stability of both trait and markers. The molecular markers described here represent a successful case of assisted-selection in coffee, indicating their potential use for breeding of caffeine-free cultivars.     

Optical properties of the adaxial and abaxial faces of leaves. Chlorophyll fluorescence, absorption and scattering coefficients.

Emission fluorescence spectra were obtained for the adaxial and abaxial faces of dicotyledonous (Ficus benjamina L., Ficus elastica, Gardenia jasminoides and Hedera helix) and monocotyledonous leaves (Gladiolus spp. and Dracaena cincta bicolor). After correction by light-re-absorption processes, using a previously published physical model, the adaxial faces of dicotyledons showed a fluorescence ratio Fred/Ffar-red rather lower than the respective values for the abaxial faces. Monocotyledons and shade-adapted-plants showed similar values for the corrected fluorescence ratio for both faces. Even when differences in experimental fluorescence emission from adaxial and abaxial leaves in dicotyledons are mostly due to light re-absorption processes, the residual dissimilarity found after application of the correction model would point to the fact that fluorescence re-absorption is not the only responsible for the observed disparity. It was concluded that light re-absorption processes does not account entirely for the differences in the experimental emission spectra between adaxial and abaxial leaves. Differences that remains still present after correction might be interpreted in terms of a different photosystem ratio (PSII/PSI). Experiments at low temperature sustained this hypothesis. In dicotyledons, light reflectance for adaxial leaves was found to be lower than for the abaxial ones. It was mainly due to an increase in the scattering coefficient for the lower leaf-side. The absorption coefficient values were slightly higher for the upper leaf-side. During senescence of Ficus benjamina leaves, the scattering coefficient increased for both the upper and lower leaf-sides. With senescence time the absorption coefficient spectra broadened while the corrected fluorescence ratio (Fred/Ffar-red) decreased for both faces. The results pointed to a preferential destruction of photosystem II relative to photosystem I during senescence.     

iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

Background  

In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques.     

Micro-scale environmental variation amplifies physiological variation among individual mussels

The contributions of temporal and spatial environmental variation to physiological variation remain poorly resolved. Rocky intertidal zone populations are subjected to thermal variation over the tidal cycle, superimposed with micro-scale variation in individuals'' body temperatures. Using the sea mussel (Mytilus californianus), we assessed the consequences of this micro-scale environmental variation for physiological variation among individuals, first by examining the latter in field-acclimatized animals, second by abolishing micro-scale environmental variation via common garden acclimation, and third by restoring this variation using a reciprocal outplant approach. Common garden acclimation reduced the magnitude of variation in tissue-level antioxidant capacities by approximately 30% among mussels from a wave-protected (warm) site, but it had no effect on antioxidant variation among mussels from a wave-exposed (cool) site. The field-acclimatized level of antioxidant variation was restored only when protected-site mussels were outplanted to a high, thermally stressful site. Variation in organismal oxygen consumption rates reflected antioxidant patterns, decreasing dramatically among protected-site mussels after common gardening. These results suggest a highly plastic relationship between individuals'' genotypes and their physiological phenotypes that depends on recent environmental experience. Corresponding context-dependent changes in the physiological mean–variance relationships within populations complicate prediction of responses to shifts in environmental variability that are anticipated with global change.     

Differential Left Hippocampal Activation during Retrieval with Different Types of Reminders: An fMRI Study of the Reconsolidation Process

Consolidated memories return to a labile state after the presentation of cues (reminders) associated with acquisition, followed by a period of stabilization (reconsolidation). However not all cues are equally effective in initiating the process, unpredictable cues triggered it, predictable cues do not. We hypothesize that the different effects observed by the different reminder types on memory labilization-reconsolidation depend on a differential neural involvement during reminder presentation. To test it, we developed a declarative task and compared the efficacy of three reminder types in triggering the process in humans (Experiment 1). Finally, we compared the brain activation patterns between the different conditions using functional magnetic resonance imaging (fMRI) (Experiment 2). We confirmed that the unpredictable reminder is the most effective in initiating the labilization-reconsolidation process. Furthermore, only under this condition there was differential left hippocampal activation during its presentation. We suggest that the left hippocampus is detecting the incongruence between actual and past events and allows the memory to be updated.     

Heterogeneous Distribution of Fetal Microchimerism in Local Breast Cancer Environment

Fetal cells enter maternal circulation during pregnancy and persist in the woman’s body for decades, achieving a form of physiological microchimerism. These cells were also evidenced in tumors. We investigated the frequency and concentration of fetal microchimerism in the local breast cancer environment. From 19 patients with confirmed breast neoplasia, after breast surgical resection, we collected three fresh specimens from the tumor core, breast tissue at tumor periphery, and adjacent normal breast tissue. The presence of male DNA was analyzed with a quantitative PCR assay for the sex determining region gene (SRY) gene. In the group of women who had given birth to at least one son, we detected fetal microchimerism in 100% of samples from tumors and their periphery and in 64% (9 of 14) of those from normal breast tissue. The tissues from the tumor and its periphery carry a significantly increased number of SRY copies compared to its neighboring common breast tissue (p = 0.005). The median of the normalized SRY-signal was about 77 (range, 3.2–21467) and 14-fold (range, 1.3–2690) greater in the tumor and respectively in the periphery than in the normal breast tissue. In addition, the relative expression of the SRY gene had a median 5.5 times larger in the tumor than in its periphery (range, 1.1–389.4). We found a heterogeneous distribution of fetal microchimerism in breast cancer environment. In women with sons, breast neoplasia harbors male cells at significantly higher levels than in peripheral and normal breast tissue.     

Susceptibility and lack of evidence for a viremic state of rabies in the night owl monkey, Aotus nancymaae

ABSTRACT: BACKGROUND: Rabies causes an acute fatal encephalomyelitis in most mammals following infection with rhabdovirus of the genus Lyssavirus. Little is known about rabies virus infection in species of New World Primates. To investigate the suitability of the Aotus nancymaae owl monkey as a viable animal model for rhabdovirus candidate vaccine testing, we used clinical presentation, serology, viral isolation, and PCR to evaluate the incubation period, immunity, and pathogenesis of infected animals. We tested the hypothesis that no viremic state exists for rabies virus. METHOD: S Eight monkeys divided into two equal groups were inoculated intramuscularly either in the neck or footpad with 105 pfu of rabies virus (Pasteur/ V-13R) and observed for >130 days. Oral and blood samples were collected and analyzed. RESULTS: Two monkeys inoculated in the neck displayed classic paralytic rabies. The mean incubation period was 11.5 days. The average maximum IgG response (antibody titer >0.200 O.D.) was achieved at day 10.0 and 62.3 in the clinical rabies and non-clinical rabies cases, respectively (p=0.0429). No difference in IgM or IgG time to seroconversion or average maximum IgM level was observed between neck versus footpad inoculation groups. No viremia or viral shedding was detected by PCR or viral isolation during the observation period, including within the two symptomatic animals three days after disease onset. Tissue sections examined were unremarkable for inflammation or other histologic signs of rabies. None of the brain sections exhibited immunoreactivity for rabies virus antibody. DISCUSSION This study demonstrates there is no difference in time to immune response between inoculation sites and distance to the brain; however, immune response tends to be more rapid in cases of clinically apparent disease and prolonged in cases infected at sites further from the brain. CONCLUSIONS: Our findings support the hypothesis that a viremic state for rabies does not exist in the New World Monkey, Aotus nancymaae, and it appears that this species may be refractory to infection. The species does provide a suitable model to assess post infection immune responses. Additional studies that address the limitations of sample size, length of observation, and lack of measurable infection should be conducted.