High-Throughput Sequencing of a South American Amerindian

The emergence of next-generation sequencing technologies allowed access to the vast amounts of information that are contained in the human genome. This information has contributed to the understanding of individual and population-based variability and improved the understanding of the evolutionary history of different human groups. However, the genome of a representative of the Amerindian populations had not been previously sequenced. Thus, the genome of an individual from a South American tribe was completely sequenced to further the understanding of the genetic variability of Amerindians. A total of 36.8 giga base pairs (Gbp) were sequenced and aligned with the human genome. These Gbp corresponded to 95.92% of the human genome with an estimated miscall rate of 0.0035 per sequenced bp. The data obtained from the alignment were used for SNP (single-nucleotide) and INDEL (insertion-deletion) calling, which resulted in the identification of 502,017 polymorphisms, of which 32,275 were potentially new high-confidence SNPs and 33,795 new INDELs, specific of South Native American populations. The authenticity of the sample as a member of the South Native American populations was confirmed through the analysis of the uniparental (maternal and paternal) lineages. The autosomal comparison distinguished the investigated sample from others continental populations and revealed a close relation to the Eastern Asian populations and Aboriginal Australian. Although, the findings did not discard the classical model of America settlement; it brought new insides to the understanding of the human population history. The present study indicates a remarkable genetic variability in human populations that must still be identified and contributes to the understanding of the genetic variability of South Native American populations and of the human populations history.     

Expression of DNA methyltransferases is involved in Quercus suber cork quality

Cork oak (Quercus suber) is an important Portuguese species, mainly due to the economic value of the cork it produces. Cork results from phellogen, a meristematic tissue, which can locally produce lenticels or have discontinuities, originating “defects”: pores and nail inclusions that are detrimental to cork industrial use. Epigenetic processes control plant development and its deregulation can lead to altered phenotypes; therefore, the study of epigenetic players in the phellogen is important to understand the emergence of cork's defects. DNA methyltransferases (DNMTs) and one protein associated to MET1 (DMAP1) were characterized in Q. suber, and their gene expression was analyzed in phellogen and contiguous differentiating cell layers of trees producing high and low quality cork, after the evaluation of their defects by physical and image analysis methods. All classes of DNMTs (MET, DRM, and CMT) with the respective canonical motifs were identified in Q. suber. The expression analyses of these genes showed that QsDRM2 was the most active methyltransferases in the cells analyzed, and that all the genes were differentially expressed in trees with distinct cork quality, with a tendency for higher expression levels in low quality producers. Interestingly, the global methylation level was higher in cells with low expression of DNA methyltransferases. A positive and significant correlation was obtained between QsDMAP1 gene expression and the percentage of cork defects. This work provides the first evidence that cork quality in Q. suber is likely influenced by epigenetic mechanisms.     

Different assembly of acid and salt tolerance response in two dairy Listeria monocytogenes wild strains

A lack on the association between acid tolerance response (ATR) and osmotolerance response (OTR) among Listeria monocytogenes dairy isolates was found. In order to evaluate how wild L. monocytogenes isolates mount tolerance responses under a sub-lethal pH and a low sodium chloride concentration (pH 5.5 and 3.5 % [w/v] NaCl), a proteomic approach was used. The ATR and OTR of two L. monocytogenes cheese dairy isolates (strain T8, serotype 4b and A9, serotype 1/2b or 3b) were determined. The proteomes of the adapted and non-adapted cultures were evaluated by 2-DE. One strain displayed an ATR, but not an OTR and the other displayed an OTR, but not an ATR. The ATR positive strain showed the over-production of proteins related with protein synthesis, protein folding, attainment of reduction power, ribose production and cell wall. In contrast, in the OTR-positive-strain proteins related with glycolysis, general stress and detoxification were identified.     

Ca2+ Signals Generated by CatSper and Ca2+ Stores Regulate Different Behaviors in Human Sperm

[Ca²⁺]_i signaling regulates sperm motility, enabling switching between functionally different behaviors that the sperm must employ as it ascends the female tract and fertilizes the oocyte. We report that different behaviors in human sperm are recruited according to the Ca²⁺ signaling pathway used. Activation of CatSper (by raising pH_i or stimulating with progesterone) caused sustained [Ca²⁺]_i elevation but did not induce hyperactivation, the whiplash-like behavior required for progression along the oviduct and penetration of the zona pellucida. In contrast, penetration into methylcellulose (mimicking penetration into cervical mucus or cumulus matrix) was enhanced by activation of CatSper. NNC55-0396, which abolishes CatSper currents in human sperm, inhibited this effect. Treatment with 5 μm thimerosal to mobilize stored Ca²⁺ caused sustained [Ca²⁺]_i elevation and induced strong, sustained hyperactivation that was completely insensitive to NNC55-0396. Thimerosal had no effect on penetration into methylcellulose. 4-Aminopyridine, a powerful modulator of sperm motility, both raised pH_i and mobilized Ca²⁺ stored in sperm (and from microsomal membrane preparations). 4-Aminopyridine-induced hyperactivation even in cells suspended in Ca²⁺-depleted medium and also potentiated penetration into methylcellulose. The latter effect was sensitive to NNC55-039, but induction of hyperactivation was not. We conclude that these two components of the [Ca²⁺]_i signaling apparatus have strikingly different effects on sperm motility. Furthermore, since stored Ca²⁺ at the sperm neck can be mobilized by Ca²⁺-induced Ca²⁺ release, we propose that CatSper activation can elicit functionally different behaviors according to the sensitivity of the Ca²⁺ store, which may be regulated by capacitation and NO from the cumulus.     

Differences in Al tolerance between Plantago algarbiensis and P. almogravensis reflect their ability to respond to oxidative stress

We evaluated the impact of low pH and aluminum (Al) on the leaves and roots of Plantago almogravensis Franco and Plantago algarbiensis Samp., focusing on energy partitioning in photosystem II, H₂O₂ levels, lipid peroxidation, electrolyte leakage (EL), protein oxidation, total soluble protein content and antioxidant enzyme activities. In both species, Al triggered more changes in oxidative metabolism than low pH alone, particularly in the roots. We found that Al increased the levels of H₂O₂ in P. algarbiensis roots, but reduced the levels of H₂O₂ in P. almogravensis leaves and roots. Neither low pH nor Al affected the spatial heterogeneity of chlorophyll fluorescence, the maximum photochemical efficiency of PSII (F_v/F_m), the actual quantum efficiency of PSII (?_PSII) or the quantum yields of regulated (?_NPQ) and nonregulated (?_NO) energy dissipation, and there was no significant change in total soluble protein content and EL. In P. algarbiensis, Al increased the carbonyl content and the activities of superoxide dismutase (SOD) and catalase (CAT) in the roots, and also CAT, ascorbate peroxidase and guaiacol peroxidase activities in the leaves. In P. almogravensis, Al reduced the level of malondialdehyde in the roots as well as SOD activity in the leaves and roots. We found that P. almogravensis plantlets could manage the oxidative stress caused by low pH and Al, whereas the P. algarbiensis antioxidant system was unable to suppress Al toxicity completely, leading to the accumulation of H₂O₂ and consequential protein oxidation in the roots.     

Influence of seasonal variation on the phenology and liriodenine content of Annona lutescens (Annonaceae)

Annona lutescens Saff. (Annonaceae) grows as a native tree in Chiapas, Mexico in Tropical Dry Forest habitat. Like most Annonaceae, it biosynthesizes benzylisoquinoline alkaloids, mostly liriodenine. To determine the influence of seasonal changes in the accumulation of liriodenine, the monthly variation of liriodenine content in roots, stems and leaves of mature and young trees was observed. These parts of young and mature A. lutescens trees were collected monthly over a 1 year period and the alkaloids were extracted; the liriodenine was quantified by high-resolution liquid chromatography. The phenological stages of the species were also assessed (leaf development, flowering and fruiting) using the Biologische Bundesanstalt, Bundessortenamt und Chemische Industrie (BBCH) scale. The analysis of both young and mature trees showed a significant increase in the liriodenine concentration occurs within roots during the dry season, which coincides with leaf fall. A significant decrease also occurred at the beginning of the rainy season (the period of leaf growth); the liriodenine content for the next rainy season did not reach the levels of the previous dry season. The climatic variation induced phenological and physiological changes in this species.     

A New Anaesthetic Protocol for Adult Zebrafish (Danio rerio): Propofol Combined with Lidocaine

Background

The increasing use of zebrafish model has not been accompanied by the evolution of proper anaesthesia for this species in research. The most used anaesthetic in fishes, MS222, may induce aversion, reduction of heart rate, and consequently high mortality, especially during long exposures. Therefore, we aim to explore new anaesthetic protocols to be used in zebrafish by studying the quality of anaesthesia and recovery induced by different concentrations of propofol alone and in combination with different concentrations of lidocaine.

Material and Methods

In experiment A, eighty-three AB zebrafish were randomly assigned to 7 different groups: control, 2.5 (2.5P), 5 (5P) or 7.5 μg/ml (7.5P) of propofol; and 2.5 μg/ml of propofol combined with 50, (P/50L), 100 (P/100L) or 150 μg/ml (P/150L) of lidocaine. Zebrafish were placed in an anaesthetic water bath and time to lose the equilibrium, reflex to touch, reflex to a tail pinch, and respiratory rate were measured. Time to gain equilibrium was also assessed in a clean tank. Five and 24 hours after anaesthesia recovery, zebrafish were evaluated concerning activity and reactivity. Afterwards, in a second phase of experiments (experiment B), the best protocol of the experiment A was compared with a new group of 8 fishes treated with 100 mg/L of MS222 (100M).

Results

In experiment A, only different concentrations of propofol/lidocaine combination induced full anaesthesia in all animals. Thus only these groups were compared with a standard dose of MS222 in experiment B. Propofol/lidocaine induced a quicker loss of equilibrium, and loss of response to light and painful stimuli compared with MS222. However zebrafish treated with MS222 recovered quickly than the ones treated with propofol/lidocaine.

Conclusion

In conclusion, propofol/lidocaine combination and MS222 have advantages in different situations. MS222 is ideal for minor procedures when a quick recovery is important, while propofol/lidocaine is best to induce a quick and complete anaesthesia.     

Circadian rhythm in locomotor activity in the burrower crayfish Procambarus acanthophorus (Villalobos 1948)

Crayfish Procambarus acanthophorus is a burrower that spends long periods building deep tunnels to reach the water table during the dry season; thus, its survival entertains a close ecological relationship with the sediment. The aim of this work was to determine whether the properties of the circadian rhythm of locomotor activity could be modified by the sediment availability. Experiments were conducted in both aquaria filled with sediment or filled with water, under cycles of Bright and Dim Illumination (BI:DI, 12:12 h) or under continuous DI:DI. The rhythm of locomotor activity was entrained with the photoperiod in aquaria with sediment or water; however, statistical differences between conditions were obtained comparing the period and the level of activity under free-running. These data suggest that the substrate’s sensorial perception could be encoded as a significant ecological parameter that exerts influence in the physiological mechanisms that control the temporal order in P. acanthophorus.     

Performance of the eclipse monitor unit objective tool utilizing volumetric modulated arc therapy for rectal cancer

AimTo assess the performance of the monitor unit (MU) Objective tool in Eclipse treatment planning system (TPS) utilizing volumetric modulated arc therapy (VMAT) for rectal cancer.BackgroundEclipse VMAT planning module includes a tool to control the number of MUs delivered: the MU Objective tool. This tool could be utilized to reduce the total number of MUs in rectal cancer treatments.Materials and methods20 rectal cancer patients were retrospectively studied using VMAT and the MU Objective tool. The baseline plan for each patient was selected as the one with no usage of the MU Objective tool. The number of MUs of this plan was set to be the reference number of MUs (MU_ref). Five plans were re-optimized for each patient only varying the Max MU parameter. The selected values were 30%, 60%, 90%, 120% and 150% of MU_ref for each patient. Differences with respect to the baseline plan were evaluated regarding MU number and parameters for PTVs coverage evaluation, PTVs homogeneity and OARs doses assessment. A two-tailed, paired-samples t-test was used to quantify these differences.ResultsAverage relative differences in MU number obtained was 10% for Max MU values of 30% and 60% of MU_ref, respectively (p < 0.03). PTVs coverage and homogeneity were not compromised and discrepancies obtained with respect to baseline plans were not significant. Furthermore, maximum OARs doses deviations were also not significant.ConclusionsA 10% reduction in the MU number could be obtained without an alteration of PTV coverage and OARs doses for rectal cancer.