The administration of methyl and butyl parabens interferes with the enzymatic antioxidant system and induces genotoxicity in rat testis: possible relation to male infertility

Parabens are esters of p-hydroxybenzoic acid, used for decades as a preservative in many products, including agrochemicals, pharmaceuticals, foods and cosmetics. Concerns regarding parabens toxicity include adverse effects on endocrine activity, carcinogenesis, infertility, spermatogenesis, and adipogenesis. The present study aimed to investigate the in vivo administration of methyl and butylparaben at concentrations of 100 and 200 mg/kg body weight, by subcutaneous injection, in variable murinometric measurements, antioxidant systems and genotoxicity. The administration of parabens did not affect the consumption of water and food. However, there was a decrease in the weight of the testes and the seminal vesicle (p < 0.05). The administration of parabens caused an increase in superoxide dismutase for methylparaben (200 mg/kg) and both concentrations of butylparaben (p < 0.05). Catalase showed increased activity in all groups treated with parabens. In contrast, glutathione reductase and glutathione S-transferase suffered a decrease in the groups treated with both parabens. These results show that parabens, especially butyl, can affect the rat testis enzymatic antioxidant system, decreasing the cellular antioxidant capacity, which was confirmed by the decrease in the glutathione reducing power, expressed by the reduced glutathione/oxidized glutathione ratio. Therefore, an increase in lipid peroxidation was observed, which was significant in the case of butyl. Genetic Damage Indicator values show that butylparaben treatments displayed significantly higher values than the control. This study shows for the first time that parabens can induce genotoxicity in the rat male reproductive organ.

Mathematical kinetic modelling followed by in vitro and in vivo assays reveal the bifunctional rice GTPCHII/DHBPS enzymes and demonstrate the key roles of OsRibA proteins in the vitamin B2 pathway

BACKGROUND

Riboflavin is the precursor of several cofactors essential for normal physical and cognitive development, but only plants and some microorganisms can produce it. Humans thus rely on their dietary intake, which at a global level is mainly constituted by cereals (> 50%). Understanding the riboflavin biosynthesis players is key for advancing our knowledge on this essential pathway and can hold promise for biofortification strategies in major crop species. In some bacteria and in Arabidopsis, it is known that RibA1 is a bifunctional protein with distinct GTP cyclohydrolase II (GTPCHII) and 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) domains. Arabidopsis harbors three RibA isoforms, but only one retained its bifunctionality. In rice, however, the identification and characterization of RibA has not yet been described.

RESULTS

Through mathematical kinetic modeling, we identified RibA as the rate-limiting step of riboflavin pathway and by bioinformatic analysis we confirmed that rice RibA proteins carry both domains, DHBPS and GTPCHII. Phylogenetic analysis revealed that OsRibA isoforms 1 and 2 are similar to Arabidopsis bifunctional RibA1. Heterologous expression of OsRibA1 completely restored the growth of the rib3∆ yeast mutant, lacking DHBPS expression, while causing a 60% growth improvement of the rib1∆ mutant, lacking GTPCHII activity. Regarding OsRibA2, its heterologous expression fully complemented GTPCHII activity, and improved rib3∆ growth by 30%. In vitro activity assays confirmed that both OsRibA1 and OsRibA2 proteins carry GTPCHII/DHBPS activities, but that OsRibA1 has higher DHBPS activity. The overexpression of OsRibA1 in rice callus resulted in a 28% increase in riboflavin content.

CONCLUSIONS

Our study elucidates the critical role of RibA in rice riboflavin biosynthesis pathway, establishing it as the rate-limiting step in the pathway. By identifying and characterizing OsRibA1 and OsRibA2, showcasing their GTPCHII and DHBPS activities, we have advanced the understanding of riboflavin biosynthesis in this staple crop. We further demonstrated that OsRibA1 overexpression in rice callus increases its riboflavin content, providing supporting information for bioengineering efforts.

Handheld and benchtop vis/NIR spectrometer combined with PLS regression for fast prediction of cocoa shell in cocoa powder

The fermented and dried cocoa beans are peeled, either before or after the roasting process, as peeled nibs are used for chocolate production, and shell content in cocoa powders may result from economically motivated adulteration (EMA), cross-contamination or misfits in equipment in the peeling process. The performance of this process is carefully evaluated, as values above 5% (w/w) of cocoa shell can directly affect the sensory quality of cocoa products. In this study chemometric methods were applied to near-infrared (NIR) spectra from a handheld (900-1700 nm) and a benchtop (400-1700 nm) spectrometers to predict cocoa shell content in cocoa powders. A total of 132 binary mixtures of cocoa powders with cocoa shell were prepared at several proportions (0 to 10% w/w). Partial least squares regression (PLSR) was used to develop the calibration models and different spectral preprocessing were investigated to improve the predictive performance of the models. The ensemble Monte Carlo variable selection (EMCVS) method was used to select the most informative spectral variables. Based on the results obtained with both benchtop (R²_P = 0.939, RMSE_P = 0.687% and RPD_P = 4.14) and handheld (R²_P = 0.876, RMSE_P = 1.04% and RPD_P = 2.82) spectrometers, NIR spectroscopy combined with the EMCVS method proved to be a highly accurate and reliable tool for predicting cocoa shell in cocoa powder. Even with a lower predictive performance than the benchtop spectrometer, the handheld spectrometer has potential to specify whether the amount of cocoa shell present in cocoa powders is in accordance with the Codex Alimentarius specifications.

Effects of the juçara fruit (Euterpe edulis Martius) pulp and lyophilized extract on NRF2, KEAP1, SOD1, and GPX2 expression in human colorectal cancer cell lines

We investigated the effects of the juçara fruit (Euterpe edulis Martius) pulp and lyophilized extract on the expression of cytoprotective genes nuclear factor erythroid 2 (NF-E2)-related factor 2 (NRF2), kelch-like ECH-associated protein 1 (KEAP1), superoxide dismutase (SOD1), and glutathione peroxidase (GPX2) in human colorectal cancer cell lines (HT-29 and Caco-2). Cells were cultured for 24 h in Dulbecco's Modified Eagle's Medium containing juçara fruit pulp (5, 10, or 50 mg/mL) or lyophilized extract (0.05, 0.1, or 0.5 mg/mL), and gene expression was quantified using real-time quantitative reverse transcription polymerase chain reaction. All studied genes showed significant variation in gene expression among different concentrations of pulp or lyophilized extract. Overall, the expression of the selected genes decreased in both cell lines following exposure to the pulp or lyophilized extract in a dose-dependent manner for most of the concentrations studied. In summary, our study showed that the compounds in juçara fruit inhibited the expression of cytoprotective genes associated with the antioxidant response and that, although not cytotoxic at the concentrations studied, they could potentially block the activation of the NRF2/KEAP1 pathway.

Reversible down-regulation of photosystems I and II leads to fast photosynthesis recovery after long-term drought in Jatropha curcas

Jatropha curcas is a drought-tolerant plant that maintains its photosynthetic pigments under prolonged drought, and quickly regains its photosynthetic capacity when water is available. It has been reported that drought stress leads to increased thermal dissipation in PSII, but that of PSI has been barely investigated, perhaps due to technical limitations in measuring the PSI absolute quantum yield. In this study, we combined biochemical analysis and spectroscopic measurements using an integrating sphere, and verified that the quantum yields of both photosystems are temporarily down-regulated under drought. We found that the decrease in the quantum yield of PSII was accompanied by a decrease in the core complexes of PSII while light-harvesting complexes are maintained under drought. In addition, in drought-treated plants, we observed a decrease in the absolute quantum yield of PSI as compared with the well-watered control, while the amount of PSI did not change, indicating that non-photochemical quenching occurs in PSI. The down-regulation of both photosystems was quickly lifted in a few days upon re-watering. Our results indicate, that in J. curcas under drought, the down-regulation of both PSII and PSI quantum yield protects the photosynthetic machinery from uncontrolled photodamage.

The Combined Effect of Heat and Osmotic Stress on Suberization of Arabidopsis Roots

The simultaneous occurrence of heat stress and drought is becoming more regular as a consequence of climate change, causing extensive agricultural losses. The application of either heat or osmotic stress increase cell-wall suberization in different tissues, which may play a role in improving plant resilience. In this work, we studied how the suberization process is affected by the combination of drought and heat stress by following the expression of suberin biosynthesis genes, cell-wall suberization and the chemical composition in Arabidopsis roots. The Arabidopsis plants used in this study were at the onset of secondary root development. At this point, one can observe a developmental gradient in the main root, with primary development closer to the root tip and secondary development, confirmed by the suberized phellem, closer to the shoot. Remarkably, we found a differential response depending on the root zone. The combination of drought and heat stress increased cell wall suberization in main root segments undergoing secondary development and in lateral roots (LRs), while the main root zone, at primary development stage, was not particularly affected. We also found differences in the overall chemical composition of the cell walls in both root zones in response to combined stress. The data gathered showed that, under combined drought and heat stress, Arabidopsis roots undergo differential cell wall remodeling depending on developmental stage, with modifications in the biosynthesis and/or assembly of major cell wall components.

Diclidophora luscae (Monogenea: Diclidophoridae) in pouting, Trisopterus luscus (Linnaeus, 1758) from the northeast Atlantic; epidemiology, morphology, molecular and phylogenetic analysis

Diclidophora (Monogenea) species are gill parasites with a stenoxenic specificity occurring only in Gadiformes. Epidemiological, morphological, molecular and phylogenetic studies were performed on 594 Diclidophora specimens collected from 213 Trisopterus luscus captured in the northeast Atlantic off the Portuguese coast during 2012, 2013 and 2020. Prevalence, parasite abundance and infection intensity were determined. Positive correlation between fish weight and length and infection intensity was observed. The effects of preservation on the parasite morphological features were studied, highlighting that specimen's identification should be reinforced by molecular studies. A sequence of D. luscae capelanii from T. capelanus captured in the Mediterranean Sea included in the 28S rDNA molecular analysis was nested within a robust D. luscae clade. Data analysis suggested that this species is in fact D. luscae, which is compatible with T. luscus and T. capelanus. The identity of fish hosts was confirmed by barcoding. For the first time, data on the infection parameters is shown, highlighting the importance of including this parasite in the monitoring plans for a holistic approach with possible effects for the management of pouting resources aiming of attaining sustainable development and biodiversity conservation measures, according to the 14th objective of the 2030 agenda.

Spatiotemporal development of suberized barriers in cork oak taproots

The longevity and high activity of the cork cambium (or phellogen) from Quercus suber L. (cork oak) are the cornerstones for the sustainable exploitation of a unique raw material. Cork oak is a symbolic model to study cork development and cell wall suberization, yet most genetic and molecular studies on these topics have targeted other model plants. In this study, we explored the potential of taproots as a model system to study phellem development and suberization in cork oak, thereby avoiding the time constraints imposed when studying whole plants. In roots, suberin deposition is found in mature endodermis cells during primary development and in phellem cells during secondary development. By investigating the spatiotemporal characteristics of both endodermis and phellem suberization in young seedling taproots, we demonstrated that secondary growth and phellogen activity are initiated very early in cork oak taproots (approx. 8 days after sowing). We further compared the transcriptomic profile of root segments undergoing primary (PD) and secondary development (SD) and identified multiple candidate genes with predicted roles in cell wall modifications, mainly lignification and suberization, in addition to several regulatory genes, particularly transcription factor- and hormone-related genes. Our results indicate that the molecular regulation of suberization and secondary development in cork oak roots is relatively conserved with other species. The provided morphological characterization creates new opportunities to allow a faster assessment of phellogen activity (as compared with studies using stem tissues) and to tackle fundamental questions regarding its regulation.

Translational profile of developing phellem cells in Arabidopsis thaliana roots

The phellem is a specialized boundary tissue providing the first line of defense against abiotic and biotic stresses in organs undergoing secondary growth. Phellem cells undergo several differentiation steps, which include cell wall suberization, cell expansion, and programmed cell death. Yet, the molecular players acting particularly in phellem cell differentiation remain poorly described, particularly in the widely used model plant Arabidopsis thaliana. Using specific marker lines we followed the onset and progression of phellem differentiation in A. thaliana roots and further targeted the translatome of newly developed phellem cells using translating ribosome affinity purification followed by mRNA sequencing (TRAP-SEQ). We showed that phellem suberization is initiated early after phellogen (cork cambium) division. The specific translational landscape was organized in three main domains related to energy production, synthesis and transport of cell wall components, and response to stimulus. Novel players in phellem differentiation related to suberin monomer transport and assembly as well as novel transcription regulators were identified. This strategy provided an unprecedented resolution of the translatome of developing phellem cells, giving a detailed and specific view on the molecular mechanisms acting on cell differentiation in periderm tissues of the model plant Arabidopsis.

A novel panel of yeast assays for the assessment of thiamin and its biosynthetic intermediates in plant tissues

Thiamin (or thiamine), known as vitamin B1, represents an indispensable component of human diets, being pivotal in energy metabolism. Thiamin research depends on adequate vitamin quantification in plant tissues. A recently developed quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) method is able to assess the level of thiamin, its phosphorylated entities and its biosynthetic intermediates in the model plant Arabidopsis thaliana, as well as in rice. However, their implementation requires expensive equipment and substantial technical expertise. Microbiological assays can be useful in deter-mining metabolite levels in plant material and provide an affordable alternative to MS-based analysis. Here, we evaluate, by comparison to the LC-MS/MS reference method, the potential of a carefully chosen panel of yeast assays to estimate levels of total vitamin B1, as well as its biosynthetic intermediates pyrimidine and thiazole in Arabidopsis samples. The examined panel of Saccharomyces cerevisiae mutants was, when implemented in microbiological assays, capable of correctly assigning a series of wild-type and thiamin biofortified Arabidopsis plant samples. The assays provide a readily applicable method allowing rapid screening of vitamin B1 (and its biosynthetic intermediates) content in plant material, which is particularly useful in metabolic engineering approaches and in germplasm screening across or within species.

Evaluating Root Mechanosensing Response in Rice

Unable to move, plants are physically restrained to the place where they grow. Remarkably, plants have developed a myriad of mechanisms to perceive the surrounding environment in order to maximize growth and survival. One of those mechanisms is the ability to perceive mechanical stimulus such as touch (thigmomorphogenesis), in order to adjust growth patterns (in different organs) to either attach to or surround an object. Roots are able to perceive several mechanical forces (e.g., gravity, touch). However, being the "hidden part" of a plant, it is difficult to assess their response to mechanical stimulation. In this chapter, our team presents a simple method to evaluate rice (Oryza sativa L.) root mechanosensing response that can be used to test different conditions (e.g., hormones) affecting rice root response to touch stimulus. This method is affordable to any lab and can be upgraded with a fully automated image recording system. We provide a detailed protocol with several notes for a more comprehensive application.

Screening for Abiotic Stress Response in Rice

Rice (Oryza sativa L.) is the staple food for over half of the world population. However, most rice varieties are severely injured by abiotic stresses, with strong social and economic impacts. Understanding rice responses to stress may guide breeding for more tolerant varieties. However, the lack of consistency in the design of the stress experiments described in the literature limits comparative studies and output assessments. The use of identical setups is the only way to generate comparable data. This chapter comprises three sections, describing the experimental conditions established at the Genomics of Plant Stress (GPlantS) unit of ITQB NOVA to assess the response of rice plants to different abiotic stresses-high salinity, cold, drought, simulated drought, and submergence-and their recovery capacity when intended. All sections include a detailed description of the materials and methodology and useful notes gathered from our team experience. We use seedlings since rice plants at this stage show high sensitivity to abiotic stresses. For the salt, cold, and simulated drought (PEG, polyethylene glycol) stress assays, we grow rice seedlings in a hydroponic system, while for the drought assay, plants are grown in soil and subjected to water withholding. For submergence, we use water-filled Magenta boxes. All setups enable visual score determination and are suitable for sample collection during stress imposition and also recovery. The proposed methodologies are affordable and straightforward to implement in most labs, allowing the discrimination of several rice genotypes at the molecular and phenotypic levels.

Heart rate variability as a biomarker in chronic chagas cardiomyopathy patients with or without concomitant digestive involvement, for prediction of rassi score risk classes

Introduction

The pathogenesis of Chronic Chagas Cardiomyopathy (CCC) is not yet fully elucidated. However, dysautonomia is one of the factors involved, in addition to being the essential mechanism in the pathogenesis of the Digestive Form of Chagas Disease (DFCD). The prognostic value of dysautonomia remains speculative, and there are no correlative studies of dysautonomia in CCC and DFCD.

Purpose

This study has three aims: a) to investigate in patients with CCC the relationship between cardiac dysautonomia, indirectly studied by heart rate variability (HRV), and the prognostic stratification assessed by the Rassi score; b) to compare the HRV in groups with isolated CCC and with the mixed form, i.e. CCC associated with DFCD; c) to evaluate the power of combining HRV indices to predict the risk class of each patient, using machine learning.

Methods

Thirty-one patients with CCC were classified into three risk groups (low, intermediate and high) according to their Rassi score and had two electrocardiograms (ECG) recorded, i.e. the conventional 12-lead and a single lead, the latter for a period of 10 to 20 minutes. From the single lead ECG, two equally sized RR series were generated and 31 HRV indices were calculated from each. The HRV was then compared between the three risk groups and also regarding the presence or not of concomitant digestive impairment. Taking HRV indices as inputs, four machine learning models were compared in its ability to predict the risk class of each patient. A previous step of attribute selection (sequential feature selection) was applied to identify the most relevant HRV indices for each algorithm.

Results

Comparing the HRV indices in the three risk groups obtained with the Rassi score, the phase entropy is decreased [0.91 (0.90, 0.91) vs 0.87 (0.86, 0.89); p=0.039] and the percentage of inflection points is increased [66.4 (63.5, 71.2) vs 58.2 (53.4, 63.3); p=0.032] in patients in the high-risk group, compared to the low-risk group. Of the 31 patients with CCC, 14 had the mixed form of the disease, i.e. with associated digestive impairment. In the latter, the triangular interpolation of the RR interval histogram decreased significantly [78.1 (62.5, 101.6) vs 121.1 (80.1, 146.5), p=0.046], while the absolute power in the low-frequency band decreased with strong trend to statistical significance [28.5 (17.1, 97.5) vs 86.9 (44.1, 171.7), p=0.06]. The best predictive model for each risk group was obtained with the Support Vector Machine, reaching an overall F1-score of 0.61.

Conclusions

The worst prognosis, indicated by the Rassi score, is associated with increased heart rate fragmentation. The combination of HRV indices enhanced the accuracy of the risk stratification. Compared to CCC the mixed form of Chagas' disease displays a decrease in the components of slow heart rate oscillation, suggesting a higher degree of sympathetic autonomic denervation associated with parasympathetic impairment.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): São Paulo Research Foundation (FAPESP)

Carbon/nitrogen metabolism and stress response networks - calcium-dependent protein kinases as the missing link?

Calcium-dependent protein kinases (CDPKs) play essential roles in plant development and stress responses. CDPKs have a conserved kinase domain, followed by an auto-inhibitory junction connected to the calmodulin-like domain that binds Ca2+. These structural features allow CDPKs to decode the dynamic changes in cytoplasmic Ca2+ concentrations triggered by hormones and by biotic and abiotic stresses. In response to these signals, CDPKs phosphorylate downstream protein targets to regulate growth and stress responses according to the environmental and developmental circumstances. The latest advances in our understanding of the metabolic, transcriptional, and protein-protein interaction networks involving CDPKs suggest that they have a direct influence on plant carbon/nitrogen (C/N) balance. In this review, we discuss how CDPKs could be key signaling nodes connecting stress responses with metabolic homeostasis, and acting together with the sugar and nutrient signaling hubs SnRK1, HXK1, and TOR to improve plant fitness.

ZmOrphan94 Transcription Factor Downregulates ZmPEPC1 Gene Expression in Maize Bundle Sheath Cells

Spatial separation of the photosynthetic reactions is a key feature of C₄ metabolism. In most C₄ plants, this separation requires compartmentation of photosynthetic enzymes between mesophyll (M) and bundle sheath (BS) cells. The upstream region of the gene encoding the maize PHOSPHOENOLPYRUVATE CARBOXYLASE 1 (ZmPEPC1) has been shown sufficient to drive M-specific ZmPEPC1 gene expression. Although this region has been well characterized, to date, only few trans-factors involved in the ZmPEPC1 gene regulation were identified. Here, using a yeast one-hybrid approach, we have identified three novel maize transcription factors ZmHB87, ZmCPP8, and ZmOrphan94 as binding to the ZmPEPC1 upstream region. Bimolecular fluorescence complementation assays in maize M protoplasts unveiled that ZmOrphan94 forms homodimers and interacts with ZmCPP8 and with two other ZmPEPC1 regulators previously reported, ZmbHLH80 and ZmbHLH90. Trans-activation assays in maize M protoplasts unveiled that ZmHB87 does not have a clear transcriptional activity, whereas ZmCPP8 and ZmOrphan94 act as activator and repressor, respectively. Moreover, we observed that ZmOrphan94 reduces the trans-activation activity of both activators ZmCPP8 and ZmbHLH90. Using the electromobility shift assay, we showed that ZmOrphan94 binds to several cis-elements present in the ZmPEPC1 upstream region and one of these cis-elements overlaps with the ZmbHLH90 binding site. Gene expression analysis revealed that ZmOrphan94 is preferentially expressed in the BS cells, suggesting that ZmOrphan94 is part of a transcriptional regulatory network downregulating ZmPEPC1 transcript level in the BS cells. Based on both this and our previous work, we propose a model underpinning the importance of a regulatory mechanism within BS cells that contributes to the M-specific ZmPEPC1 gene expression.

Modulation of Abiotic Stress Responses in Rice by E3-Ubiquitin Ligases: A Promising Way to Develop Stress-Tolerant Crops

Plants are unable to physically escape environmental constraints and have, therefore, evolved a range of molecular and physiological mechanisms to maximize survival in an ever-changing environment. Among these, the post-translational modification of ubiquitination has emerged as an important mechanism to understand and improve the stress response. The ubiquitination of a given protein can change its abundance (through degradation), alter its localization, or even modulate its activity. Hence, ubiquitination increases the plasticity of the plant proteome in response to different environmental cues and can contribute to improve stress tolerance. Although ubiquitination is mediated by different enzymes, in this review, we focus on the importance of E3-ubiquitin ligases, which interact with the target proteins and are, therefore, highly associated with the mechanism specificity. We discuss their involvement in abiotic stress response and place them as putative candidates for ubiquitination-based development of stress-tolerant crops. This review covers recent developments in this field using rice as a reference for crops, highlighting the questions still unanswered.

The influence of Castanea sativa Mill. flower extract on hormonally and chemically induced prostate cancer in a rat model

Prostate cancer (PCa) is one of the most common cancers in men, with a huge impact on their health. The use of Castanea sativa Mill. flowers (CFs) in beverages has been reported, through ancestral claims, as having health benefits. In vitro research has evidenced the properties of CFs, such as antitumor and antioxidant activities. This study aimed to evaluate the effects of CF extract in an animal model of PCa. Forty male Wistar Unilever rats were randomly assigned to four groups: control, induced, control + CF, and induced + CF groups. Animals from the induced groups were exposed to a multistep protocol for PCa induction. The CF extract, rich in trigalloyl-HHDP-glucoside and obtained via decoction, was administered to the CF groups in drinking water (3 mg per animal per day) for 49 weeks. Animals were sacrificed at 61 weeks of age. Regarding the effects of CFs on dorsolateral prostate tumorigenesis, no significant differences were observed between the induced and induced + CF groups. However, animals exposed to the CF extract showed fewer inflammation areas on the dorsolateral prostate lobe than those not exposed to CF. Moreover, the CF extract alleviated the hepatic oxidative stress associated with the multistep protocol, resulting in lower levels of lipid peroxidation. These results suggest that CF extract has antioxidant and anti-inflammatory properties.

Seven years of evaluation of ectoparasites and vector-borne pathogens among ring-tailed coatis in an urban park in southeastern Brazil

Wild animals have been recognized as potential reservoirs of vector-borne pathogens. Proximity between these animals and urban areas increases the need to know which pathogens these are and whether they can infect domestic animals and humans. In Mangabeiras Municipal Park in Belo Horizonte, Brazil, coatis live near the urban area, which is mainly occupied by human residents and their domestic animals. Therefore, the objective of this study was to detect, through molecular and direct methods, the presence of ectoparasites and hemoparasites in coatis. A total of 216 samples were collected, of which 209 samples were from first-captures and seven were from recaptures. The following parasites were found: ticks of the genus Amblyomma, lice of the species Neotrichodectes pallidus and fleas of the species Rhopalopsyllus lutzi lutzi and Ctenocephalides felis felis. All the samples were negative for the family Anaplasmataceae and the species Leishmania sp. and Trypanosoma cruzi. The hemoparasites Trypanosoma evansi, Hepatozoon procyonis, Babesia sp. and Sarcocystis neurona were found. The area of the present study is not endemic for T. evansi, which therefore suggests that these coatis may be acting as reservoirs or sentinels of this parasite. This finding is of great epidemiological importance and should be investigated more closely. Thus, this study showed that there is a great variety of pathogens in the park that transit among coatis and, probably, among other animals that inhabit or live close to the park.

P542Cardiac autonomic dysfunction and inflammatory response in heart failure - markers for cardiac resynchronization therapy response?

Funding Acknowledgements

FCP

Introduction

Cardiac sympathetic activation and inflammatory response are involved in chronic heart failure (HF) pathophysiology. The severity of autonomic dysfunction and inflammation might be responsible for different responses to HF treatment.

Aim

To evaluate the impact of cardiac autonomic dysfunction, and it´s association with systemic inflammation, on cardiac resynchronization therapy (CRT) response in severe HF patients.

Methods

Single centre, prospective, longitudinal study, including consecutive patients, referred to CRT. Demographic data, HF aetiology and NYHA class were evaluated. Left ventricular (LV) function data (LV ejection fraction - LVEF) by echocardiography, heart to mediastinum early ratio (HMRe) by 123I-MIBG cardiac scintigraphy, and plasmatic TNF-α levels (pg/mL) were determined, at baseline and 4 months after CRT implantation. CRT response was defined by an absolute increase of at least 5% in LVEF at 4 months evaluation after CRT. Patients were divided in 4 groups according to HMRe and TNF-α cut-points: Group I (TNF-α &gt; 2.0 pg/ml + HMRe ≥ 1.6), Group II (TNF-α &gt; 2.0 pg/ml + HMRe &lt; 1.6), Group III (TNF-α ≤ 2.0 pg/ml + HMRe ≥ 1.6) and Group IV (TNF-α ≤ 2.0 pg/ml + HMRe &lt; 1.6). Data was analyzed using descriptive statistics and groups were compared by Fisher"s exact test.

Results

A total of 95 patients were included (age 68.6 ± 10.2 years), 67.4% male and 32.6% female, 40% with diabetes mellitus, 30.5% with ischemic cardiomyopathy, 23.2% in NYHA III/IV, baseline LVEF - 26 ± 7%. At 4 months, LVEF was 40 ± 11%. In total, 73.7% were responders and 26.3% were non-responders to CRT. There were 28 patients (29.5%) with HMRe ≥ 1.6, with 25 responders (89.3%) and 48 patients (50.5%) with TNF-α ≤ 2.0 pg/ml, with 38 responders (79.2%). Group I had 16 patients (16.8%), with 81.2% responders; Group II had 31 patients (32.7%), with 61.3% responders; Group III had 12 patients (12.6%), with 100% responders, and Group IV had 36 patients (37.9%), with 72.2% responders. Conclusion: In patients with severe HF submitted to CRT, combining cardiac autonomic dysfunction and inflammation, associated to high rate of CRT non response. Contrarily, those with preserved cardiac autonomic function and no increased levels of inflammation identified most significantly CRT responders.

CRT response according to HMRe and TNFα HMRe ≥ 1.6 (n = 28) HMRe &lt; 1.6 (n = 67) Responders NO Respondersn (%) Responders NO Respondersn (%) TNF α &gt; 2 pg/mL (n = 47) G I: 13 (81.2%) 3 (18.8%) GII: 19 (61.3%) 12 (38.7%) * TNF α ≤ 2 pg/mL (n = 48) G III: 12 (100%) 0 (0%)* G IV: 26 (72.2%) 10 (27.8%)

0493 Use of Sleep Aid Medication is Associated with Memory Deficits: A Population-Based Study

Introduction

Use of medications to treat sleep complaints is a common practice that may incur in cognitive deficits. Evidence, beyond the well-described effects of benzodiazepines on cognition, still needs expansion. This study assessed the use of sleep aid medications of different classes and associated factors on prospective and retrospective memory in a representative populational sample from São Paulo.

Methods

Volunteers in the EPISONO study underwent evaluation through questionnaires and a complete polysomnography exam. A subsample of 500 volunteers (Mean Age=42.9 years; 307 women) was included. Users (N=250) and non-users (N=250; randomly selected among the non-using volunteers) of sleep medication were evaluated regarding scores in 8 subscales and the overall score of the Prospective and Retrospective Memory Questionnaire (PRMQ). Afterwards, users of classes of medications were compared. Covariates, including scores in psychiatric evaluation scales and polysomnographic findings, were added in both segments to identify the factors with highest interference in the results obtained.

Results

Medication users consistently performed worse in prospective memory and short-term internal-cued retrospective memory even when covariates were added. Scores in Beck Anxiety and Depression Inventories, Insomnia Severity Index and variables related to wakefulness and sleep architecture were the covariates with the highest interference in the results. When comparing types of medication, few differences were seen, suggesting that for such analysis, a sample with higher power would be appropriate.

Conclusion

Users of sleep medication presented impairment in prospective memory. Factors such as sleep architecture and continuity, as well as insomnia, anxiety and depression symptoms must be considered when evaluating cognitive deficits and pharmacological treatment in patients with sleep complaints, as they may participate in this relationship. Future studies are necessary to characterize the impact of different medication classes on prospective and retrospective memory.

Support

Our studies are supported by Associação Fundo de Incentivo à Pesquisa (AFIP) and Conselho Nacional de Desenvolvimento Científico Tecnológico (CNPq - Grant #133397/2017-3); S.T. and M.L.A. received CNPq fellowships.

Genomic history and ecology of the geographic spread of rice

Rice (Oryza sativa) is one of the world's most important food crops, and is comprised largely of japonica and indica subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical japonica rice during a global cooling event about 4,200 yr ago. Soon after, tropical japonica rice reached Southeast Asia, where it rapidly diversified, starting about 2,500 yr BP. The history of indica rice dispersal appears more complicated, moving into China around 2,000 yr BP. We also identify extrinsic factors that influence genome diversity, with temperature being a leading abiotic factor. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptations associated with the spread of a key domesticated species.

Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance

Chromatin structure, DNA methylation, and histone modifications act in a concerted manner to influence gene expression and therefore plant phenotypes. Environmental stresses are often associated with extensive chromatin rearrangements and modifications of epigenetic levels and patterns. Stress-tolerant plants can be a good tool to unveil potential connections between specific epigenetic modifications and stress tolerance capacity. We analyzed genome wide DNA methylation of a salt-tolerant rice variety under salinity and identified a set of differentially methylated regions (DMRs) between control and stress samples using high-throughput sequencing of DNA immunoprecipitated with the 5-methylcytosine antibody (MeDIP-Seq). The examination of DNA methylation pattern at DMRs regions revealed a general tendency for demethylation events in stress samples as compared to control. In addition, DMRs appear to influence the expression of genes located in their vicinity. We hypothesize that short regions as DMRs can shape the chromatin landscape of specific genomic regions and, therefore, may modulate the function of several genes. In this sense, the identification of DMRs represents one step towards to uncover new players in the regulation of stress-responsive genes and new target genes with potential application in enhancement of plant salinity-tolerance.

Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases

BACKGROUND

SUMOylation is an essential eukaryotic post-translation modification that, in plants, regulates numerous cellular processes, ranging from seed development to stress response. Using rice as a model crop plant, we searched for potential regulatory points that may influence the activity of the rice SUMOylation machinery genes.

RESULTS

We analyzed the presence of putative cis-acting regulatory elements (CREs) within the promoter regions of the rice SUMOylation machinery genes and found CREs related to different cellular processes, including hormone signaling. We confirmed that the transcript levels of genes involved in target-SUMOylation, containing ABA- and GA-related CREs, are responsive to treatments with these hormones. Transcriptional analysis in Nipponbare (spp. japonica) and LC-93-4 (spp. indica), showed that the transcript levels of all studied genes are maintained in the two subspecies, under normal growth. OsSUMO3 is an exceptional case since it is expressed at low levels or is not detectable at all in LC-93-4 roots and shoots, respectively. We revealed post-transcriptional regulation by alternative splicing (AS) for all genes studied, except for SUMO coding genes, OsSIZ2, OsOTS3, and OsELS2. Some AS forms have the potential to alter protein domains and catalytic centers. We also performed the molecular and phenotypic characterization of T-DNA insertion lines of some of the genes under study. Knockouts of OsFUG1 and OsELS1 showed increased SUMOylation levels and non-overlapping phenotypes. The fug1 line showed a dwarf phenotype, and significant defects in fertility, seed weight, and panicle architecture, while the els1 line showed early flowering and decreased plant height. We suggest that OsELS1 is an ortholog of AtEsd4, which was also supported by our phylogenetic analysis.

CONCLUSIONS

Overall, we provide a comprehensive analysis of the rice SUMOylation machinery and discuss possible effects of the regulation of these genes at the transcriptional and post-transcriptional level. We also contribute to the characterization of two rice SUMO proteases, OsELS1 and OsFUG1.

Metal loads and biomarker suite responses in a tropical carnivorous fish indicative of anthropogenic impacts in a Southeastern Brazilian lagoon

Tropical coastal lagoons are highly productive environments exhibiting high biodiversity. However, the use of these ecosystems by local communities is of concern, since this generally leads to environmental degradation. The Imboassica coastal lagoon, located in Macaé city, in Northern Rio de Janeiro, is an important ecosystem in the state, however, already displaying signs of anthropogenic impacts. Carnivorous fish Hoplias malabaricus specimens were sampled from this impacted site, as well as from a reference area. Fish from Imboassica Lagoon presented lower condition factor, lower cholinesterase activity, and higher percentage of erythrocyte micronuclei when compared to fish from the reference site. Metals in fish from Imboassica Lagoon were always higher than Encantada Lagoon, with some seasonal differences, where some metals were higher in the rainy season compared to the dry season in muscle tissue, with the exception of Cu, Fe, Sr, and Zn; and in the liver, except for Ba, Cd, Cr, Ni, and Sr. Cr and Mn in the edible muscle portion of the fish were higher than the limits established by Brazilian and International legislations as permissible for human consumption, thus leading to concerns regarding public health risks for the local population that use fish as their main protein source.

Gluconacin from Gluconacetobacter diazotrophicus PAL5 is an active bacteriocin against phytopathogenic and beneficial sugarcane bacteria

AIMS

This study aimed to explore the possibility of using the Gluconacin from Gluconacetobacter diazotrophicus strain PAL5 in the biological control of diverse sugarcane phytopathogenic bacteria.

METHODS AND RESULTS

An in silico analysis was first employed to determine the phylogenetic relationship between Gram-negative/positive bacteriocin producers and Gluconacin. The analysis showed that this trait is widespread among tested bacterial species and a well-conserved gene within the Acetobacteraceae family. The bacteriocin gene (GDI_0415) present in the genome of strain PAL5 was than cloned in pDEST™17 and expressed in Escherichia coli BL21-AI™. A bioassay showed growth inhibition of Xanthomonas albilineans by the recombinant bacteriocin. Subsequent bioassays indicated different levels of antagonistic activity against the majority of the sugarcane phytopathogenic bacteria (Xanthomonas axonopodis pv. vasculorum, Acidovorax avenae subsp. avenae, Pseudomonas syringae pv. syringae, Xanthomonas vasicola pv. vasculorum). In addition, the bacteriocin was also antagonistic to some beneficial bacterial strains belonging to G. diazotrophicus and endophytic Bacillus species, which also colonize sugarcane plants.

CONCLUSIONS

The GDI_0415 gene, responsible for the production of Gluconacin, is well conserved within the Acetobacteraceae family and presented antagonistic activity against phytopathogenic and a few beneficial sugarcane bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

The production of a recombinant protein, named Gluconacin, opens new avenues for the agro-biotechnology application in agriculture, mainly with regard to the sugarcane crop.

The draft genome sequence of cork oak

Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.

The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications

Plant calcium-dependent protein kinases (CDPKs) are key proteins implicated in calcium-mediated signaling pathways of a wide range of biological events in the organism. The action of each particular CDPK is strictly regulated by many mechanisms in order to ensure an accurate signal translation and the activation of the adequate response processes. In this work, we investigated the regulation of a CDPK involved in rice cold stress response, OsCPK17, to better understand its mode of action. We identified two new alternative splicing (AS) mRNA forms of OsCPK17 encoding truncated versions of the protein, missing the CDPK activation domain. We analyzed the expression patterns of all AS variants in rice tissues and examined their subcellular localization in onion epidermal cells. The results indicate that the AS of OsCPK17 putatively originates truncated forms of the protein with distinct functions, and different subcellular and tissue distributions. Additionally, we addressed the regulation of OsCPK17 by post-translational modifications in several in vitro experiments. Our analysis indicated that OsCPK17 activity depends on its structural rearrangement induced by calcium binding, and that the protein can be autophosphorylated. The identified phosphorylation sites mostly populate the OsCPK17 N-terminal domain. Exceptions are phosphosites T107 and S136 in the kinase domain and S558 in the C-terminal domain. These phosphosites seem conserved in CDPKs and may reflect a common regulatory mechanism for this protein family.

Outcomes from patients with presumed drug resistant tuberculosis in five reference centers in Brazil

Background

The implementation of rapid drug susceptibility testing (DST) is a current global priority for TB control. However, data are scarce on patient-relevant outcomes for presumptive diagnosis of drug-resistant tuberculosis (pDR-TB) evaluated under field conditions in high burden countries.

Methods

Observational study of pDR-TB patients referred by primary and secondary health units. TB reference centers addressing DR-TB in five cities in Brazil. Patients age 18 years and older were eligible if pDR-TB, culture positive results for Mycobacterium tuberculosis and, if no prior DST results from another laboratory were used by a physician to start anti-TB treatment. The outcome measures were median time from triage to initiating appropriate anti-TB treatment, empirical treatment and, the treatment outcomes.

Results

Between February,16th, 2011 and February, 15th, 2012, among 175 pDR TB cases, 110 (63.0%) confirmed TB cases with DST results were enrolled. Among study participants, 72 (65.5%) were male and 62 (56.4%) aged 26 to 45 years. At triage, empirical treatment was given to 106 (96.0%) subjects. Among those, 85 were treated with first line drugs and 21 with second line. Median time for DST results was 69.5 [interquartile - IQR: 35.7–111.0] days and, for initiating appropriate anti-TB treatment, the median time was 1.0 (IQR: 0–41.2) days. Among 95 patients that were followed-up during the first 6 month period, 24 (25.3%; IC: 17.5%–34.9%) changed or initiated the treatment after DST results: 16/29 MDRTB, 5/21 DR-TB and 3/45 DS-TB cases. Comparing the treatment outcome to DS-TB cases, MDRTB had higher proportions changing or initiating treatment after DST results (p = 0.01) and favorable outcomes (p = 0.07).

Conclusions

This study shows a high rate of empirical treatment and long delay for DST results. Strategies to speed up the detection and early treatment of drug resistant TB should be prioritized.

Rice calcium-dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose-phosphate synthase and is required for a proper cold stress response

Calcium-dependent protein kinases (CDPKs) are involved in plant tolerance mechanisms to abiotic stresses. Although CDPKs are recognized as key messengers in signal transduction, the specific role of most members of this family remains unknown. Here, we test the hypothesis that OsCPK17 plays a role in rice cold stress response by analysing OsCPK17 knockout, silencing and overexpressing rice lines under low temperature. Altered OsCPK17 gene expression compromises cold tolerance performance, without affecting the expression of key cold stress-inducible genes. A comparative phosphoproteomic approach led to the identification of six potential in vivo OsCPK17 targets, which are associated with sugar and nitrogen metabolism, and with osmotic regulation. To test direct interaction, in vitro kinase assays were performed, showing that the sucrose-phosphate synthase OsSPS4 and the aquaporin OsPIP2;1/OsPIP2;6 are phosphorylated by OsCPK17 in a calcium-dependent manner. Altogether, our data indicates that OsCPK17 is required for a proper cold stress response in rice, likely affecting the activity of membrane channels and sugar metabolism.

Evaluation of genetic diversity among soybean (Glycine max) genotypes using univariate and multivariate analysis

The genetic diversity study has paramount importance in breeding programs; hence, it allows selection and choice of the parental genetic divergence, which have the agronomic traits desired by the breeder. This study aimed to characterize the genetic divergence between 24 soybean genotypes through their agronomic traits, using multivariate clustering methods to select the potential genitors for the promising hybrid combinations. Six agronomic traits evaluated were number of days to flowering and maturity, plant height at flowering and maturity, insertion height of the first pod, and yield. The genetic divergence evaluated by multivariate analysis that esteemed first the Mahalanobis' generalized distance (D2), then the clustering using Tocher's optimization methods, and then the unweighted pair group method with arithmetic average (UPGMA). Tocher's optimization method and the UPGMA agreed with the groups' constitution between each other, the formation of eight distinct groups according Tocher's method and seven distinct groups using UPGMA. The trait number of days for flowering (45.66%) was the most efficient to explain dissimilarity between genotypes, and must be one of the main traits considered by the breeder in the moment of genitors choice in soybean-breeding programs. The genetic variability allowed the identification of dissimilar genotypes and with superior performances. The hybridizations UFU 18 x UFUS CARAJÁS, UFU 15 x UFU 13, and UFU 13 x UFUS CARAJÁS are promising to obtain superior segregating populations, which enable the development of more productive genotypes.

Regulation of Na+ and K+ homeostasis in plants: towards improved salt stress tolerance in crop plants

Soil salinity is a major abiotic stress that results in considerable crop yield losses worldwide. However, some plant genotypes show a high tolerance to soil salinity, as they manage to maintain a high K⁺/Na⁺ ratio in the cytosol, in contrast to salt stress susceptible genotypes. Although, different plant genotypes show different salt tolerance mechanisms, they all rely on the regulation and function of K⁺ and Na⁺ transporters and H⁺ pumps, which generate the driving force for K⁺ and Na⁺ transport. In this review we will introduce salt stress responses in plants and summarize the current knowledge about the most important ion transporters that facilitate intra- and intercellular K⁺ and Na⁺ homeostasis in these organisms. We will describe and discuss the regulation and function of the H⁺-ATPases, H⁺-PPases, SOS1, HKTs, and NHXs, including the specific tissues where they work and their response to salt stress.

Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities

BACKGROUND

Cynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in various biological properties such as, antibacterial, antifungal, antioxidant, hepatoprotective, and anticarcinogenic activities.

RESULTS

In this work we screened a Cynara cardunculus collection for new allelic variants in key genes involved in the chlorogenic acid biosynthesis pathway. The target genes encode p-coumaroyl ester 3'-hydroxylase (C3'H) and hydroxycinnamoyl-CoA: quinate hydroxycinnamoyl transferase (HQT), both participating in the synthesis of chlorogenic acid. Using high-resolution melting, the C3'H gene proved to be highly conserved with only 4 haplotypes while, for HQT, 17 haplotypes were identified de novo. The putative influence of the identified polymorphisms in C3'H and HQT proteins was further evaluated using bioinformatics tools. We could identify some polymorphisms that may lead to protein conformational changes. Chlorogenic acid content, antioxidant and antithrombin activities were also evaluated in Cc leaf extracts and an association analysis was performed to assess a putative correlation between these traits and the identified polymorphisms.

CONCLUSION

In this work we identified allelic variants with putative impact on C3'H and HQT proteins which are significantly associated with chlorogenic acid content and antioxidant activity. Further study of these alleles should be explored to assess putative relevance as genetic markers correlating with Cynara cardunculus biological properties with further confirmation by functional analysis.

Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses

The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.

Differential DNA Methylation Patterns Are Related to Phellogen Origin and Quality of Quercus suber Cork

DNA methylation is thought to influence Quercus suber cork quality, which is the main constraint for its economic valorisation. However, a deep knowledge of the cytosine methylation patterns disclosing the epigenetic variability of trees with different cork quality types is totally missing. This study investigates the hypothesis that variations in DNA methylation contribute to differences in cork cellular characteristics directly related to original or traumatic phellogen activity. We used MSAPs (Methylation Sensitive Amplified Polymorphism) to assess DNA methylation patterns of cork and leaf tissues of Q. suber adult trees growing in three cork oak stands. The relationship between the detected polymorphisms and the diversity of cork quality traits was explored by a marker-trait analysis focusing on the most relevant quality characteristics. Populations differed widely in cork quality, but only slightly in degree of epigenetic differentiation. Four MSAP markers (1.3% of the total) were significantly associated with the most noteworthy quality traits: wood inclusions (nails) and porosity. This evidence supports the potential role of cytosine methylation in the modulation of differential phellogen activity either involved in localized cell death or in pore production, resulting in different cork qualities. Although, the underlying basis of the methylation polymorphism of loci affecting cork quality traits remain unclear, the disclosure of markers statistically associated with cork quality strengthens the potential role of DNA methylation in the regulation of these traits, namely at the phellogen level.

Regulation of Na+ and K+ homeostasis in plants: towards improved salt stress tolerance in crop plants

Soil salinity is a major abiotic stress that results in considerable crop yield losses worldwide. However, some plant genotypes show a high tolerance to soil salinity, as they manage to maintain a high K+/Na+ ratio in the cytosol, in contrast to salt stress susceptible genotypes. Although, different plant genotypes show different salt tolerance mechanisms, they all rely on the regulation and function of K+ and Na+ transporters and H+ pumps, which generate the driving force for K+ and Na+ transport. In this review we will introduce salt stress responses in plants and summarize the current knowledge about the most important ion transporters that facilitate intra- and intercellular K+ and Na+ homeostasis in these organisms. We will describe and discuss the regulation and function of the H+-ATPases, H+-PPases, SOS1, HKTs, and NHXs, including the specific tissues where they work and their response to salt stress.

Five novel transcription factors as potential regulators of OsNHX1 gene expression in a salt tolerant rice genotype

This manuscript reports the identification and characterization of five transcription factors binding to the promoter of OsNHX1 in a salt stress tolerant rice genotype (Hasawi). Although NHX1 encoding genes are known to be highly regulated at the transcription level by different abiotic stresses, namely salt and drought stress, until now only one transcription factor (TF) binding to its promoter has been reported. In order to unveil the TFs regulating NHX1 gene expression, which is known to be highly induced under salt stress, we have used a Y1H system to screen a salt induced rice cDNA expression library from Hasawi. This approach allowed us to identify five TFs belonging to three distinct TF families: one TCP (OsPCF2), one CPP (OsCPP5) and three NIN-like (OsNIN-like2, OsNIN-like3 and OsNIN-like4) binding to the OsNHX1 gene promoter. We have also shown that these TFs act either as transcriptional activators (OsPCF2, OsNIN-like4) or repressors (OsCPP5, OsNIN-like2) and their encoding genes are differentially regulated by salt and PEG-induced drought stress in two rice genotypes, Nipponbare (salt-sensitive) and Hasawi (salt-tolerant). The transactivation activity of OsNIN-like3 was not possible to determine. Increased soil salinity has a direct impact on the reduction of plant growth and crop yield and it is therefore fundamental to understand the molecular mechanisms underlying gene expression regulation under adverse environmental conditions. OsNHX1 is the most abundant K⁺-Na⁺/H⁺ antiporter localized in the tonoplast and its gene expression is induced by salt, drought and ABA. To investigate how OsNHX1 is transcriptionally regulated in response to salt stress in a salt-tolerant rice genotype (Hasawi), a salt-stress-induced cDNA expression library was constructed and subsequently screened using the yeast one-hybrid system and the OsNHX1 promoter as bait. Five transcription factors (TFs) belonging to three distinct TF families: one TCP (OsPCF2), one CPP (OsCPP5) and three NIN-like (OsNIN-like2, OsNIN-like3 and OsNIN-like4) were identified as binding to OsNHX1 promoter. Transactivation activity assays performed in Arabidopsis and rice protoplasts showed that OsPCF2 and OsNIN-like4 are activators of the OsNHX1 gene expression, while OsCPP5 and OsNIN-like2 act as repressors. The transactivation activity of OsNIN-like3 needs to be further investigated. Gene expression studies showed that OsNHX1 transcript level is highly induced by salt and PEG-induced drought stress in both shoots and roots in both Nipponbare and Hasawi rice genotypes. Nevertheless, OsNHX1 seems to play a particular role in shoots in response to drought. Most of the TFs binding to OsNHX1 promoter showed a modest transcriptional regulation under stress conditions, however, in response to most of the conditions studied, the OsPCF2 was induced earlier than OsNHX1, indicating that OsPCF2 may activate OsNHX1 gene expression. In addition, although the OsNHX1 response to salt and PEG-induced drought stress in either shoots or roots was quite similar in both rice genotypes, the expression of OsPCF2 in roots under salt stress and the OsNIN-like4 in roots subjected to PEG was mainly up-regulated in Hasawi, indicating that these TFs may be associated with the salt and drought stress tolerance observed for this genotype.

Selection of an Appropriate Protein Extraction Method to Study the Phosphoproteome of Maize Photosynthetic Tissue

Often plant tissues are recalcitrant and, due to that, methods relying on protein precipitation, such as TCA/acetone precipitation and phenol extraction, are usually the methods of choice for protein extraction in plant proteomic studies. However, the addition of precipitation steps to protein extraction methods may negatively impact protein recovery, due to problems associated with protein re-solubilization. Moreover, we show that when working with non-recalcitrant plant tissues, such as young maize leaves, protein extraction methods with precipitation steps compromise the maintenance of some labile post-translational modifications (PTMs), such as phosphorylation. Therefore, a critical issue when studying PTMs in plant proteins is to ensure that the protein extraction method is the most appropriate, both at qualitative and quantitative levels. In this work, we compared five methods for protein extraction of the C4-photosynthesis related proteins, in the tip of fully expanded third-leaves. These included: TCA/Acetone Precipitation; Phenol Extraction; TCA/Acetone Precipitation followed by Phenol Extraction; direct extraction in Lysis Buffer (a urea-based buffer); and direct extraction in Lysis Buffer followed by Cleanup with a commercial kit. Protein extraction in Lysis Buffer performed better in comparison to the other methods. It gave one of the highest protein yields, good coverage of the extracted proteome and phosphoproteome, high reproducibility, and little protein degradation. This was also the easiest and fastest method, warranting minimal sample handling. We also show that this method is adequate for the successful extraction of key enzymes of the C4-photosynthetic metabolism, such as PEPC, PPDK, PEPCK, and NADP-ME. This was confirmed by MALDI-TOF/TOF MS analysis of excised spots of 2DE analyses of the extracted protein pools. Staining for phosphorylated proteins in 2DE revealed the presence of several phosphorylated isoforms of PEPC, PPDK, and PEPCK.

Genomic prediction for tick resistance in Braford and Hereford cattle

One of the main animal health problems in tropical and subtropical cattle production is the bovine tick, which causes decreased performance, hide devaluation, increased production costs with acaricide treatments, and transmission of infectious diseases. This study investigated the utility of genomic prediction as a tool to select Braford (BO) and Hereford (HH) cattle resistant to ticks. The accuracy and bias of different methods for direct and blended genomic prediction was assessed using 10,673 tick counts obtained from 3,435 BO and 928 HH cattle belonging to the Delta G Connection breeding program. A subset of 2,803 BO and 652 HH samples were genotyped and 41,045 markers remained after quality control. Log transformed records were adjusted by a pedigree repeatability model to estimate variance components, genetic parameters, and breeding values (EBV) and subsequently used to obtain deregressed EBV. Estimated heritability and repeatability for tick counts were 0.19 ± 0.03 and 0.29 ± 0.01, respectively. Data were split into 5 subsets using k-means and random clustering for cross-validation of genomic predictions. Depending on the method, direct genomic value (DGV) prediction accuracies ranged from 0.35 with Bayes least absolute shrinkage and selection operator (LASSO) to 0.39 with BayesB for k-means clustering and between 0.42 with BayesLASSO and 0.45 with BayesC for random clustering. All genomic methods were superior to pedigree BLUP (PBLUP) accuracies of 0.26 for k-means and 0.29 for random groups, with highest accuracy gains obtained with BayesB (39%) for k-means and BayesC (55%) for random groups. Blending of historical phenotypic and pedigree information by different methods further increased DGV accuracies by values between 0.03 and 0.05 for direct prediction methods. However, highest accuracy was observed with single-step genomic BLUP with values of 0.48 for -means and 0.56, which represent, respectively, 84 and 93% improvement over PBLUP. Observed random clustering cross-validation breed-specific accuracies ranged between 0.29 and 0.36 for HH and between 0.55 and 0.61 for BO, depending on the blending method. These moderately high values for BO demonstrate that genomic predictions could be used as a practical tool to improve genetic resistance to ticks and in the development of resistant lines of this breed. For HH, accuracies are still in the low to moderate side and this breed training population needs to be increased before genomic selection could be reliably applied to improve tick resistance.

Transcriptomics and physiological analyses reveal co-ordinated alteration of metabolic pathways in Jatropha curcas drought tolerance

Jatropha curcas, a multipurpose plant attracting a great deal of attention due to its high oil content and quality for biofuel, is recognized as a drought-tolerant species. However, this drought tolerance is still poorly characterized. This study aims to contribute to uncover the molecular background of this tolerance, using a combined approach of transcriptional profiling and morphophysiological characterization during a period of water-withholding (49 d) followed by rewatering (7 d). Morphophysiological measurements showed that J. curcas plants present different adaptation strategies to withstand moderate and severe drought. Therefore, RNA sequencing was performed for samples collected under moderate and severe stress followed by rewatering, for both roots and leaves. Jatropha curcas transcriptomic analysis revealed shoot- and root-specific adaptations across all investigated conditions, except under severe stress, when the dramatic transcriptomic reorganization at the root and shoot level surpassed organ specificity. These changes in gene expression were clearly shown by the down-regulation of genes involved in growth and water uptake, and up-regulation of genes related to osmotic adjustments and cellular homeostasis. However, organ-specific gene variations were also detected, such as strong up-regulation of abscisic acid synthesis in roots under moderate stress and of chlorophyll metabolism in leaves under severe stress. Functional validation further corroborated the differential expression of genes coding for enzymes involved in chlorophyll metabolism, which correlates with the metabolite content of this pathway.

Screening for Abiotic Stress Tolerance in Rice: Salt, Cold, and Drought

Rice (Oryza sativa) is the primary source of food for more than half of the world population. Most rice varieties are severely injured by abiotic stresses, with strong social and economic impact. Understanding rice responses to stress may help breeding for more tolerant varieties. However, papers dealing with stress experiments often describe very different experimental designs, thus making comparisons difficult. The use of identical setups is the only way to generate comparable data. This chapter is organized into three sections, describing the experimental conditions established at the Genomics of Plant Stress (GPlantS) unit of ITQB to assess the response of rice plants to three different abiotic stresses--high salinity, cold stress, and drought. All sections include a detailed description of the materials and methodology, as well as useful notes gathered from the GPlantS team's experience. We use rice seedlings as plants at this stage show high sensitivity to abiotic stresses. For the salt and cold stress assays we use hydroponic cultures, while for the drought assay plants are grown in soil and subjected to water withholding. All setups enable visual score determination and are suitable for sample collection along the imposition of stress. The proposed methodologies are simple and affordable to implement in most labs, allowing the discrimination of several rice genotypes at the molecular and phenotypic level.

Floristic and phytosociology in dense "terra firme" rainforest in the Belo Monte Hydroelectric Plant influence area, Pará, Brazil

The objective of the present study was to characterise the floristic and phytosociological composition on a stretch of dense "Terra Firme" rainforest located in the Belo Monte hydroelectric plant area of influence, located in the state of Pará, Brazil. All trees with DAP >10 cm situated in 75 permanent plots of 1 ha were inventoried. 27,126 individuals trees (361 ind.ha-1), distributed in 59 botanical families, comprising 481 species were observed. The families with the largest number of species were Fabaceae (94), Araceae (65) and Arecaceae (43), comprising 43.7% of total species. The species Alexa grandiflora (4.41), Cenostigma tocantinum (2.50) and Bertholletia excelsa (2.28) showed the highest importance values (IV). The ten species with greater IV are concentrated (22%). The forest community has high species richness and can be classified as diverse age trees, heterogeneous and of medium conservation condition.

Age-dependent biochemical dysfunction in skeletal muscle of triple-transgenic mouse model of Alzheimer`s disease

The emergence of Alzheimer`s disease as a systemic pathology shifted the research paradigm toward a better understanding of the molecular basis of the disease considering the pathophysiological changes in both brain and peripheral tissues. In the present study, we evaluated the impact of disease progression on physiological relevant features of skeletal muscle obtained from 3, 6 and 12 month-old 3xTg-AD mice, a model of Alzheimer`s disease, and respective agematched nonTg mice. Our results showed that skeletal muscle functionality is already affected in 3-month-old 3xTg-AD mice as evidenced by deficient acetylcholinesterase and catalase activities as well as by alterations in fatty acid composition of mitochondrial membranes. Additionally, an age-dependent accumulation of amyloid-β_1-40 peptide occurred in skeletal muscle of 3xTg-AD mice, an effect that preceded bioenergetics mitochondrial dysfunction, which was only detected at 12 months of age, characterized by decreased respiratory control ratio and ADP/O index and by an impairment of complex I activity. HPLC-MS/MS analyses revealed significant changes in phospholipid composition of skeletal muscle tissues from 3xTg-AD mice with 12 months of age when compared with age-matched nonTg mice. Increased levels of lyso-phosphatidylcholine associated with a decrease of phosphatidylcholine molecular species containing arachidonic acid were detected in 3xTg-AD mice, indicating an enhancement of phospholipase A₂ activity and skeletal muscle inflammation. Additionally, a decrease of phosphatidylethanolamine plasmalogens content and an increase in phosphatidylinositol levels was observed in 3xTg-AD mice when compared with age-matched nonTg mice. Altogether, these observations suggest that the skeletal muscle of 3xTg-AD mice are more prone to oxidative and inflammatory events.