Comparative physiological and transcriptome analysis in cultivated and wild sugarcane species in response to hydrogen peroxide-induced oxidative stress

BACKGROUND

Sugarcane is an important energy crop grown worldwide,supplementing various renewable energy sources. Cultivated and wild sugarcane species respond differently to biotic and abiotic stresses. Generally, wild species are tolerant to various abiotic stresses. In the present study, the physiological and molecular responses of cultivated and wild sugarcane species to oxidative stress at the transcriptional levels were compared. Transcriptional responses were determined using RNAseq. The representative RNA-seq transcript values were validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and confirmed through physiological responses.

RESULTS

Oxidative stress causes leaf-rolling and -tip drying in cultivated sugarcane, but the wild species are tolerant. Higher chlorophyll fluorescence was observed in the wild species than that in the cultivated varieties under stress. Wild species can maintain a higher chlorophyll stability index than the cultivated species, which was confirmed by the lower transcripts of the chlorophyllase gene in the wild species than that in the cultivated variety. Transcription factor genes (NAC, MYB, and WRKY) were markedly expressed in response to oxidative stress, revealing their involvement in stress tolerance. The analysis revealed synchronized expression of acetyl-transferase, histone2A, cellulose synthase, and secondary cell wall biosynthetic genes in the wild species. The validation of selected genes and 15 NAC transcription factors using RT-qPCR revealed that their expression profiles were strongly correlated with RNA-seq. To the best of our knowledge, this is the first report on the oxidative stress response in cultivated and wild sugarcane species.

CONCLUSION

Physiological and biochemical changes in response to oxidative stress markedly differ between cultivated and wild sugarcane species. The differentially expressed stress-responsive genes are grouped intothe response to oxidative stress, heme-binding, peroxidase activity, and metal ion binding categories. Chlorophyll maintenance is a stress tolerance response enhanced by the differential regulation of the chlorophyllase gene.There is a considerable difference in the chlorophyll stability index between wild and cultivated varieties. We observed a substantial regulation of secondary wall biosynthesis genes in the wild species compared with that in the cultivated variety, suggesting differences in stress tolerance mechanisms.

Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, two sugarcane genotypes were subjected to three water-deficit levels (mild, moderate, and severe) and subsequent recovery and leaf transcriptome was generated using Illumina NextSeq sequencing. Among the differentially expressed genes, the tolerant genotype Co 06022 generated 2970 unigenes (p ≤ 0.05, functionally known, non-redundant DEGs) at 2-day stress, and there was a progressive decrease in the expressed genes as the stress period increased with 2109 unigenes at 6-day stress and 2307 unigenes at 10-day stress. There was considerable reduction at recovery with 1334 unigenes expressed at 10 days after recovery. However, in the susceptible genotype Co 8021, the number of unigenes expressed at 2 days was lower (2025) than the tolerant genotype and a further reduction was seen at 6-day stress (1552). During recovery, more differentially expressed genes were observed in the susceptible cultivar indicating that the cultivar has to activate more functions/processes to recover from the damage caused by stress. Comparison of DEGs between all stages of stress and recovery in both genotypes revealed that, the commonly up- and down-regulated genes across different stages were approximately double in the tolerant genotype. The most enriched gene ontology classes were heme binding, peroxidase activity and metal ion binding in the biological process and response to oxidative stress, hydrogen peroxide catabolic process and response to stress in the molecular function category. The cellular component was enriched with DEGs involved in extracellular region followed by integral component of membrane. The KEGG pathway analysis revealed important metabolic activities and functionally important genes involved in mitigating water-deficit stress in both the varieties. In addition, several unannotated genes in important pathways were detected and together may provide novel insights into water-deficit tolerance mechanisms in sugarcane. The reliability of the observed expression patterns was confirmed by qRT-PCR. The results of this study will help to identify useful genes for improving drought tolerance in sugarcane.

Advanced Glycation end Products: Specific Fluorescence Changes of Pentosidine-Like Compounds during Short Daily Hemodialysis

Background

Advanced glycation end products (AGE) accumulate in uremia and represent an important etiopathogenetic cause of morbidity in dialyzed patients. Conventional hemodialysis treatment seems to be ineffective in lowering AGE levels. We wished to investigate whether daily hemodialysis (DHD), a treatment that seems to result in better clinical condition in end-stage renal disease patients, is effective in the reduction of these compounds.

Methods

We evaluated 10 non-diabetic patients on standard hemodialysis (SHD = 3 × 4h/week) for more than 6 months by a crossover study. These patients were assigned randomly to 6 months of DHD (6 × 2h/week) or 6 months of SHD. Then, they were switched to 6 months of the alternative treatment. At the end of these two periods, we studied pentosidine-like AGE compounds by measuring the total fluorescence at a wavelength characteristic for these substances: Ex: 335nm / Em:385nm; we also measured protein-linked pentosidine at the same time points. Finally, we determined the AGE-related total fluorescence in the deproteinized serum of 13 uremic patients on peritoneal dialysis (CAPD) and of 10 healthy controls.

Results

Pre-HD AGE-related total fluorescence obtained after 6 months of DHD was significantly lower than that obtained with standard HD (DHD = 201.3 ± 36.4 AU/ml vs. SHD = 267.5 ± 141.4 AU/ml, p=0.03). The extraction rate per minute of dialysis was slightly, but not significantly higher during DHD than SHD (0.29 ± 0.11% vs. 0.23 ± 0.04, p = 0.07). AGE-related total fluorescence pre-HD values in patients treated by SHD and DHD were about 20-fold higher than in control subjects. They did not differ from CAPD patients. The pre-dialysis level of protein-linked pentosidine was significantly lower in DHD than in SHD (DHD = 16.12 ± 4.71 pmol/mg protein, SHD = 22.64 ± 6.86 pmol/mg protein, p < 0.01).

Conclusions

DHD showed a reduction in AGE-related total fluorescence, although the mean value remained higher than in control subjects. DHD is also accompanied by a decrease in protein-linked pentosidine.

Potentiality of yeast Candida sp. SMN04 for degradation of cefdinir, a cephalosporin antibiotic: kinetics, enzyme analysis and biodegradation pathway

A new yeast strain isolated from the pharmaceutical wastewater was capable of utilizing cefdinir as a sole carbon source for their growth in mineral medium. The yeast was identified and named as Candida sp. SMN04 based on morphology and 18S-ITS-D1/D2/D3 rRNA sequence analysis. The interaction between factors pH (3.0-9.0), inoculum dosage (1-7%), time (1-11 day) and cefdinir concentration (50-450 mg/L) was studied using a Box-Behnken design. The factors were studied as a result of their effect on cell dry weight (R1; g/L), extended spectrum β-lactamase (ESBL) assay (R2; mm), P450 activity (R3; U/mL) and degradation (R4; %). Maximum values of R1, R2, R3 and R4 were obtained at central values of all the parameters. The isolated yeast strain efficiently degraded 84% of 250 mg L⁻¹ of cefdinir within 6 days with a half-life of 2.97 days and degradation rate constant of 0.2335 per day. Pseudo-first-order model efficiently described the process. Among the various enzymes tested, the order of activity at the end of Day 4 was noted to be: cytochrome P450 (1.76 ± 0.03) > NADPH reductase (1.51 ± 0.20) > manganese peroxidase and amylase (0.66 ± 0.15; 0.66 ± 0.70). Intermediates were successfully characterized by liquid chromatography-mass spectrometry. The opening of the β-lactam ring involving ESBL activity was considered as one of the major steps in the cefdinir degradation process. Fourier transform-infrared spectroscopy analysis showed the absence of spectral vibrations between 1766 and 1519 cm⁻¹ confirming the complete removal of lactam ring during cefdinir degradation. The results of the present study are promising for the use of isolated yeast Candida sp. SMN04 as a potential bioremediation agent.

Synthesis and characterization of a CuS–WO3 composite photocatalyst for enhanced visible light photocatalytic activity

WO₃ nanorods and flower-like CuS were synthesized by a hydrothermal process.

[Prevention of psychosocial issues and drug addiction in workers employed in building great infrastructures: first outcomes of an experience in the Florence area]

The research on stress, mobbing, and substance dependence in workers employed in the building of the great infrastructures is part of the project Euridice-Ten. The 75% of the workers employed took part in the research through an anonymous and structured questionnaire. The Clinica del Lavoro of the University of Milan elaborated the data. They point out a high risk of stress, a low level of control, a marked risk of mobbing, a high chronic fatigue in the most exhausting jobs, sleep disorders, problems in the social life as well as at home, in nourishment and at work. Many workers drink too much alcohol and the 9% of the workers know workers who use cocaine.

Quantitative and diffusion MR imaging as a new method to assess osteoporosis

BACKGROUND AND PURPOSE

The role of advanced MR imaging techniques in demonstrating the microarchitectural changes in osteoporosis has been recently investigated. Our aim was to determine the role of quantitative and diffusion MR imaging in the diagnosis of osteoporosis compared with dual-energy x-ray absorptiometry (DEXA).

MATERIALS AND METHODS

Fifty-one subjects underwent both DEXA and conventional MR imaging with diffusion and apparent diffusion coefficient (ADC) mapping. T1, T2, diffusion signal intensity, and ADC values were calculated and compared with bone mineral attenuation (BMD). Results were obtained from L1 to L4 of each patient with a total of 204 lumbar vertebrae.

RESULTS

Both T1 and T2 signal intensities tended to increase when both diffusion and ADC values decreased with reducing BMD.

CONCLUSIONS

An inverse relationship between BMD and T1 and T2 signal intensities and a direct relationship between diffusion and ADC values were present in this pilot group. The T1/diffusion signal-intensity ratio could be a reliable diagnostic indicator of osteoporosis.

Patterns of delays in diagnosis amongst patients with smear-positive pulmonary tuberculosis at a teaching hospital in Turkey

In total, 151 newly diagnosed patients with smear-positive pulmonary tuberculosis were studied. The mean time from the onset of symptoms to the first visit to a physician was 46.4 days; the mean referral delay was 28.9 days; the mean delay in diagnosis was 2.4 days; and the mean delay in treatment initiation was 0.8 days. There was a delay in consulting a physician by 49% of patients. A low index of suspicion for tuberculosis on the part of the physician and healthcare system and laboratory delays were the most common reasons for delays in diagnosis.

The relation of the pleural thickening in tuberculosis pleurisy with the activity of adenosine deaminase

BACKGROUND

Residual pleural thickening (RPT) still occurs in most patients with tuberculosis pleurisy despite advances in the treatment of tuberculosis. The aim of this study was to evaluate the significance of RPT in tuberculosis pleurisy with the patients clinical findings, biochemical and microbiological properties of pleural effusion and with the total adenosine deaminase (ADA) and isoenzymes levels.

METHODS

121 tuberculosis pleurisy patients were evaluated retrospectively. According to posteroanterior chest x-rays, the 63 (52%) cases with the thickness 2 mm or more in lower lateral hemithorax were grouped as I and the 58 (48%) cases without pleural thickness were grouped as II. The amount of pleural effusion was classified into small, medium or massive according to their chest x-rays. In both groups; sex, age, symptoms score, bacteriological and biochemical tests and ADA levels were recorded.

RESULTS

81 (67%) male and 40 (33%) female, overall 121 patients were enrolled into the study. RPT was found higher in males (p=0.014) and the increase ran parallel with the amount of cigarette smoking (p=0.014). RPT was found to be lower in small effusions (p=0.001). The group with RPT, the serum albumin was found lower (p=0.002), pleural fluid total protein (p=0.047) and the ratio of pleural fluid protein to serum protein (p=0.002) were found higher. In group I, total ADA: 69.5 +/- 38.9 IU/L and ADA2: 41.3 +/- 31.6 IU/L were higher than the cases without RPT (p=0.032, p=0.017, respectively).

CONCLUSIONS

We suggest that the immunological mechanisms are effective in the development of pleural thickening.

Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane

The use of maize microsatellite markers as a potential cost-effective method for molecular analysis of sugarcane was evaluated. Of the 34 primer pairs obtained from maize genomic libraries, 14 showed repeatable amplifications in Saccharum species clones, commercial hybrids, and the related genera Erianthus, accounting for 41.17% cross transferability. Complex banding patterns were encountered in sugarcane with the number of amplified fragments ranging from 7 to 14 with an average of 10 per primer, indicating the high polyploidy and heterozygosity existing in sugarcane. Phenetic analysis of the SSR polymorphisms produced by nine primers could clearly differentiate the different species of Saccharum and Erianthus and revealed the relationships that existed between them. Genetic similarity co-efficient indicated low diversity existing among the S. officinarum clones (82%) and a relatively higher level of diversity in the S. spontaneum clones (69.7%). Higher level of divergence of Erianthus from Saccharum was also clearly estabilished. Five primers produced genus- and species-specific fragments for Erianthus, S. spontaneum, S. officinarum, and S. barberi. The polymorphic primers, when tested on a panel of 30 commercial sugarcane cultivars, revealed a broad range (32.4-83.3%) of pair-wise similarity values, indicating their ability to detect high levels of polymorphism. A combination of two primers could differentiate all the varieties, further emphasizing their potential in fingerprinting and varietal identification.

Advanced glycation end products: specific fluorescence changes of pentosidine-like compounds during short daily hemodialysis

BACKGROUND

Advanced glycation end products (AGE) accumulate in uremia and represent an important etiopathogenetic cause of morbidity in dialyzed patients. Conventional hemodialysis treatment seems to be ineffective in lowering AGE levels. We wished to investigate whether daily hemodialysis (DHD), a treatment that seems to result in better clinical condition in end-stage renal disease patients, is effective in the reduction of these compounds.

METHODS

We evaluated 10 non-diabetic patients on standard hemodialysis (SHD = 3 x 4 h/week) for more than 6 months by a crossover study. These patients were assigned randomly to 6 months of DHD (6 x 2 h/week) or 6 months of SHD. Then, they were switched to 6 months of the alternative treatment. At the end of these two periods, we studied pentosidine-like AGE compounds by measuring the total fluorescence at a wavelength characteristic for these substances: Ex: 335nm/Em:385nm; we also measured protein-linked pentosidine at the same time points. Finally, we determined the AGE-related total fluorescence in the deproteinized serum of 13 uremic patients on peritoneal dialysis (CAPD) and of 10 healthy controls.

RESULTS

Pre-HD AGE-related total fluorescence obtained after 6 months of DHD was significantly lower than that obtained with standard HD (DHD = 201.3 +/- 36.4 AU/ml vs. SHD = 267.5 +/- 141.4 AU/ml, p = 0.03). The extraction rate per minute of dialysis was slightly, but not significantly higher during DHD than SHD (0.29 +/- 0.11% vs. 0.23 +/- 0.04, p = 0.07). AGE-related total fluorescence pre-HD values in patients treated by SHD and DHD were about 20-fold higher than in control subjects. They did not differ from CAPD patients. The pre-dialysis level of protein-linked pentosidine was significantly lower in DHD than in SHD (DHD = 16.12 +/- 4.71 pmol/mg protein, SHD = 22.64 +/- 6.86 pmol/mg protein, p < 0.01).

CONCLUSIONS

DHD showed a reduction in AGE-related total fluorescence, although the mean value remained higher than in control subjects. DHD is also accompanied by a decrease in protein-linked pentosidine.

Angiotensin-converting enzyme gene I/D polymorphism and carotid artery disease in renovascular hypertension

There is evidence linking the activation of the renin-angiotensin system (RAS) with target organ damage in renovascular hypertension (RVH). A genetic association of the DD genotype of the angiotensin-converting enzyme (ACE) gene with cardiovascular complications has been found in various clinical conditions. The aim of our study was to determine whether the insertion/deletion (I/D) polymorphism of the ACE gene is associated with the high prevalence of target organ damage reported in RVH. A total of 65 atherosclerotic patients (age 68.2 +/- 5.2 years) with RVH and 49 atherosclerotic patients (age 68.0 +/- 6.3 years) with essential hypertension (EH) were sequentially enrolled when attending the outpatient clinic for specialist assessment of their vascular disorder. Cardiac, renal, and vascular involvement were assessed in both groups and blood was taken for genetic analysis. Patients with RVH had a higher prevalence of left ventricular hypertrophy (LVH), carotid artery disease, and albuminuria than those with EH. In RVH, but not in EH, the DD genotype was significantly associated with severe arterial disease. In RVH, carotid disease (lumen narrowing >60%) was present in 62% of DD patients versus 25% of the other genotypes (OR = 4.90, 95% CI: 1.70-14.13). Such an association was also present in peripheral vascular disease: 72.4% in DD patients versus 41.6% in the other genotypes (OR = 3.67, 95% CI = 1.29-10.36). Logistic regression analysis showed that the DD genotype was the strongest predictor of risk of severe carotid disease. We conclude that, in atherosclerotic RVH, there is an association of the severity of vascular disease with the DD genotype of the ACE gene.

Reduction of renal functional reserve in kidney transplant recipients: a possible role of arachidonic acid metabolism alterations

AIM

Renal functional reserve (RFR), resulting from an increase in glomerular filtration (GFR) after protein load, is a matter of debate. In kidney transplant recipients most studies have failed to show conclusive results, reporting either the absence, the reduction or the presence of renal reserve in normo-functioning kidneys. The aim of this study was to investigate RFR in kidney transplant patients as well as the possible hormonal vasoactive alterations underlying the reduction of renal reserve reported in some patients.

PATIENTS AND METHODS

We studied 8 controls and 25 patients, the latter with no history of acute rejection for at least 12 months and GFR >50 ml/min. The 25 patients were divided into 2 groups based on the presence (10) or the absence (15) of RFR.

RESULTS

Both the RFR group and the controls experienced a similar increase of GFR after oral protein load: 24.3 +/- 15.57% vs 24.4 +/- 10.8%. The group without RFR showed a paradoxical reduction of GFR after oral protein load: 13.3 +/- 13.2% (p <0.001). We analyzed the filtration fraction (FF) and observed that the group without RFR had higher values than the group with RFR and the controls: 0.35 +/- 0.11 vs 0.29 +/- 0.07 (p = 0.01) and vs 0.26 +/- 0.02 (p = 0.04). The hyperfiltration state observed in the group without RFR was sustained by a high level of thromboxane. The urine ratio TxB2/6ketoPgF1alpha was higher in the group without RFR than in the RFR group 0.78 +/- 0.2 vs 0.64 +/- 0.1 (p = 0.01). This ratio decreased only in the RFR group after a meat meal. In all the patients, changes of TxB2/6ketoPGF1alpha were inversely correlated to changes of GFR after a meat meal (r = -0.6, p = 0.01).

CONCLUSIONS

In conclusion, these data demonstrate that kidney transplant recipients with good organ function can be grouped according to the presence of RFR. RFR appears to be inversely correlated with the TxB2/6ketoPGF1alpha ratio, and its decrease seems to be linked to the failure of thromboxane to decrease and prostacycline to increase after a meat meal.

Renal funtional reserve in kidney transplant recipients

In the last few years different authors have observed that kidney transplant recipients with good organ function do not have a renal functional reserve (RFR). This condition is accompained by a high glomerular filtration rate (GFR). We studied RFR in patients with very good organ function under different immunosuppressive therapies, who were divided into groups based on the presence or absence of RFR.