The epigenetic diversity of six genotype groups (commercial cultivars,
S. officinarum
,
S. spontaneum
,
S. robustum
,
S. barberi
, and
Erianthus
sp.) was assessed through methylation-sensitive ...amplification polymorphism (MSAP). A total of 1341 MSAP loci were analyzed, of which 1117 (83.29%) were susceptible to cytosine methylation and responsible for a higher proportion of overall diversity among genotypes. The MSAP selective primer combinations captured different proportions of internal and external cytosine methylation loci across genotype groups, while the average external cytosine frequency was higher for all genotype groups. The genotypes were divided into two subpopulations with a high differentiation index (
φ
st = 0.086) based on epigenetic loci. The genotypes were clustered in three subgroups for both methylated and unmethylated loci, considering dissimilarity values. Four methylated fragments (MFs) were randomly selected and subsequently sequenced and compared with sugarcane public databases using BLASTN. MF alignments suggest that cytosine methylation occurs in sugarcane near CpG islands and tandem repeats within transcribed regions and putative
cis
-regulatory sequences, which assigned functions are associated with stress adaptation. These results provide the first insights about the distribution of this epigenetic mark in sugarcane genome, and suggest a biological relevance of methylated loci.
Sugarcane mosaic disease (SMD) caused by sugarcane mosaic virus, is one of the main diseases in sugarcane production areas in Brazil. Thus, the identification of new sources of resistance for use in ...future introgression crosses is key for reliable economic gains. Here, we aimed to screen a diversity panel of 98 sugarcane genotypes for SMD under natural infection conditions, to investigate virus-specific amplicons from SCMV coat protein gene (CP), and identify marker-trait associations via association mapping using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeats (SSR). The highest SMD incidence (26.53%) was observed eight months after planting, with significant differences (p<0.01) among genotypes and a means-based broad-sense heritability of 62.49% with a noticeable contribution of
Saccharum spontaneum
to SMD resistance. The CP sequence analysis revealed no variation among the four selected plant samples, which phylogenetic analysis revealed clustering with the RIB-1 strain while putative amino acid substitutions indicate a new SCMV isolate. From a subset of 135 SSR and 663 AFLP markers, selected after quality control, 91 markers were associated with response to SCMV (
p
<0.05) by simple linear regression, and 24 were significant at
p
<0.01. Four out these 24 fit in a stepwise regression at
p
<0.05, all contributing for the resistance to SMD, and are present in thirteen genotypes showing no SMD symptoms. These four markers collectively explain 29.95% of trait variation, while individually explain from 5.51 to 14.02%, and may correspond to new genomic regions conferring genetic resistance to SMD which investigation is worthwhile.
Sugarcane mosaic disease (SMD) caused by sugarcane mosaic virus, is one of the main diseases in sugarcane production areas in Brazil. Thus, the identification of new sources of resistance for use in ...future introgression crosses is key for reliable economic gains. Here, we aimed to screen a diversity panel of 98 sugarcane genotypes for SMD under natural infection conditions, to investigate virus-specific amplicons from SCMV coat protein gene (CP), and identify marker-trait associations via association mapping using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeats (SSR). The highest SMD incidence (26.53%) was observed eight months after planting, with significant differences (p<0.01) among genotypes and a means-based broad-sense heritability of 62.49% with a noticeable contribution of Saccharum spontaneum to SMD resistance. The CP sequence analysis revealed no variation among the four selected plant samples, which phylogenetic analysis revealed clustering with the RIB-1 strain while putative amino acid substitutions indicate a new SCMV isolate. From a subset of 135 SSR and 663 AFLP markers, selected after quality control, 91 markers were associated with response to SCMV (p <0.05) by simple linear regression, and 24 were significant at p <0.01. Four out these 24 fit in a stepwise regression at p <0.05, all contributing for the resistance to SMD, and are present in thirteen genotypes showing no SMD symptoms. These four markers collectively explain 29.95% of trait variation, while individually explain from 5.51 to 14.02%, and may correspond to new genomic regions conferring genetic resistance to SMD which investigation is worthwhile.
Yellow leaf disease (YLD), caused by sugarcane yellow leaf virus (SCYLV), has been reported to infect sugarcane worldwide causing significant yield losses and is considered a major disease of this ...crop. A panel composed of 98 genotypes encompassing basic germplasm, commercial cultivars, and elite clones was assayed in the nursery and a replicated field for resistance to SCYLV, combining symptom expression and virus quantification. Virus symptom intensity was evaluated using a diagrammatic scale while virus titer was estimated by DAS-ELISA (Double Antibody Sandwich-ELISA) and RT-qPCR (Reverse Transcription Quantitative PCR) in the nursery and field trials, respectively. Resistance was evaluated alongside symptom development kinetics. Based on the symptom intensity, 52 (53.06%) genotypes were classified as resistant in the nursery and 42 (42.86%) in the field. Twenty-nine (29.59%) genotypes showed no symptoms in the nursery and field trial. Moderately resistant genotypes showed a low correlation between virus titer and symptom intensity. The kinetics of symptom development increased over time in moderately susceptible and susceptible genotypes. The SCYLV incidence assessed by RT-qPCR was 92.55%, which was detected in 83% of the asymptomatic genotypes. The broad-sense heritability based on symptom expression and relative quantification was 52.62% and 68%, respectively. The virus quantification assays allowed for the identification of potential genotypes immune to SCYLV.
•Resistance evaluation combining symptom expression and virus quantification.•83% of asymptomatic but SCYLV infected genotypes.•Five potential SCYLV immune genotypes identified by DAS-ELISA and RT-qPCR.•Combination of RT-qPCR and symptom expression proven suitable for parental selection.•Moderate to high broad-sense heritability for symptom expression (52.62%) and virus titer (68%).
This study aimed to evaluate the resistance of 79 sugarcane genotypes (varieties and elite clones) artificially inoculated with a severe Sugarcane mosaic virus (SCMV) strain and to estimate genetic ...parameters associated with SCMV resistance. Symptoms were evaluated using a graded scale, and confirmation of infection was performed using the Plate Trapped Antibody-ELISA serological test in plants conducted in a greenhouse experiment and then validated under field conditions. The mean incidence of mosaic disease was low in greenhouse conditions, with higher observed incidence values when assessed in the field. Based on the field results, variance analysis was significant for genotypes and genotype × environment interaction. Tracking mosaic symptom expression over time in the different sugarcane genotypes revealed varying behavior, including recovery from disease in some genotypes. The broad-sense heritability based on the mean and individual level was 62.18% and 19.37%, respectively. Twenty-two genotypes were observed to be resistant to SCMV.
•Seventy-nine sugarcane genotypes artificially inoculated (Sugarcane mosaic virus).•Symptoms along with infection confirmation by serological test.•Incidence and severity of symptoms were higher in the field than greenhouse assay.•Broad-sense heritability at mean (62.18%) and individual (19.37%) level observed.•Twenty two genotypes were shown to be resistant to SCMV.
Mesenchymal stem cells are candidates for therapeutic strategies in periodontal repair due to their osteogenic potential. In this study, we identified epigenetic markers during osteogenic ...differentiation, taking advantage of the individual pattern of mesenchymal cells of the periodontal ligament with high (h-PDLCs) and low (l-PDLCs) osteogenic capacity. We found that the involvement of non-coding RNAs in the regulation of the RUNX2 gene is strongly associated with high osteogenic potential. Moreover, we evaluated miRs and genes that encode enzymes to process miRs and their biogenesis. Our data show the high expression of the XPO5 gene, and miRs 7 and 22 observed in the l-PDLCs might be involved in acquiring osteogenic potential, suppressing RUNX2 gene expression. Further, an inversely proportional correlation between lncRNAs (HOTAIR and HOTTIP) and RUNX2 gene expression was observed in both l- and h-PDLCs, and it was also related to the distinct osteogenic phenotypes. Thus, our results indicate the low expression of XPO5 in h-PDLC might be the limiting point for blocking the miRs biogenesis, allowing the high gene expression of RUNX2. In accordance, the low expression of miRs, HOTAIR, and HOTTIP could be a prerequisite for increased osteogenic potential in h-PDLCs. These results will help us to better understand the underlying mechanisms of osteogenesis, considering the heterogeneity in the osteogenic potential of PDLCs that might be related to a distinct transcriptional profile of lncRNAs and the biogenesis machinery.
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•Individual epigenetic profile significantly impacts the acquisition of the osteogenic phenotype.•Noncoding RNA suppresses Osteoblast differentiation of mesenchymal cells isolated from the periodontal ligament.•Individual transcriptional profile of XPO5, miRs and lncRNA as a potential marker of the osteogenic potential of human PDLC.•Bioinformatics approach to predict potential microRNAs involved in post-transcriptional control of RUNX2 and SP7 genes.
Cancer immunotherapies provide survival benefits in responding patients, but many patients fail to respond. Identifying the biology of treatment response and resistance are a priority to optimize ...drug selection and improve patient outcomes. We performed transcriptomic and immune profiling on 158 tumor biopsies from melanoma patients treated with anti-PD-1 monotherapy (n = 63) or combined anti-PD-1 and anti-CTLA-4 (n = 57). These data identified activated T cell signatures and T cell populations in responders to both treatments. Further mass cytometry analysis identified an EOMES+CD69+CD45RO+ effector memory T cell phenotype that was significantly more abundant in responders to combined immunotherapy compared with non-responders (n = 18). The gene expression profile of this population was associated with longer progression-free survival in patients treated with single agent and greater tumor shrinkage in both treatments.
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•Activated T cell signatures/populations drive response to anti-PD-1-based therapies•EOMES+CD69+CD45RO+ effector memory T cells are associated with response•EOMES+CD69+CD45RO+ expression is associated with longer PFS and tumor shrinkage•Non-responders with TIL-hot tumors express other immune drug targets
Gide et al. characterize melanoma samples from patients treated with anti-PD-1 alone or with anti-CTLA-4. Tumors from non-responders to monotherapy often express other immune checkpoints and higher gene expression profile of EOMES+CD69+CD45RO+ T cells is associated with greater tumor shrinkage in both therapies.
Summary Background Based on observational studies, administration of surgical antimicrobial prophylaxis (SAP) for the prevention of surgical site infection (SSI) is recommended within 60 min before ...incision. However, the precise optimum timing is unknown. This trial compared early versus late administration of SAP before surgery. Methods In this phase 3 randomised controlled superiority trial, we included general surgery adult inpatients (age ≥18 years) at two Swiss hospitals in Basel and Aarau. Patients were randomised centrally and stratified by hospital according to a pre-existing computer-generated list in a 1:1 ratio to receive SAP early in the anaesthesia room or late in the operating room. Patients and the outcome assessment team were blinded to group assignment. SAP consisted of single-shot, intravenous infusion of 1·5 g of cefuroxime, a commonly used cephalosporin with a short half-life, over 2–5 min (combined with 500 mg metronidazole in colorectal surgery). The primary endpoint was the occurrence of SSI within 30 days of surgery. The main analyses were by intention to treat. The trial is registered with ClinicalTrials.gov , number NCT01790529. Findings Between Feb 21, 2013, and Aug 3, 2015, 5580 patients were randomly assigned to receive SAP early (2798 patients) or late (2782 patients). 5175 patients (2589 in the early group and 2586 in the late group) were analysed. Median administration time was 42 min before incision in the early group (IQR 30–55) and 16 min before incision in the late group (IQR 10–25). Inpatient follow-up rate was 100% (5175 of 5175 patients); outpatient 30-day follow-up rate was 88·8% (4596 of 5175), with an overall SSI rate of 5·1% (234 of 4596). Early administration of SAP did not significantly reduce the risk of SSI compared with late administration (odds ratio 0·93, 95% CI 0·72–1·21, p=0·601). Interpretation Our findings do not support any narrowing of the 60-min window for the administration of a cephalosporin with a short half-life, thereby obviating the need for increasingly challenging SAP timing recommendations. Funding Swiss National Science Foundation, Hospital of Aarau, University of Basel, Gottfried und Julia Bangerter-Rhyner Foundation, Hippocrate Foundation, and Nora van Meeuwen-Häfliger Foundation.
Brain Long non-coding RNA (lncRNA) and microRNAs (miRs) play essential roles in the regulation of several important biological processes, including neuronal activity, cognitive processes, ...neurogenesis, angiogenesis, and neuroinflammation. In this context, the transcriptional repressor, RE1 silencing transcription factor (Rest), acts regulating the expression of neuronal genes as well as of lncRNAs and multiple miRNAs in the central nervous system. Nevertheless, its role in neuroinflammation was less explored. Here, we demonstrate, using an in vivo model of neuroinflammation induced by i.p. injection of LPS (0.33 mg/kg), that neuroinflammation increases gene expression of pro-inflammatory cytokines concomitant with the native and truncated forms of Rest and of non-coding RNAs. Additionally, the increased expression of enzymes Drosha ribonuclease III) (Drosha), Exportin 5 (Xpo5) and Endoribonuclease dicer (Dicer), associated with high expression of neuroprotective miRs 22 and 132 are indicative that the activation of biogenesis of miRs in the hippocampal region is a Central Nervous System (CNS) protective mechanism for the deleterious effects of neuroinflammation. Our results indicate that positive regulation of Rest gene expression in the hippocampal region by neuroinflammation correlates directly with the expression of miRs 22 and 132 and inversely with miR 335. In parallel, the confirmation of the possible alignment between the lncRNAs with miR 335 by bioinformatics corroborates with the sponge effect of Hottip and Hotair hybridizing and inhibiting the pro-inflammatory action of miR 335. This suggests the existence of a possible correlation between the activation of miR biogenesis machinery with increased expression of the transcription factor Rest, contributing to neuroprotection.
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•Involvement of ncRNAs in the neuroprotective response LPS-induced inflammation hippocampal.•Neuroinflammation activates the miRs biogenesis machinery in the hippocampus.•LPS-induced inflammation modulates miR22, 132 and 355 expressions in the hippocampus.•Hippocampal neuroinflammation modifies the transcriptional profile of lncRNA Hotair and Hottip.
The objective of this study was to determine whether curcumin and a commercial microencapsulated phytogenic supplement containing thymol, cinnamaldehyde and carvacrol in broiler chicken feed would ...improve health and meat quality (fatty acid profile), as well as to determine the coccidiostatic and bactericidal potential of the additives. The broiler chickens were divided into five groups: NC – negative control feed; PC – positive control; CU – with 50 mg/kg of curcumin, PHY – 100 mg/kg phytogenic; and PHY + CU, a combination of both additives at 50 mg/kg (curcumin) and 100 mg/kg (phytogenic). We observed significantly higher levels of total proteins associated with increased circulating globulins, as well as lower levels of uric acid, cholesterol and triglycerides in the PHY + CU group than in the NC. There were significantly fewer oocysts in birds supplemented with additives in the NC group on day 21; on day 35, the NC, PHY and PHY + CU groups had significantly lower counts than the PC and CU groups; however, at 44 days, the lowest counts were in PC group. The bacterial counts were significantly lower on day 21 in all groups that received additives than those of the control group; however, at 44 days, the bacterial and Escherichia coli counts in these groups were significantly higher than those of the control. Curcumin with or without phytogenic agent improved meat quality, with increased antioxidant levels and reduction of lipid peroxidation. There were significantly lower total saturated fatty acid levels and significantly greater monounsaturated/polyunsaturated fatty acid levels in broilers that consumed additives individually and in combination. The combination of additives significantly increased the crypt/villus ratio, a marker of improved intestinal health and performance. Additives potentiated their individual effects, suggesting they can replace conventional growth promoters without compromising health, intestinal mucosa or meat quality.
•Curcumin and microencapsulated phytogenics (carvacrol, thymol and cinnamaldehyde) in feed of broilers.•These components in diet favored the zootechnical performance and health of the birds.•This component in the diet also improved meat quality, highlighting the increase in unsaturated fatty acids.•Birds that ingested these herbal components had lower bacterial and coccidial load.
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