Local and systemic transcriptome and spliceome reprogramming induced by the root-knot nematode Meloidogyne incognita in tomato.

Root-knot nematodes (Meloidogyne spp.) are widely spread root parasites that infect thousands of vascular plant species. These highly polyphagous nematodes engage in sophisticated interactions with host plants that results in the formation of knot-like structures known as galls whose ontogeny remains largely unknown. Here, we determined transcriptome changes and alternative splicing variants induced by Megalaima incognita in galls and neighboring root cells at two distinct infective stages. M. incognita induced substantial transcriptome changes in tomato roots both locally in galls and systemically in neighboring cells. A considerable parallel regulation of gene expression in galls and neighboring cells were detected, indicative of effective intercellular communications exemplified by suppression of basal defense responses particularly during the early stage of infection. The transcriptome analysis also revealed that M. incognita exerts a tight control over the cell cycle process as a whole that results in an increase of ploidy levels in the feeding sites and accelerated mitotic activity of the gall cells. Alternative splicing analysis indicated that M. incognita significantly modulates pre-mRNA splicing as a total of 9064 differentially spliced events from 2898 genes were identified where intron retention and exon skipping events were largely suppressed. Furthermore, a number of differentially spliced events were functionally validated using transgenic hairy root system and found to impact gall formation and nematode egg mass production. Together, our data provide unprecedented insights into the transcriptome and spliceome reprogramming induced by M. incognita in tomato with respect to gall ontogeny and nematode parasitism.

Conceptual Framework of Epigenetic Analyses of Plant Responses to Sedentary Endoparasitic Nematodes.

Epigenetic modifications including miRNA regulation, DNA methylation, and histone modifications play fundamental roles in establishing the interactions between host plants and parasitic nematodes. Over the past decade, an increasing number of studies revealed the key functions of various components of the plant epigenome in the regulation of gene expression and shaping plant responses to nematode infection. In this chapter, we provide a conceptual framework for methods used to investigate epigenetic regulation during plant-nematode interactions. We focus specifically on current and emerging methods used to study miRNA regulation and function. We also highlight various methods and analytical tools used to profile DNA methylation patterns and histone modification marks at the genome level. Our intention is simply to explain the advantages of various methods and how to overcome some limitations. With rapid development of single-cell sequencing technology and genome editing, advanced and new methodologies are expected to emerge in the near future to further improve our understanding of epigenetic regulation and function during plant-nematode interactions.

Strain Echocardiographic Evaluation of Myocardial Involvement in Patients with Continuing Chest Pain after COVID-19 Infection. / Avaliação Ecocardiográfica com Strain do Envolvimento Miocárdico em Pacientes com Dor Torácica Contínua após Infecção por COVID-19.

BACKGROUND: A new clinical manifestation called post or long coronavirus disease (p/l COVID) has walked into our lives after the acute COVID-19 phase. P/l COVID may lead to myocardial injury with subsequent cardiac problems. Diagnosing these patients quickly and simply has become more important due to the increasing number of patients with p/l COVID. OBJECTIVES: We compared strain echocardiography (SE) parameters of patients who suffered from atypical chest pain and had sequel myocarditis findings on cardiac magnetic resonance (CMR). We aimed to investigate the value of SE for detection of myocardial involvement in patients with p/l COVID. METHODS: A total of 42 patients were enrolled. Our population was separated into two groups. The CMR(-) group (n = 21) had no myocardial sequelae on CMR, whereas the CMR(+) group had myocardial sequelae on CMR (n = 21). The predictive value of SE for myocarditis was also evaluated by age-adjusted multivariate analysis. P values < 0.05 were considered statistically significant. RESULTS: When compared with left ventricular ejection fraction (LVEF), global longitudinal strain (GLS) and global circumferential strain (GCS) had a stronger relationship (LVEF, p = 0.05; GLS, p < 0.001; GCS, p < 0.001) with p/l COVID associated myocardial involvement. GLS < 20.35 had 85.7% sensitivity and 81% specificity; GCS < 21.35 had 81% sensitivity and 81% specificity as diagnostic values for myocardial sequelae detected with CMR. While there was no difference between the groups in terms of inflammatory markers (C-reactive protein, p = 0.31), a difference was observed between biochemical markers, which are indicators of cardiac involvement (brain natriuretic peptide, p < 0.001). CONCLUSION: SE is more useful than traditional echocardiography for making diagnosis quickly and accurately in order not to delay treatment in the presence of myocardial involvement.

FUNDAMENTO: Tem surgido uma nova manifestação clínica chamada pós-COVID ou COVID longa (COVID p/l) após a fase aguda da COVID-19. COVID p/l pode levar à lesão miocárdica com problemas cardíacos subsequentes. Diagnosticar esses pacientes de forma rápida e simples é cada vez mais importante devido ao número crescente de pacientes com COVID p/l. OBJETIVOS: Comparamos os parâmetros de ecocardiografia com strain (ES) de pacientes que apresentaram dor torácica atípica e achados de sequelas de miocardite na ressonância magnética cardíaca (RMC). Nosso objetivo foi investigar o valor da ES para detecção de envolvimento miocárdico em pacientes com COVID p/l. MÉTODOS: Foram incluídos um total de 42 pacientes. Nossa população foi separada em 2 grupos. O grupo RMC(-) (n = 21) não apresentou sequelas miocárdicas na RMC, enquanto o grupo RMC(+) apresentou sequelas miocárdicas na RMC (n = 21). O valor preditivo da ES para miocardite também foi avaliado por análise multivariada ajustada por idade. Valores de p < 0,05 foram considerados estatisticamente significativos. RESULTADOS: Quando comparado com a fração de ejeção do ventrículo esquerdo (FEVE), o strain longitudinal global (SLG) e o strain circunferencial global (SCG) tiveram uma relação mais forte (FEVE, p = 0,05; SLG, p < 0,001; SCG, p < 0,001) com envolvimento miocárdico associado à COVID p/l. SLG < 20,35 apresentou sensibilidade de 85,7% e especificidade de 81%; SCG < 21,35 apresentou sensibilidade de 81% e especificidade de 81% como valores diagnósticos para sequelas miocárdicas detectadas com RMC. Enquanto não houve diferença entre os grupos quanto aos marcadores inflamatórios (proteína C-reativa, p = 0,31), houve diferença entre os marcadores bioquímicos, que são indicadores de envolvimento cardíaco (peptídeo natriurético cerebral, p < 0,001). CONCLUSÃO: A ES é mais útil do que a ecocardiografia tradicional para diagnosticar com rapidez e precisão, a fim de não atrasar o tratamento na presença de envolvimento miocárdico.

Avaliação Ecocardiográfica com Strain do Envolvimento Miocárdico em Pacientes com Dor Torácica Contínua após Infecção por COVID-19 / Strain Echocardiographic Evaluation of Myocardial Involvement in Patients with Continuing Chest Pain after COVID-19 Infection

Resumo Fundamento Tem surgido uma nova manifestação clínica chamada pós-COVID ou COVID longa (COVID p/l) após a fase aguda da COVID-19. COVID p/l pode levar à lesão miocárdica com problemas cardíacos subsequentes. Diagnosticar esses pacientes de forma rápida e simples é cada vez mais importante devido ao número crescente de pacientes com COVID p/l. Objetivos Comparamos os parâmetros de ecocardiografia com strain (ES) de pacientes que apresentaram dor torácica atípica e achados de sequelas de miocardite na ressonância magnética cardíaca (RMC). Nosso objetivo foi investigar o valor da ES para detecção de envolvimento miocárdico em pacientes com COVID p/l. Métodos Foram incluídos um total de 42 pacientes. Nossa população foi separada em 2 grupos. O grupo RMC(-) (n = 21) não apresentou sequelas miocárdicas na RMC, enquanto o grupo RMC(+) apresentou sequelas miocárdicas na RMC (n = 21). O valor preditivo da ES para miocardite também foi avaliado por análise multivariada ajustada por idade. Valores de p < 0,05 foram considerados estatisticamente significativos. Resultados Quando comparado com a fração de ejeção do ventrículo esquerdo (FEVE), o strain longitudinal global (SLG) e o strain circunferencial global (SCG) tiveram uma relação mais forte (FEVE, p = 0,05; SLG, p < 0,001; SCG, p < 0,001) com envolvimento miocárdico associado à COVID p/l. SLG < 20,35 apresentou sensibilidade de 85,7% e especificidade de 81%; SCG < 21,35 apresentou sensibilidade de 81% e especificidade de 81% como valores diagnósticos para sequelas miocárdicas detectadas com RMC. Enquanto não houve diferença entre os grupos quanto aos marcadores inflamatórios (proteína C-reativa, p = 0,31), houve diferença entre os marcadores bioquímicos, que são indicadores de envolvimento cardíaco (peptídeo natriurético cerebral, p < 0,001). Conclusão A ES é mais útil do que a ecocardiografia tradicional para diagnosticar com rapidez e precisão, a fim de não atrasar o tratamento na presença de envolvimento miocárdico.

Abstract Background A new clinical manifestation called post or long coronavirus disease (p/l COVID) has walked into our lives after the acute COVID-19 phase. P/l COVID may lead to myocardial injury with subsequent cardiac problems. Diagnosing these patients quickly and simply has become more important due to the increasing number of patients with p/l COVID. Objectives We compared strain echocardiography (SE) parameters of patients who suffered from atypical chest pain and had sequel myocarditis findings on cardiac magnetic resonance (CMR). We aimed to investigate the value of SE for detection of myocardial involvement in patients with p/l COVID. Methods A total of 42 patients were enrolled. Our population was separated into two groups. The CMR(-) group (n = 21) had no myocardial sequelae on CMR, whereas the CMR(+) group had myocardial sequelae on CMR (n = 21). The predictive value of SE for myocarditis was also evaluated by age-adjusted multivariate analysis. P values < 0.05 were considered statistically significant. Results When compared with left ventricular ejection fraction (LVEF), global longitudinal strain (GLS) and global circumferential strain (GCS) had a stronger relationship (LVEF, p = 0.05; GLS, p < 0.001; GCS, p < 0.001) with p/l COVID associated myocardial involvement. GLS < 20.35 had 85.7% sensitivity and 81% specificity; GCS < 21.35 had 81% sensitivity and 81% specificity as diagnostic values for myocardial sequelae detected with CMR. While there was no difference between the groups in terms of inflammatory markers (C-reactive protein, p = 0.31), a difference was observed between biochemical markers, which are indicators of cardiac involvement (brain natriuretic peptide, p < 0.001). Conclusion SE is more useful than traditional echocardiography for making diagnosis quickly and accurately in order not to delay treatment in the presence of myocardial involvement.

The Value of Carotid Intima-Media Thickness in the Detection of Atherosclerosis in HIV (+) Patients Subclinical Atherosclerosis in HIV (+).

BACKGROUND:  To evaluate the role of the traditional risk scoring system (TRSS) in detecting subclinical atherosclerosis in HIV (+) patients. STUDY DESIGN: Cohort study. PLACE AND DURATION OF STUDY: Infectious Diseases Clinic, Izmir Katip Çelebi University, Atatürk Training and Research Hospital, from March 2017 to January 2018. METHODOLOGY: The patient group was formed with 52 HIV (+) patients, aged 18-60 years, and a control group was formed with 52 HIV (-) healthy volunteers. For all groups, there was no comorbid diseases or family history. Diabetes mellitus, hypertension, chronic kidney disease and cardiovascular disease were excluded from the two groups. Carotid intima-media thickness (CIMT) measurements were performed with high resolution B mode Doppler USG and patients with subclinical atherosclerosis were identified by the presence of atheroma plaque. RESULTS: The median right CIMT measurement was 0.91 (0.73-0.97) mm and the median left CIMT was 0.90 (0.73-0.98) mm in HIV (+) patients. The median values of CIMT on right and left sides in the control group were 0.77 (0.67-0.81) mm and 0.76 (0.70-0.81) mm. Atheroma plaque was detected in 13.5% of the HIV (+) patients and in none of the control group. Subclinical atherosclerosis was found in 51.9% of HIV (+) patients and this rate was 7.7% in the HIV (-) group (p<0.001). There was a weak correlation between CIMT and TRSS. CONCLUSION: In this study, the scoring systems (Framingham, ACC/AHA CVHRS) that determine the risk of cardiovascular disease recommended in current practice and the results of CIMT measurements were not found to be compatible. The development of new scoring systems including CIMT testing for the determination of this risk will open important new horizons. Key Words: AIDS, Cardiovascular disease, Subclinical atherosclerosis, CIMT.

Three-Dimensional Soft-Tissue Evaluation in Patients with Cleft Lip and Palate.

BACKGROUND In cleft lip and palate (CLP) patients, the shape of the facial soft tissues shows variety in 3 dimensions (3D). Two-dimensional (2D) photographs and radiographs are insufficient in the examination of these anomalies. The aim of this retrospective study was to examine the soft tissue and craniofacial characteristics of individuals with nonsyndromic unilateral cleft lip and palate (UCLP), bilateral cleft lip and palate (BCLP), skeletal Class III malocclusions, or skeletal Class I malocclusions using 3D facial imaging. MATERIAL AND METHODS The entire study group consisted of a total of 158 patients, aged 8-32 years: 29 of the patients had UCLP, 22 BCLP, 54 had skeletal Class III malocclusions, and 53 had skeletal Class I malocclusions. 3D stereophotogrammetric soft-tissue recordings of all patients were analyzed. ANOVA and the Kruskal-Wallis test were performed to compare the groups. RESULTS Statistically significant differences were observed among the groups in terms of linear, angular, proportional. and volumetric measurements. While nasal differences were not observed in the Class III group, nose and upper-lip deformities were common in the CLP groups. Upper-lip projection was reduced in all 3 groups. In the Class III patients, the lower lip and chin were more prominent than in the other groups. The facial convexity angle was increased in the CLP and Class III groups. The upper-lip volume was decreased in the BCLP, the UCLP, and the Class III groups. CONCLUSIONS Patients with skeletal Class III or CLP anomalies showed significantly different soft-tissue characteristics than the Class I control group. 3D stereophotogrammetric facial imaging is an easy and noninvasive method that can be used in examination and recording of these facial deformities. It is possible to make volumetric measurements using this method.

Effects of low-dose doxycycline and bisphosphonate clodronate on alveolar bone loss and gingival levels of matrix metalloproteinase-9 and interleukin-1ß in rats with diabetes: a histomorphometric and immunohistochemical study.

BACKGROUND: Bisphosphonates (BPs) and low-dose doxycycline (LDD) have been shown to inhibit bone resorption and to improve the levels of proinflammatory mediators and destructive enzymes in gingival tissues, respectively. The purpose of this study is to evaluate the effect of mono and combined BP clodronate and LDD therapies in reducing gingival levels of matrix metalloproteinase-9 (MMP-9), interleukin-1ß (IL-1ß), and alveolar bone loss in rats with diabetes. METHODS: Fifty adult Wistar rats were divided into five study groups as follows: 1) group 1 = diabetes control; 2) group 2 = diabetes + periodontitis; 3) group 3 = diabetes + periodontitis + LDD; 4) group 4 = diabetes + periodontitis + clodronate; and 5) group 5 = diabetes + periodontitis + LDD + clodronate. LDD and clodronate were given as a single agent or as combination therapy during the 7 days of the post-experimental periodontitis period. On day 7, the rats were sacrificed, the mobility of the tooth was recorded, and block biopsies were removed. The gingival tissues were analyzed histologically and immunohistochemically for expression of MMP-9 and IL-1ß. Alveolar bone loss was evaluated morphometrically under a light microscope. Data analysis was performed statistically by Kruskal-Wallis and post hoc Tukey and Spearman correlation tests. RESULTS: Alveolar bone loss was significantly greater in groups 2 through 5 than group 1 (P <0.05) but was not significantly different among groups 2 through 5 (P >0.05). Animals with periodontitis (group 2) expressed significantly higher levels of MMP-9 and IL-1ß compared with those without periodontitis (group 1) (P <0.05). MMP-9 expression was significantly lower in group 3 than groups 1, 2, and 5 (P <0.05). IL-1ß expression was significantly lower in the groups 1, 3, 4, and 5 than 2 (P <0.01) but was not significantly different among groups 1, 3, 4, and 5. Positive correlations were found between alveolar bone loss and density of inflammation (ρ = 0.319, P = 0.021) and between MMP-9 and IL-1ß (ρ = 0.418, P = 0.002), respectively. CONCLUSION: Our findings suggest that ligature-induced periodontitis in animals with diabetes results in significantly higher levels of MMP-9 and IL-1ß expression in gingiva. The use of mono and combined clodronate and LDD administrations may significantly reduce levels of MMP-9 and IL-1ß expression. However, drug administration did not affect alveolar bone levels during the study period.

Double-application of platelet-rich plasma on bone healing in rabbits.

OBJECTIVE: Platelet-rich plasma (PRP) is considered to enhance bone formation especially at early stages of wound healing, depending on the limited and short life-span of platelets and growth factors. The aim of this study was to evaluate efficacy of double-application of PRP (DA-PRP) on bone healing in a rabbit calvarial defect model. STUDY DESIGN: Twenty-eight rabbits, each had two surgically prepared calvarial bone defects (10mm diameter), were included in this study and randomly divided into six groups. Defects (n=56) were treated with single-application of PRP (SA-PRP)(n=10), SA-PRP and beta-tricalciumphosphate (SA-PRP+TCP)(n=10), DA-PRP (n=8), DA-PRP and beta-tricalciumphosphate (DA-PRP+TCP)(n=8), beta-tricalciumphosphate (TCP)(n=10) or left empty (Control)(n=10). Animals were sacrificed at 30 days postoperatively. RESULTS: The new bone (NB%) and defect fill (DF%) percentages were calculated from histological slides by image-analyzer software and statistically analysed. All test groups showed higher NB% than control, but differences among all groups were insignificant. The TCP treated groups had significantly higher DF% than groups treated without TCP, however the DF% differences between control, SA-PRP and DA-PRP or TCP, SA-PRP+TCP or DA-PRP+TCP were insignificant. CONCLUSION: Although new bone formation was histomorphologically remarkable at double-application PRP groups, statistical analyses of the histomorphometric data revealed no significant difference.