Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

Background: Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds of whole genome duplication events. Therefore, it has become possible to generate a high-quality genome sequence. Furthermore, cultivars exists that rival sugarcane in levels of stem sugar so that a genetic approach can be used to investigate which genes are differentially expressed to achieve high levels of stem sugar. Results: Here, we characterized the small RNA component of the transcriptome from grain and sweet sorghum stems, and from F2 plants derived from their cross that segregated for sugar content and flowering time. We found that variation in miR172 and miR395 expression correlated with flowering time whereas variation in miR169 expression correlated with sugar content in stems. Interestingly, genotypic differences in the ratio of miR395 to miR395* were identified, with miR395* species expressed as abundantly as miR395 in sweet sorghum but not in grain sorghum. Finally, we provided experimental evidence for previously annotated miRNAs detecting the expression of 25 miRNA families from the 27 known and discovered 9 new miRNAs candidates in the sorghum genome. Conclusions: Sequencing the small RNA component of sorghum stem tissue provides us with experimental evidence for previously predicted microRNAs in the sorghum genome and microRNAs with a potential role in stem sugar accumulation and flowering time

Microbial community structure of vineyard soils with different pH and copper content

The phospholipid fatty acid (PLFA) pattern of vineyard soils from the Northwest of the Iberian Peninsula was studied to identify soil factors determining the microbial community structure, with special emphasis on effects of Cu pollution and pH. A wide range of soil samples, collected from six winegrowing regions (Rías Baixas, Ribeiro, Ribeira Sacra, Monterrei, Valdeorras and Vinhos Verdes) was analyzed. Physico-chemical properties, including total Cu content, five different Cu fractions and available Cu, were also determined. Total Cu varied between 33 and 1120 mg kg1 and pHwater between 4.3 and 7.3. Soil pH rather than Cu content was most important in determining the composition of the microbial community. An increase in the relative concentrations of the monounsaturated PLFAs 16:1ω5, 16:1ω7c, 17:1ω8 and 18:1ω7 and a decrease of br18:0, i17:0, 17:0 and cy19:0 was correlated to an increase in pH. A significant effect of Cu was also found, with an increase in the branched fatty acids 10Me17:0, i16:0, 10Me18:0, a17:0 and br17:0 as consequence of Cu pollution. This change in the PLFA pattern was correlated to both the total and available fractions of Cu. Although the PLFA pattern was a useful tool to assess factors affecting the microbial composition, it is difficult to differentiate between these factors.Xunta de Galicia | Ref. 09MDS013291P

Variabilidad entre el ángulo de Clarke y el índice de Chippaux- Smirak para el diagnóstico de pie plano

[Abstract] Background: The measurements used in diagnosing biomechanical pathologies vary greatly. The aim of this study was to determine the concordance between Clarke's angle and Chippaux-Smirak index, and to determine the validity of Clarke's angle using the Chippaux-Smirak index as a reference. Methods: Observational study in a random population sample (n= 1,002) in A Coruña (Spain). After informed patient consent and ethical review approval, a study was conducted of anthropometric variables, Charlson comorbidity score, and podiatric examination (Clarke's angle and Chippaux-Smirak index). Descriptive analysis and multivariate logistic regression were performed. Results: The prevalence of flat feet, using a podoscope, was 19.0% for the left foot and 18.9% for the right foot, increasing with age. The prevalence of flat feet according to the Chippaux-Smirak index or Clarke's angle increases significantly, reaching 62.0% and 29.7% respectively. The concordance (kappa I) between the indices according to age groups varied between 0.25-0.33 (left foot) and 0.21-0.30 (right foot). The intraclass correlation coefficient (ICC) between the Chippaux-Smirak index and Clarke's angle was -0.445 (left foot) and -0.424 (right foot). After adjusting for age, body mass index (BMI), comorbidity score and gender, the only variable with an independent effect to predict discordance was the BMI (OR= 0.969; 95% CI: 0.940-0.998). Conclusion: There is little concordance between the indices studied for the purpose of diagnosing foot arch pathologies. In turn, Clarke's angle has a limited sensitivity in diagnosing flat feet, using the Chippaux-Smirak index as a reference. This discordance decreases with higher BMI values.[Resumen] Introducción: Existe una gran variabilidad en las mediciones para el diagnóstico de la patología biomecánica. El objetivo de este estudio fue determinar la concordancia entre el ángulo de Clarke y el índice de Chippaux-Smirak, para determinar la validez del ángulo de Clarke utilizando como referencia el índice de Chippaux-Smirak. Métodos: Se realizó un estudio observacional en una muestra aleatoriamente seleccionada (n= 1,002) en A Coruña (España). Tras el consentimiento informado del paciente y la aprobación del comité de ética, se estudiaron variables, antropométricas, índice de comorbilidad de Charlson y un examen podológico (ángulo de Clarke, índice de Chippaux-Smirak). Se realizó un estudio descriptivo y un análisis multivariado de regresión logística. Resultados: La prevalencia de pie plano utilizando el podoscopio fue de 19.0%(pie izquierdo) y 18.9%(pie derecho), incrementándose con la edad. La prevalencia de pie plano según el índice ChippauxSmirak o el ángulo de Clarke se incrementan considerablemente llegando a 62.0% y 29.7%. La concordancia (kappa I) entre los índices según grupos de edad oscila entre 0.25-0.33 (pie izquierdo) y 0.210.30 (pie derecho). El coeficiente de correlación intraclase (CCI) entre el índice de Chippaux-Smirak y el ángulo de Clarke es -0.445 (pie izquierdo) y 0.424 (pie derecho). Tras ajustar por edad, índice de masa corporal (IMC), score de comorbilidad y sexo la única variable con un efecto independiente para predecir discordancia es el IMC (OR= 0.969; IC 95%: 0.94-0.998). Conclusiones: La concordancia entre los índices estudiados para el diagnóstico de la patología del arco plantar es reducida. Existe a su vez una reducida sensibilidad del ángulo de Clarke para el diagnóstico de pie plano, utilizando como referencia el índice de Chippaux-Smirak. Esta discordancia disminuye con valores más altos de IMC

Clarithromycin Effect in Microbial Communities

Financiaciado para publicación en acceso aberto: Universidade de Vigo/CISUGA laboratory experiment was carried out to investigate the response of the microbial communities in acid agricultural soils located in the NW Iberian Peninsula to the presence of clarithromycin. Four soils, with different organic C content and similar pH, and seven different concentrations of clarithromycin (0.49, 1.95, 7.81, 31.25, 125, 500 and 2,000 mg kg−1 of soil) were used, and microbial estimates were made after 8 and 42 incubation days. The phospholipid fatty acids (PLFA) technique was used to estimate the total microbial biomass and biomass of specific microbial groups as well as the microbial community structure (PLFA pattern). The microbial biomass (total and specific groups) was different in the four studied soils, the lowest values being exhibited by soils with the lowest organic C. The antibiotic addition showed a positive effect on microbial biomass (total and specific groups), especially at the highest dose; the effect being similar or even more accentuated with time passed after the addition (42 days ≥8 days). Principal component analysis (PCA) of the PLFA data carried out with the whole data set showed that the main determining factors of the microbial structure followed the order: soil > time incubation ≥ antibiotic dose. When the PCA was performed individually for each incubation time, the results indicated that microbial communities of the four soils were different. Likewise, for each soil, different microbial communities were observed depending on antibiotic concentration. The microbial biomass and PLFA pattern data were coincidentally showing that the clarithromycin addition favored fungi and G− bacteria more that bacteria and G+ bacteria; the effect being dose-dependent. Our data (microbial biomass, PLFA pattern) also demonstrated that the effect of clarithromycin addition on microbial communities in these four acid agricultural soils persisted even after 42 incubation days.Xunta de Galicia | Ref. ED481B-2022-081Ministerio de Ciencia, Innovación y Universidades | Ref. RTI2018-099574-B-C21Ministerio de Ciencia, Innovación y Universidades | Ref. RTI2018-099574-B-C22Ministerio de Ciencia, Innovación y Universidades | Ref. FPU21/0420

A randomized clinical trial to determine the effectiveness of CO-oximetry and anti-smoking brief advice in a cohort of kidney transplant patients who smoke: study protocol for a randomized controlled trial

Randomized controlled trial[Abstract]Background: The cardiovascular risk in renal transplant patients is increased in patients who continue to smoke after transplantation. The aim of the study is to measure the effectiveness of exhaled carbon monoxide (CO) measurement plus brief advisory sessions, in comparison to brief advice, to reduce smoking exposure and smoking behavior in kidney transplant recipients who smoke. The effectiveness will be measured by: (1) abandonment of smoking, (2) increase in motivation to stop smoking, and (3) reduction in the number of cigarettes smoked per day. Design: a randomized, controlled, open clinical trial with blinded evaluation. Scope: A Coruña Hospital (Spain), reference to renal transplantation in the period 2012-2015. Inclusion criteria: renal transplant patients who smoke in the precontemplation, contemplation or preparation stages according to the Prochaska and DiClemente's Stages of Change model, and who give their consent to participate. Exclusion criteria: smokers attempting to stop smoking, patients with terminal illness or mental disability that prevents them from participating. Randomization: patients will be randomized to the control group (brief advisory session) or the intervention group (brief advisory session plus measuring exhaled CO). The sample target size is n = 112, with 56 patients in each group. Allowing for up to 10 % loss to follow-up, this would provide 80 % power to detect a 13 % difference in attempting to give up smoking outcomes at a two-tailed significance level of 5 %. Measurements: sociodemographic characteristics, cardiovascular risk factors, treatment, rejection episodes, infections, self-reported smoking habit, drug use, level of dependence (the Fagerström test), stage of change (Prochaska and DiClemente's Stages of Change model), and motivation to giving up smoking (the Richmond test). Response: the effectiveness will be evaluated every 3, 6, 9 and 12 months as: pattern of tobacco use (self-reported tobacco use), smoking cessation rates, carbon monoxide (CO) levels in exhaled air measured by CO-oximetry, urinary cotinine tests, nicotine dependence (Fagerström test), motivational stages of change (Prochaska and DiClemente's stages) and motivation to stop smoking (the Richmond test). Analysis: descriptive statistics and linear/logistic multiple regression models will be performed. Clinical relevance will be measured as relative risk reduction, absolute risk reduction and the number needed to treat. Ethics: informed consent of the patients and Ethical Review Board was obtained (code 2011/061). Discussion: Tobacco is a modifiable risk factor that increase the risk of morbidity and mortality in kidney transplant recipients. If effectiveness of CO-oximetry is confirmed to reduce tobacco exposure, we would have an intervention that is easy to use, low cost and with great implications about cardiovascular risk prevention in these patients.Instituto de Salud Carlos III; PI11/0135

Long-term results of heart transplant in recipients older and younger than 65 years: a comparative study of mortality, rejections, and neoplasia in a cohort of 445 patients

[Resumen] Background. Whether being older than 65 years should be considered an absolute counterindication to heart transplant (HT), as it is in some centers, is controversial. In our centre, patients older than 65 years are accepted for HT if they satisfy stringent conditions. The aim of this study was to examine whether heart recipients older than 65 years have a greater risk of rejection, neoplasia, or mortality than younger ones. Methods. We studied 445 patients who underwent HT between April 1991 and December 2003, 42 of whom were older than 65 years and 403 who were 65 years or younger. The parameters evaluated were the cumulative incidences of neoplasias and rejections (ISHLT grade ≥ 3A), and the survival rates 1 month, 1 year, and 5 years post-HT. Results. The two groups had similar percentages of patients with at least one rejection episode (≤65 years 56.9%, >65 years 51.3%; P > .05), and although there were proportionally almost twice as many tumors in the older group (14.2%) as in the younger (7.9%), this difference was not statistically significant either. Nor were there any significant differences in survival, the 1-month, 1-year, and 5-year rates being 87.8%, 82.1%, and 68.8%, respectively, in the younger group and 85.7%, 78.6%, and 73.4%, respectively, in the older. Conclusions. Among carefully selected patients aged more than 65 years, HT can be performed without incurring greater risk of rejection, malignancy, or death than is found among recipients younger than 65 years

CAR density influences antitumoral efficacy of BCMA CAR T cells and correlates with clinical outcome

Identification of new markers associated with long-term efficacy in patients treated with CAR T cells is a current medical need, particularly in diseases such as multiple myeloma. In this study, we address the impact of CAR density on the functionality of BCMA CAR T cells. Functional and transcriptional studies demonstrate that CAR T cells with high expression of the CAR construct show an increased tonic signaling with up-regulation of exhaustion markers and increased in vitro cytotoxicity but a decrease in in vivo BM infiltration. Characterization of gene regulatory networks using scRNA-seq identified regulons associated to activation and exhaustion up-regulated in CARHigh T cells, providing mechanistic insights behind differential functionality of these cells. Last, we demonstrate that patients treated with CAR T cell products enriched in CARHigh T cells show a significantly worse clinical response in several hematological malignancies. In summary, our work demonstrates that CAR density plays an important role in CAR T activity with notable impact on clinical response

Diagnosis delay and follow-up strategies in colorectal cancer. Prognosis implications: a study protocol

<p>Abstract</p> <p>Background</p> <p>Controversy exists with regard to the impact that the different components of diagnosis delay may have on the degree of invasion and prognosis in patients with colorectal cancer. The follow-up strategies after treatment also vary considerably. The aims of this study are: a) to determine if the symptoms-to-diagnosis interval and the treatment delay modify the survival of patients with colorectal cancer, and b) to determine if different follow-up strategies are associated with a higher survival rate.</p> <p>Methods/Design</p> <p>Multi-centre study with prospective follow-up in five regions in Spain (Galicia, Balearic Islands, Catalonia, Aragón and Valencia) during the period 2010-2012. Incident cases are included with anatomopathological confirmation of colorectal cancer (International Classification of Diseases 9th revision codes 153-154) that formed a part of a previous study (n = 953).</p> <p>At the time of diagnosis, each patient was given a structured interview. Their clinical records will be reviewed during the follow-up period in order to obtain information on the explorations and tests carried out after treatment, and the progress of these patients.</p> <p>Symptoms-to-diagnosis interval is defined as the time calculated from the diagnosis of cancer and the first symptoms attributed to cancer. Treatment delay is defined as the time elapsed between diagnosis and treatment. In non-metastatic patients treated with curative intention, information will be obtained during the follow-up period on consultations performed in the digestive, surgery and oncology departments, as well as the endoscopies, tumour markers and imaging procedures carried out.</p> <p>Local recurrence, development of metastases in the follow-up, appearance of a new tumour and mortality will be included as outcome variables.</p> <p>Actuarial survival analysis with Kaplan-Meier curves, Cox regression and competitive risk survival analysis will be performed.</p> <p>Discussion</p> <p>This study will make it possible to verify if the different components of delay have an impact on survival rate in colon cancer and rectal cancer. In consequence, this multi-centre study will be able to detect the variability present in the follow-up of patients with colorectal cancer, and if this variability modifies the prognosis. Ideally, this study could determine which follow-up strategies are associated with a better prognosis in colorectal cancer.</p