Selection of a CTAB protocol for high-quality DNA extraction in Oryza sativa L. validated for application in genotyping process based on Illumina sequencing

Pérez-Pazos Jazmin Vanessa,Romero-Ferrer Jorge Luis,Berdugo-Cely Jhon A. 한국작물학회 2023 Journal of crop science and biotechnology Vol.26 No.4

Rice genotypes with possible tolerance to biotic and abiotic stresses are interested in genomic studies for their use in breeding programs. Colombian Plant Germplasm Bank (CPGB) has preserved local rice genotypes without genomic analysis yet. Considering the need to develop genomic studies with these genotypes and minimize costs in the genotyping process, in this research, fve CTAB DNA extraction protocols (P1-P5) were evaluated and compared with a commercial kit. Four local rice accessions from the CPGB were used, and DNA concentration (fuorescence and absorbance), quality (absorbance, integrity, and enzymatic digestion), and cost analysis were determined. A selection index (SI) was established to choose the best DNA protocol. Finally, the selected protocol was validated in 14 local rice genotypes through Illumina sequencing. The six evaluated DNA extraction protocols presented signifcant diferences in quantifcation and quality variables. From the SI established, the protocol selected was the P4 (SI=147.7); this protocol allows obtaining DNA with high concentrations and quality levels at a 50% lower cost than the commercial kit. The sequences generated from the DNA obtained with the P4 protocol presented 7 million reads with high levels of quality (Q30) and length (>50 pb) per evaluated accession; On average, 98.9% of these sequences mapped to the rice genome and identifed up to 15,436 SNP markers without missing data. These results confrm that the DNA from rice local genotypes obtained with the P4 CTAB protocol has the requirements for routine use in genomic studies based on genotyping processes that require Illumina sequencing.

Relationship Between Psychological Factors and Pain Intensity in Temporomandibular Disorders with or without Central Sensitization: A Cross-Sectional Observational Study Using Multiple Regression Analysis

Pérez Sebastián Eustaquio Martín,Pérez Sebastián Eustaquio Martín,Córdova José Andrés Díaz,Cortés Leidy Milena Posada 대한안면통증∙구강내과학회 2023 Journal of Oral Medicine and Pain Vol.48 No.3

Purpose: To quantify the relationship between perceived pain intensity and psychological variables in a sample of participants with temporomandibular disorder, with or without central sensitization (CS). Methods: A cross-sectional study with nonprobability convenience sampling was conducted from January 1, 2022, to June 30, 2023. Pain intensity (Numeric Pain Rating Scale), anxiety (State-Trait Anxiety Questionnaire, STAI), catastrophizing (Pain Catastrophizing Scale, PCS), perceived stress (Perceived Stress Scale, PSS), and sleep quality (Pittsburgh Sleep Quality Index, PSQI) were assessed. Statistical analysis was performed using IBM SPSS Statistics for Windows, Version 20.0 (IBM Co.), which included descriptive and normality analyses and the calculation of strength of multiple correlational regression. Results: A total of 52 (n=34 female 65.4%; n=18 male 34.6%) subjects with diagnosis of temporomandibular disorders (TMD) were finally included. A total of 26 participants (n=26, 50.0%) were cases suffered from CS (TMD-CS mean=46.62±11.24) while the remaining participants (n=26, 50.0%) were the controls (TMD-nCS mean=26.77, standard deviation [SD]=8.42). The pain intensity was moderate in both groups TMDCS (mean=7.62, SD=0.83) and TMD-nCS (mean=7.05, SD=0.86), anxiety (TMD-CS STAI mean=53.27, SD=11.54; TMD-nCS STAI mean=49, SD=11.55), catastrophizing (TMD-CS PCS mean=46.27, SD=9.75; TMD-nCS PCS mean=26.69, SD=4.97), perceived stress (TMDCS PSS mean=30.35, SD=4.91; TMD-nCS PSS mean=26.12, SD=6.60) and sleep quality (TMD-CS PSQI mean=15.81, SD=3.65; TMD-nCS PSQI mean=12.77, SD=2.76) levels were measured in both groups. In TMD-CS and TMD-nCS, higher anxiety levels were moderately and significantly associated with greater pain intensity β=0.4467 (t=2.477, p=0.021) and β=0.5087 (t=2.672, p=0.014). Nevertheless, catastrophizing, perceived stress and sleep quality were not associated to pain intensity in neither of group. Conclusions: In both TMD-CS and TMD-nCS patients, elevated anxiety levels were moderately and significantly associated with increased pain intensity. However, heightened levels of pain catastrophizing, perceived stress, and poor sleep quality were not significantly associated with increased pain intensity in either of the two analyzed groups.

Osteomyelitis: A Descriptive Study

Laura Prieto-Pérez,Ramón Pérez-Tanoira,Elizabet Petkova-Saiz,Concepción Pérez-Jorge,Cristina Lopez-Rodriguez,Beatriz Alvarez-Alvarez,Jorge Polo-Sabau,Jaime Esteban 대한정형외과학회 2014 Clinics in Orthopedic Surgery Vol.6 No.1

Background: To analyze the incidence and clinical-microbiological characteristics of osteomyelitis (OM) in a tertiary Spanish hospital. Methods: All cases diagnosed with OM between January 2007 and December 2010 were retrospectively reviewed. The variablesexamined include epidemiological characteristics, risk factors, affected bone, radiographic changes, histology, microbiological cultureresults, antibiotic treatment, and the need for surgery. Results: Sixty-three cases of OM were diagnosed. Twenty-six patients (41.3%) had acute OM whereas 37 patients (58.7%) wereclassified as chronic OM. OM may result from haematogenous or contiguous microbial seeding. In this group, 49 patients (77.8%)presented with OM secondary to a contiguous source of infection and 14 patients had hematogenous OM (22.2%). Staphylococcusaureus was the most commonly found microorganism. Conclusions: OM mainly affected patients with risk factors related to the presence of vascular diseases. Antibiotic treatmentmust be guided by susceptibility patterns of individual microorganisms, although it must be performed together with surgery inmost of the cases.

Acute Effects of Turmeric Extracts on Knee Joint Pain: A Pilot, Randomized Controlled Trial

Lorena Calderón-Pérez,Elisabet Llauradó,Judit Companys,Laura Pla-Pagà,Noemí Boqué,Francesc Puiggrós,Rosa-M Valls,Anna Pedret,Josep Manuel Llabrés,Lluís Arola,Rosa Solà 한국식품영양과학회 2021 Journal of medicinal food Vol.24 No.4

Turmeric extracts (TEs) have been shown to be suitable as a pain treatment for human joint arthritis. In a pilot, randomized clinical trial, 68 individuals with mild/moderate knee joint pain (KJP) consumed a new formulation of water-soluble TEs and insoluble curcuminoids (B-Turmactive®) or brewer's yeast as a placebo for 1 week. Our hypothesis was that B-Turmactive would have a short-term analgesic effect on KJP measured by the self-reported Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). After 3 days and 1 week, both treatments reduced pain when walking on a flat surface (P < .01), going up or down stairs (P < .001), and sitting or lying (P < .05), but only B-Turmactive reduced pain at night while in bed and in an upright standing position (P < .01). Concerning global KJP, it was reduced by both treatments after 3 days and 1 week of the intervention (P < .001), being less with B-Turmactive after 1 week (P = .012 vs. 3 weeks). Although no intertreatment differences were observed, only B-Turmactive decreased high-sensitivity C-reactive protein levels (P = .045) at 1 week, which indicates a prompt analgesic effect mediated by a decrease in inflammatory status.

The Phospholipid Linoleoylglycerophosphocholine as a Biomarker of Directly Measured Insulin Resistance

Maria Camila Pérez-Matos,Martha Catalina Morales-Álvarez,Freddy Jean Karlo Toloza,Maria Laura Ricardo-Silgado,Jose Oscar Mantilla-Rivas,Jairo Arturo Pinzón-Cortes,Maritza Perez-Mayorga,Elizabeth Jimén 대한당뇨병학회 2017 Diabetes and Metabolism Journal Vol.41 No.6

Background: Plasma concentrations of some lysophospholipids correlate with metabolic alterations in humans, but their potential as biomarkers of insulin resistance (IR) is insufficiently known. We aimed to explore the association between plasma linoleoylglycerophosphocholine (LGPC) and objective measures of IR in adults with different metabolic profiles. Methods: We studied 62 men and women, ages 30 to 69 years, (29% normal weight, 59% overweight, 12% obese). Participants underwent a 5-point oral glucose tolerance test (5p-OGTT) from which we calculated multiple indices of IR and insulin secretion. Fifteen participants additionally underwent a hyperinsulinemic-euglycemic clamp for estimation of insulin-stimulated glucose disposal. Plasma LGPC was determined using high performance liquid chromatography/time-of-flight mass spectrometry. Plasma LGPC was compared across quartiles defined by the IR indices. Results: Mean LGPC was 15.4±7.6 ng/mL in women and 14.1±7.3 ng/mL in men. LGPC did not correlate with body mass index, percent body fat, waist circumference, blood pressure, glycosylated hemoglobin, log-triglycerides, or high density lipoprotein cholesterol. Plasma LGPC concentrations was not systematically associated with any of the studied 5p-OGTT-derived IR indices. However, LGPC exhibited a significant negative correlation with glucose disposal in the clamp (Spearman r=–0.56, P=0.029). Despite not being diabetic, participants with higher plasma LGPC exhibited significantly higher post-challenge plasma glucose excursions in the 5p-OGTT (P trend=0.021 for the increase in glucose area under the curve across quartiles of plasma LGPC). Conclusion: In our sample of Latino adults without known diabetes, LGPC showed potential as a biomarker of IR and impaired glucose metabolism.

Anti-inflammatory and utero-relaxant effect of α-bisabolol on the pregnant human uterus

Victor Manuel Muñoz-Pérez,Mario I. Ortiz,Héctor A. Ponce-Monter,Vicente Monter-Pérez,Guillermo Barragán-Ramírez 대한약리학회 2018 The Korean Journal of Physiology & Pharmacology Vol.22 No.4

The aim of this study was to evaluate the in vitro anti-inflammatory and utero-relaxant effect of α-bisabolol on the pregnant human myometrium. Samples from the pregnant human myometrium were used in functional tests to evaluate the inhibitory effect of α-bisabolol (560, 860, 1,200 and 1,860 µM) on spontaneous myometrial contractions. The intracellular cyclic adenosine monophosphate (cAMP) levels generated in response to α-bisabolol in human myometrial homogenates were measured by ELISA. The anti-inflammatory effect of α-bisabolol was determined through the measurement of two pro-inflammatory cytokines, tumor necrosis factor-α (TNFα) and interleukin (IL)-1β, and the anti-inflammatory cytokine IL-10, in pregnant human myometrial explants stimulated with lipopolysaccharide (LPS). Forskolin was used as a positive control to evaluate the cAMP and cytokine levels. α-Bisabolol was found to induce a significant inhibition of spontaneous myometrial contractions at the highest concentration level (p<0.05). α-Bisabolol caused a concentration-dependent decrease in myometrial cAMP levels (p<0.05) and a concentration-dependent decrease in LPS-induced TNFα and IL-1β production, while IL-10 production did not increase significantly (p>0.05). The anti-inflammatory and utero-relaxant effects induced by α-bisabolol were not associated with an increase in cAMP levels in pregnant human myometrial samples. These properties place α-bisabolol as a potentially safe and effective adjuvant agent in cases of preterm birth, an area of pharmacological treatment that requires urgent improvement.

Body fat composition and miR-378 expression profiling in patients with type 1 diabetes

Lissette Duarte,Diego F. García-Díaz,Francisco Pérez-Bravo 대한소아내분비학회 2020 Annals of Pediatirc Endocrinology & Metabolism Vol.25 No.2

Purpose: Type 1 diabetes (T1D) is an autoimmune disease that involves genetic, epigenetic, and environmental factors. Change in body composition is a potential mechanism for explaining the increased incidence of T1D. Micro RNA-378 (miRNA-378) is a positive regulator of adipogenesis that has yet to be studied in such patients. This study aims to evaluate the miRNA-378 expression profile in peripheral mononuclear cells of T1D patients and controls and to determine its possible association with levels of body fat, interleukin-6 (IL-6), and tumor necrosis factor alpha (TNF-α). Methods: Twenty-four T1D subjects and 20 controls under 18 years of age without autoimmune diseases were studied. miRNA-378 expression profile was determined by TaqMan probes. Body composition was determined by multifrequency bioimpedance. IL-6 and TNF-α serum levels were determined by LUMINEX. Anti-GAD65, anti-IA2, and anti-ZnT8 antibodies were quantified in serum by enzyme immunoassays. Statistical significance was considered P<0.05. Results: Similar body mass index and body fat (kg) were observed between the T1D and control subjects (P=0.55 and P=0.69, respectively). The miRNA-378 expression profile was significantly higher in T1D patients compared with the controls (P<0.05). Lower miRNA-378 expression in prepubertal controls was observed compared to pubertal controls, prepubertal T1D, and pubertal T1D (P<0.05). AntiGAD65, AntilA2, and AntiZnT8 were positively correlated with miRNA-378 (P=0.002, P=0.053, and P=0.007). No statistically significant correlation was observed between miRNA-378 expression and IL-6, TNF-α, or body fat. Conclusion: Elevated miRNA-378 expression in T1D patients compared with controls is linked to pubertal stage but is not associated with proinflammatory status or body composition.

Understanding a Core Pilin of the Type IVa Pili of Acidithiobacillus thiooxidans, PilV

( Araceli Hernández-sánchez ),( Edgar D. Páez-pérez ),( Elvia Alfaro-saldaña ),( Vanesa Olivares-illana ),( J. Viridiana García-meza ) 한국미생물생명공학회 2024 Journal of microbiology and biotechnology Vol.34 No.3

Pilins are protein subunits of pili. The pilins of type IV pili (T4P) in pathogenic bacteria are well characterized, but anything is known about the T4P proteins in acidophilic chemolithoautotrophic microorganisms such as the genus Acidithiobacillus. The interest in T4P of A. thiooxidans is because of their possible role in cell recruitment and bacterial aggregation on the surface of minerals during biooxidation of sulfide minerals. In this study we present a successful ad hoc methodology for the heterologous expression and purification of extracellular proteins such as the minor pilin PilV of the T4P of A. thiooxidans, a pilin exposed to extreme conditions of acidity and high oxidation-reduction potentials, and that interact with metal sulfides in an environment rich in dissolved minerals. Once obtained, the model structure of A. thiooxidans PilV revealed the core basic architecture of T4P pilins. Because of the acidophilic condition, we carried out in silico characterization of the protonation status of acidic and basic residues of PilV in order to calculate the ionization state at specific pH values and evaluated their pH stability. Further biophysical characterization was done using UV-visible and fluorescence spectroscopy and the results showed that PilV remains soluble and stable even after exposure to significant changes of pH. PilV has a unique amino acid composition that exhibits acid stability, with significant biotechnology implications such as biooxidation of sulfide minerals. The biophysics profiles of PilV open new paradigms about resilient proteins and stimulate the study of other pilins from extremophiles.

De Novo San Luis Valley Syndrome-like der(8) Chromosome With a Concomitant dup(8p22) in a Mexican Girl

Alma Laura Sánchez-Casillas,Horacio Rivera,Anna Gabriela Castro-Martínez,José Elías García-Ortiz,Carlos Córdova-Fletes,Paul Mendoza-Pérez 대한진단검사의학회 2017 Annals of Laboratory Medicine Vol.37 No.1

Dear Editor, The rec(8)dup(8q)inv(8)(p23.1q22.1) chromosome associated with San Luis Valley Syndrome (SLVS OMIM 179613) is usually diagnosed in Hispanic patients from the USA Southwest where a founder carrier Spaniard lived around 1800 [1, 2]. This rec(8) has an 8q duplication of 47.90 Mb and an 8p deletion of 11.65 Mb [3, 4]. Excluding two de novo rec(8)dup q chromosomes characterized only by G-bands and included in a recent compilation [5], cytogenomic analyses identified nine comparable de novo der(8)dup q/del p chromosomes with or without a simultaneous 8p gain. We describe a Mexican mestizo girl with a de novo SLVS-like der(8) but with a concomitant 8p22p23.1 duplication.

Splenic myeloid metaplasia in warm autoimmune hemolytic anemia (wAIHA): a retrospective study

Víctor Manuel Anguiano-Álvarez,Alonso Hernández-Company,Nashla Hamdan-Pérez,Daniel Montante-M,Diego A. Zúñiga-Tamayo,Sergio Rodríguez-Rodríguez,Alan Pomerantz,Elena J. Tuna-Aguilar 대한혈액학회 2018 Blood Research Vol.53 No.1

BackgroundSplenic myeloid metaplasia (SMM) is a kind of extramedullary hematopoiesis, whereasits clinical significance in wAIHA remains unclear. The aim of this study is evaluating thefrequency and clinical characteristics of SMM, compared with splenic-congestion (SC). MethodsWe included patients with wAIHA treated in a Mexican tertiary hospital between January1992 and December 2015. All patients received steroids as first-line treatment and splenectomyas second-line treatment. ResultsAmong the thirty-six splenectomized patients, 15 (41.6%) and 21 (58.4%) were diagnosedas SMM and SC, respectively. No differences were found in clinical characteristicsbetween two groups. SMM patients showed lower platelet count (147×109/L vs. 240×109/L, P=0.02) and higher presence of anti-dsDNA antibodies (40% vs. 4.7%,P=0.01) than SC patients. Although the complete response (CR) rate with first-line treatmentwas lower in SMM patients (13.3% vs. 47.6%; P=0.04), post-splenectomy mediandisease-free-survival (DFS) was longer (16.2 mo vs. 5.1 mo; P=0.19). Univariate/multivariateanalysis showed that achieving CR during first-line treatment (OR 0.3, 95% CI:0.03‒0.94, P=0.03) and higher platelet count (OR 0.99, 95% CI: 0.98‒0.99, P=0.03)were protective factors for SMM; and anti-dsDNA titer higher than 9.6 IU/dL was a riskfactor for SMM (OR 2.76, 95% CI: 1.48‒5.14, P<0.001). ConclusionThe wAIHA patients with SMM have different biological profiles with those without SMM. This study is the first trial evaluating the significance of histopathological spleen findingsand their association with rheumatologic profile.