Technological advances involving RNA-Seq and Bioinformatics allow quantifying the transcriptional levels of genes in cells, tissues, and cell lines, permitting the identification of Differentially ...Expressed Genes (DEGs). DESeq2 and edgeR are well-established computational tools used for this purpose and they are based upon generalized linear models (GLMs) that consider only fixed effects in modeling. However, the inclusion of random effects reduces the risk of missing potential DEGs that may be essential in the context of the biological phenomenon under investigation. The generalized linear mixed models (GLMM) can be used to include both effects.
We present DEGRE (Differentially Expressed Genes with Random Effects), a user-friendly tool capable of inferring DEGs where fixed and random effects on individuals are considered in the experimental design of RNA-Seq research. DEGRE preprocesses the raw matrices before fitting GLMMs on the genes and the derived regression coefficients are analyzed using the Wald statistical test. DEGRE offers the Benjamini-Hochberg or Bonferroni techniques for
-value adjustment.
The datasets used for DEGRE assessment were simulated with known identification of DEGs. These have fixed effects, and the random effects were estimated and inserted to measure the impact of experimental designs with high biological variability. For DEGs' inference, preprocessing effectively prepares the data and retains overdispersed genes. The biological coefficient of variation is inferred from the counting matrices to assess variability before and after the preprocessing. The DEGRE is computationally validated through its performance by the simulation of counting matrices, which have biological variability related to fixed and random effects. DEGRE also provides improved assessment measures for detecting DEGs in cases with higher biological variability. We show that the preprocessing established here effectively removes technical variation from those matrices. This tool also detects new potential candidate DEGs in the transcriptome data of patients with bipolar disorder, presenting a promising tool to detect more relevant genes.
DEGRE provides data preprocessing and applies GLMMs for DEGs' inference. The preprocessing allows efficient remotion of genes that could impact the inference. Also, the computational and biological validation of DEGRE has shown to be promising in identifying possible DEGs in experiments derived from complex experimental designs. This tool may help handle random effects on individuals in the inference of DEGs and presents a potential for discovering new interesting DEGs for further biological investigation.
Effective protocols for in vitro rooting for woody fruit trees are still a challenge for in vitro seedling production, especially when there is a need to insert new cultivars or rootstocks. These ...protocols are essential to accelerate studies in plant breeding programs and for seedling distribution. This study evaluated the use of 6-Benzylaminopurine (IBA) in in vitro rooting of Pyruscomunnis rootstocks, clones ‘OHxF87’ and Pyrodwarf. Explant exposure times (0, 24, 48, 72, and 96 hours) to 20 mg L-1 IBA were tested for in vitro rooting. The exposure to IBA resulted in rooting rates above 80%, surpassing some results reported in the literature. The 24-hour treatment provided 81,81% survival, leading to an average growth of five roots with 19 mm length, for ‘OHxF87’ rootstock. The same exposure time resulted in the highest survival rate (75%) and the highest mean root number, seven roots per plant with 10 mm length, for ‘PDW’ rootstock. Root formation did not occur in the absence of synthetic auxin. Therefore, it can be concluded that a 24-hour exposure at 20 mg L-1 IBA was sufficient to promote in vitro rooting in ‘OHxF87’ and Pyrodwarf rootstocks’.
RESUMO: Protocolos eficazes de enraizamento in vitro de frutíferas lenhosas ainda são um desafio para produção de mudas in vitro, especialmente quando há necessidade de inserção de novas cultivares ou porta-enxerto. Esses protocolos são essenciais para acelerar estudos nos programas de melhoramento genético e também para distribuição posterior das mudas. Nesse sentido, o objetivo deste estudo foi avaliar a utilização da 6-Benzilaminopurina no enraizamento in vitro de porta-enxerto Pirus comunnis, clones ‘OHxF87’ e Pyrodwarf. Para o enraizamento, foi testado o tempo de exposição dos explantes ao AIB. Para tanto, foram utilizados 20 mg L-1 do fitohormônio nas horas 0, 24, 48, 72 e 96 horas. A exposição ao AIB resultou em taxas de enraizamento acima de 80%, superando alguns resultados encontrados na literatura. Para o porta-enxerto ‘OHxF87’, o tratamento de 24 horas proporcionou 81,81% de sobrevivência, promovendo em média cinco raízes com comprimento de 19 mm. O mesmo tratamento para o porta-enxerto ‘PDW’ resultou na maior taxa de sobrevivência (75%), bem como no maior número médio de raízes, sete raízes por planta, com comprimento de 10 mm. Na ausência de auxina sintética, a formação de raízes não ocorreu. Assim sendo, podemos concluir que o tempo de exposição de 24 horas a 20 mg L-1 de IBA foi suficiente para promover o enraizamento de porta-enxertos Pyrus communis de ‘OHxF87’ e ‘PDW’.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The onset of leaf senescence is a highly regulated developmental change that is controlled by both genetics and the environment. Senescence is triggered by massive transcriptional reprogramming, but ...functional information about its underlying regulatory mechanisms is limited. In the current investigation, we performed a functional analysis of the soybean (Glycine max) osmotic stress- and endoplasmic reticulum (ER) stress-induced NAC transcription factor GmNAC81 during natural leaf senescence using overexpression studies and reverse genetics. GmNAC81-overexpressing lines displayed accelerated flowering and leaf senescence but otherwise developed normally. The precocious leaf senescence of GmNAC81-overexpressing lines was associated with greater Chl loss, faster photosynthetic decay and higher expression of hydrolytic enzyme-encoding GmNAC81 target genes, including the vacuolar processing enzyme (VPE), an executioner of vacuole-triggered programmed cell death (PCD). Conversely, virus-induced gene silencing-mediated silencing of GmNAC81 delayed leaf senescence and was associated with reductions in Chl loss, lipid peroxidation and the expression of GmNAC81 direct targets. Promoter-reporter studies revealed that the expression pattern of GmNAC81 was associated with senescence in soybean leaves. Our data indicate that GmNAC81 is a positive regulator of age-dependent senescence and may integrate osmotic stress- and ER stress-induced PCD responses with natural leaf senescence through the GmNAC81/VPE regulatory circuit.
To assess whether there the final range of motion (ROM) results achieved by patients undergoing total knee arthroplasty (TKA) with prosthesis using Medial Pivot design are predictable.
Between ...January and August of 2014, 155 patients with primary osteoarthritis of knee who underwent TKA using the prosthesis ADVANCE
Medial Pivot were prospectively assessed. All ROM measures were made and recorded before, during, and after surgery. All patients were clinically assessed preoperatively and postoperatively (15, 45 days, three months, six months, one year, and annually thereafter after surgery); their functional status was assessed using the WOMAC questionnaire.
Significant differences (
< 0.001) were observed between the means and medians of ROM in the preoperative when compared with those during the perioperative; the perioperative values, when compared with those after six months postoperative, were also different (
< 0.001). No significant differences were found between the means and medians ROM between the intraoperative period and at the 45-day assessment (ns) and between the means and medians ROM between the preoperative period and at the six-month evaluation (ns).
The final ROM achieved by patients that underwent TKA with medial pivot prosthesis can be predicted. The perioperative ROM correlates with that at 45 days after surgery. The final ROM is correlated with that of the pre-operative period.
Effective protocols for in vitro rooting for woody fruit trees are still a challenge for in vitro seedling production, especially when there is a need to insert new cultivars or rootstocks. These ...protocols are essential to accelerate studies in plant breeding programs and for seedling distribution. This study evaluated the use of 6-Benzylaminopurine (IBA) in in vitro rooting of Pyrus comunnis rootstocks, clones 'OHxF87' and Pyrodwarf. Explant exposure times (0, 24, 48, 72, and 96 hours) to 20 mg L.sup.-1 IBA were tested for in vitro rooting. The exposure to IBA resulted in rooting rates above 80%, surpassing some results reported in the literature. The 24-hour treatment provided 81,81% survival, leading to an average growth of five roots with 19 mm length, for 'OHxF87' rootstock. The same exposure time resulted in the highest survival rate (75%) and the highest mean root number, seven roots per plant with 10 mm length, for 'PDW' rootstock. Root formation did not occur in the absence of synthetic auxin. Therefore, it can be concluded that a 24-hour exposure at 20 mg L.sup.-1 IBA was sufficient to promote in vitro rooting in 'OHxF87' and Pyrodwarf rootstocks'. Key words: 'OHxF87', 'PDW', plant tissue culture, Pyrodwarf, seedling production, 6-Benzylaminopurine. Protocolos eficazes de enraizamento in vitro de frutiferas lenhosas ainda sao um desafio para producao de mudas in vitro, especialmente quando ha necessidade de insercao de novas cultivares ou porta-enxerto. Esses protocolos sao essenciais para acelerar estudos nos programas de melhoramento genetico e tambem para distribuicao posterior das mudas. Nesse sentido, o objetivo deste estudo foi avaliar a utilizacao da 6-Benzilaminopurina no enraizamento in vitro de porta-enxerto Pirus comunnis, clones 'OHxF87' e Pyrodwarf. Para o enraizamento, foi testado o tempo de exposicao dos explantes ao AIB. Para tanto, foram utilizados 20 mg L.sup.-1 do fitohormonio nas horas 0, 24, 48, 72 e 96 horas. A exposicao ao AIB resultou em taxas de enraizamento acima de 80%, superando alguns resultados encontrados na literatura. Para o porta-enxerto 'OHxF87', o tratamento de 24 horas proporcionou 81,81% de sobrevivencia, promovendo em media cinco raizes com comprimento de 19 mm. O mesmo tratamento para o porta-enxerto 'PDW' resultou na maior taxa de sobrevivencia (75%), bem como no maior numero medio de raizes, sete raizes por planta, com comprimento de 10 mm. Na ausencia de auxina sintetica, a formacao de raizes nao ocorreu. Assim sendo, podemos concluir que o tempo de exposicao de 24 horas a 20 mg L.sup.-1 de IBA foi suficiente para promover o enraizamento de porta-enxertos Pyrus communis de 'OHxF87' e 'PDW'. Palavras-chave: cultura de tecidos vegetais, OHxF87, PDW, Pyrodwarf; Producao de mudas, 6-Benzylaminopurine.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Avaliar se há previsibilidade da amplitude de movimentos alcançada por pacientes submetidos a artroplastia total do joelho com prótese que usa desenho medial pivot.
Entre janeiro e agosto de 2014 foi ...feita avaliação prospectiva de 155 pacientes com osteoartrose primária do joelho submetidos a artroplastia total do joelho com o uso da prótese Advance® Medial Pivot. Todas as medidas da amplitude de movimentos foram feitas antes, durante e após a cirurgia. Todos os pacientes foram avaliados clinicamente no pré‐ e pós‐operatório (15, 45 dias, três meses, seis meses, um ano e depois anualmente após a cirurgia) para a análise de seu estado funcional. O questionário Western Ontario and McMaster Universities Osteoarthritis Index (Womac) foi usado.
Diferenças significativas (p<0,001) foram relatadas entre as médias e medianas da amplitude de movimentos no pré‐operatório em comparação com as medidas obtidas no período intraoperatório. As medidas do pré‐operatório também se mostraram diferentes quando comparadas com aquelas após seis meses de pós‐operatório (p<0,001). Não foram encontradas diferenças significativas entre as médias e medianas da amplitude de movimento na comparação do intraoperatório e as medidas feitas aos 45 dias (ns) e entre as médias e medianas das medidas pré‐operatórias e aquelas observadas aos seis meses (ns).
Há previsibilidade da amplitude de movimentos obtida por pacientes submetidos a artroplastia total do joelho com prótese medial pivot. A amplitude aos 45 dias é semelhante àquela observada nas medidas intraoperatórias. A amplitude final está relacionada à amplitude pré‐operatória.
To assess whether there the final range of motion (ROM) results achieved by patients undergoing total knee arthroplasty (TKA) with prosthesis using Medial Pivot design are predictable.
Between January and August of 2014, 155 patients with primary osteoarthritis of knee who underwent TKA using the prosthesis ADVANCE® Medial Pivot were prospectively assessed. All ROM measures were made and recorded before, during, and after surgery. All patients were clinically assessed preoperatively and postoperatively (15, 45 days, three months, six months, one year, and annually thereafter after surgery); their functional status was assessed using the WOMAC questionnaire.
Significant differences (p<0.001) were observed between the means and medians of ROM in the preoperative when compared with those during the perioperative; the perioperative values, when compared with those after six months postoperative, were also different (p<0.001). No significant differences were found between the means and medians ROM between the intraoperative period and at the 45‐day assessment (ns) and between the means and medians ROM between the preoperative period and at the six‐month evaluation (ns).
The final ROM achieved by patients that underwent TKA with medial pivot prosthesis can be predicted. The perioperative ROM correlates with that at 45 days after surgery. The final ROM is correlated with that of the pre‐operative period.
Under the adverse remodeling of the right ventricle and interventricular septum in pulmonary arterial hypertension (PAH) the left ventricle (LV) dynamics is impaired. Despite the benefits of combined ...aerobic and resistance physical trainings to individuals with PAH, its impact on the LV is not fully understood.
To test whether moderate-intensity combined physical training performed during the development of PAH induced by MCT in rats is beneficial to the LV's structure and function.
Male Wistar rats were divided into two groups: Sedentary Hypertensive Survival (SHS, n = 7); and Exercise Hypertensive Survival (EHS, n = 7) to test survival. To investigate the effects of combined physical training, another group of rats were divided into three groups: Sedentary Control (SC, n = 7); Sedentary Hypertensive (SH, n = 7); and Exercise Hypertensive (EH, n = 7). PAH was induced through an intraperitoneal injection of MCT (60 mg/kg). Echocardiographic evaluations were conducted on the 22nd day after MCT administration. Animals in the EHS and EH groups participated in a combined physical training program, alternating aerobic (treadmill running: 50 min, 60% maximum running speed) and resistance (ladder climbing: 15 climbs with 1 min interval, 60% maximum carrying load) exercises, one session/day, 5 days/week for approximately 4 weeks.
The physical training increased survival and tolerance to aerobic (i.e., maximum running speed) and resistance (i.e., maximum carrying load) exertions and prevented reductions in ejection fraction and fractional shortening. In addition, the physical training mitigated oxidative stress (i.e., CAT, SOD and MDA) and inhibited adverse LV remodeling (i.e., Collagen, extracellular matrix, and cell dimensions). Moreover, the physical training preserved the amplitude and velocity of contraction and hindered the reductions in the amplitude and velocity of the intracellular Ca
transient in LV single myocytes.
Moderate-intensity combined physical training performed during the development of MCT-induced PAH in rats protects their LV from damages to its structure and function and hence increases their tolerance to physical exertion and prolongs their survival.
Resumo Fundamento A hipertrofia e a dilatação do ventrículo direito observadas na hipertensão arterial pulmonar (HAP) prejudicam a dinâmica do ventrículo esquerdo (VE) achatando o septo ...interventricular. Objetivo Investigar se o treinamento físico resistido (TFR) de intensidade baixa a moderada é benéfico para funções contráteis do VE e de cardiomiócitos em ratos durante o desenvolvimento de HAP induzida por monocrotalina (MCT). Métodos Foram usados ratos Wistar machos (Peso corporal: ~ 200 g). Para avaliar o tempo até o possível surgimento de insuficiência cardíaca (ou seja, ponto de desfecho), os ratos foram divididos em dois grupos, hipertensão com sedentarismo até a insuficiência (HSI, n=6) e hipertensão com treinamento até a insuficiência (HTI, n=6). Para testar os efeitos do TFR, os ratos foram divididos entre grupos de controle sedentários (CS, n=7), hipertensão com sedentarismo (HS, n=7) e hipertensão com treinamento (HT, n=7). A HAP foi induzida por duas injeções de MCT (20 mg/kg, com um intervalo de 7 dias). Os grupos com treinamento foram submetidos a um protocolo de TFR (subir escadas; 55-65% da máxima carga carregada), 5 dias por semana. A significância estatística foi definida em p <0,05. Resultados O TFR prolongou o ponto de desfecho (~25%), melhorou a tolerância ao esforço físico (~55%) e atenuou as disfunções de contratilidade de VE e de cardiomiócitos promovidas pela MCT preservando a fração de ejeção e o encurtamento fracional, a amplitude do encurtamento, e as velocidades de contração e relaxamento nos cardiomiócitos. O TFR também preveniu os aumentos de fibrose e colágeno tipo I no ventrículo esquerdo causados pela MCT, além de manter as dimensões de miócitos e colágeno tipo III reduzidas por MCT. Conclusão O TFR de intensidade baixa a moderada é benéfico para funções contráteis de VE e cardiomiócitos em ratos durante o desenvolvimento de HAP induzida por MCT.
We tested the effects of low- to moderate-intensity resistance exercise training (RT) on the structure and function of pulmonary, right ventricle (RV), and skeletal muscle tissues in rats with stable ...pulmonary artery hypertension (PAH).
After the first monocrotaline (MCT; 20 mg/kg) injection, male rats were submitted to a RT program (Ladder climbing; 55–65 % intensity), 5 times/week. Seven days later rats received the second MCT dose. Physical effort tolerance test and echocardiographic examination were performed. After euthanasia, lung, heart, and biceps brachii were processed for histological, single myocyte, and biochemical analysis.
RT improved survival and physical effort tolerance (i.e., maximum carrying load), mitigated the pulmonary artery resistance increase (i.e., TA/TE), and preserved cardiac function (i.e., fractional shortening, ejection fraction, stroke volume and TAPSE). RT counteracted oxidative stress (i.e., CAT, SOD, GST, MDA and NO) and adverse remodeling in lung (i.e., collapsed alveoli) and in biceps brachii (i.e., atrophy and total collagen) tissues. RT delayed RV adverse remodeling (i.e., hypertrophy, extracellular matrix, collagen types I and III, and fibrosis) and impairments in single RV myocyte contractility (i.e., amplitude and velocity to peak and relaxation). RT improved the expression of gene (i.e., miRNA 214) and intracellular Ca2+ cycling regulatory proteins (i.e., PLBser16); and of pathological (i.e., α/β-MHC and Foxo3) and physiological (i.e., Akt, p-Akt, mTOR, p-mTOR, and Bcl-xL) hypertrophy pathways markers in RV tissue.
Low- to moderate-intensity RT benefits the structure and function of pulmonary, RV, and skeletal muscle tissues in rats with stable pulmonary artery hypertension.
BACKGROUNDThe right ventricular hypertrophy and dilation observed in pulmonary artery hypertension (PAH) damages the left ventricle (LV) dynamics by flattening the interventricular septum. ...OBJECTIVETo investigate whether low- to moderate-intensity resistance exercise training (RT) is beneficial to LV and cardiomyocyte contractile functions in rats during the development of monocrotaline (MCT)-induced PAH. METHODSMale Wistar rats (Body weight: ~ 200 g) were used. To assess the time to potential heart failure onset (i.e., end point), rats were divided into sedentary hypertension until failure (SHF, n=6) and exercise hypertension until failure (EHF, n=6) groups. To test RT effects, rats were divided into sedentary control (SC, n = 7), sedentary hypertension (SH, n=7), and exercise hypertension (EH, n=7) groups. PAH was induced by two MCT injections (20 mg/kg, with 7 days interval). Exercise groups were submitted to an RT protocol (Ladder climbing; 55-65% of carrying maximal load), 5 times/week. Statistical significance was assumed at P < 0.05. RESULTSRT prolonged the end point (~25 %), enhanced the physical effort tolerance (~ 55%), and mitigated the LV and cardiomyocyte contractility dysfunctions promoted by MCT by preserving the ejection fraction and fractional shortening, the amplitude of shortening, and the velocities of contraction and relaxation in cardiomyocytes. RT also prevented increases in left ventricle fibrosis and type I collagen caused by MCT, and maintained the type III collagen and myocyte dimensions reduced by MCT. CONCLUSIONLow- to moderate-intensity RT benefits LV and cardiomyocyte contractile functions in rats during the development of MCT-induced PAH.
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