Expression analysis of transcription factors in sugarcane during cold stress / Análise de expressão de fatores de transcrição em cana-de-açúcar sob estresse por frio

Abstract Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.

Resumo Fatores de transcrição (FT) são uma ampla classe de genes em plantas e podem regular a expressão de outros genes em resposta a vários estresses ambientais (estresses bióticos e abióticos). No presente estudo, a atividade do fator de transcrição na cana-de-açúcar foi examinada durante o estresse pelo frio. Inicialmente, as leituras de transcrição de RNA de duas cultivares de cana-de-açúcar (ROC22 e GT08-1108) sob estresse frio foram baixadas do banco de dados SRA NCBI. As leituras foram alinhadas em um genoma de referência e as análises de expressão diferencial foram realizadas com o pacote R / Bioconductor edgeR. Com base em nossas análises no cultivar ROC22, 963 genes TF foram significativamente regulados positivamente sob estresse pelo frio entre um total de 5.649 genes regulados positivamente, enquanto 293 genes TF foram regulados negativamente entre um total de 3.289 genes regulados negativamente. No cultivar GT08-1108, 974 genes TF foram identificados entre 5.649 genes regulados positivamente e 283 genes TF foram encontrados entre 3.289 genes regulados negativamente. Os fatores de transcrição, em sua maioria, foram anotados com categorias GO relacionadas à ligação de proteína, ligação de fator de transcrição, ligação específica de sequência de DNA, complexo de fator de transcrição, atividade de fator de transcrição em RNA polimerase II, atividade de fator de transcrição de ligação de ácido nucleico, atividade de corepressor de transcrição, sequência específica da região reguladora, atividade do fator de transcrição da RNA polimerase II, atividade do cofator do fator de transcrição, atividade do fator de transcrição do promotor do plastídio, atividade do fator de transcrição do promotor da RNA polimerase I, polimerase II e RNA polimerase III. As descobertas dos resultados acima ajudarão a identificar fatores de transcrição expressos diferencialmente durante o estresse pelo frio. Ele também fornece uma análise abrangente da regulação da atividade de transcrição de muitos genes. Portanto, este estudo fornece base molecular para melhorar a tolerância ao frio em cana-de-açúcar e outras gramíneas economicamente importantes.

Expression analysis of transcription factors in sugarcane during cold stress / Análise de expressão de fatores de transcrição em cana-de-açúcar sob estresse por frio

Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.

Fatores de transcrição (FT) são uma ampla classe de genes em plantas e podem regular a expressão de outros genes em resposta a vários estresses ambientais (estresses bióticos e abióticos). No presente estudo, a atividade do fator de transcrição na cana-de-açúcar foi examinada durante o estresse pelo frio. Inicialmente, as leituras de transcrição de RNA de duas cultivares de cana-de-açúcar (ROC22 e GT08-1108) sob estresse frio foram baixadas do banco de dados SRA NCBI. As leituras foram alinhadas em um genoma de referência e as análises de expressão diferencial foram realizadas com o pacote R / Bioconductor edgeR. Com base em nossas análises no cultivar ROC22, 963 genes TF foram significativamente regulados positivamente sob estresse pelo frio entre um total de 5.649 genes regulados positivamente, enquanto 293 genes TF foram regulados negativamente entre um total de 3.289 genes regulados negativamente. No cultivar GT08-1108, 974 genes TF foram identificados entre 5.649 genes regulados positivamente e 283 genes TF foram encontrados entre 3.289 genes regulados negativamente. Os fatores de transcrição, em sua maioria, foram anotados com categorias GO relacionadas à ligação de proteína, ligação de fator de transcrição, ligação específica de sequência de DNA, complexo de fator de transcrição, atividade de fator de transcrição em RNA polimerase II, atividade de fator de transcrição de ligação de ácido nucleico, atividade de corepressor de transcrição, sequência específica da região reguladora, atividade do fator de transcrição da RNA polimerase II, atividade do cofator do fator de transcrição, atividade do fator de transcrição do promotor do plastídio, atividade do fator de transcrição do promotor da RNA polimerase I, polimerase II e RNA polimerase III. As descobertas dos resultados acima ajudarão a identificar fatores de transcrição expressos diferencialmente durante o estresse pelo frio. Ele também fornece uma análise abrangente da regulação da atividade [...].

Expression analysis of transcription factors in sugarcane during cold stress

Abstract Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.

Resumo Fatores de transcrição (FT) são uma ampla classe de genes em plantas e podem regular a expressão de outros genes em resposta a vários estresses ambientais (estresses bióticos e abióticos). No presente estudo, a atividade do fator de transcrição na cana-de-açúcar foi examinada durante o estresse pelo frio. Inicialmente, as leituras de transcrição de RNA de duas cultivares de cana-de-açúcar (ROC22 e GT08-1108) sob estresse frio foram baixadas do banco de dados SRA NCBI. As leituras foram alinhadas em um genoma de referência e as análises de expressão diferencial foram realizadas com o pacote R / Bioconductor edgeR. Com base em nossas análises no cultivar ROC22, 963 genes TF foram significativamente regulados positivamente sob estresse pelo frio entre um total de 5.649 genes regulados positivamente, enquanto 293 genes TF foram regulados negativamente entre um total de 3.289 genes regulados negativamente. No cultivar GT08-1108, 974 genes TF foram identificados entre 5.649 genes regulados positivamente e 283 genes TF foram encontrados entre 3.289 genes regulados negativamente. Os fatores de transcrição, em sua maioria, foram anotados com categorias GO relacionadas à ligação de proteína, ligação de fator de transcrição, ligação específica de sequência de DNA, complexo de fator de transcrição, atividade de fator de transcrição em RNA polimerase II, atividade de fator de transcrição de ligação de ácido nucleico, atividade de corepressor de transcrição, sequência específica da região reguladora, atividade do fator de transcrição da RNA polimerase II, atividade do cofator do fator de transcrição, atividade do fator de transcrição do promotor do plastídio, atividade do fator de transcrição do promotor da RNA polimerase I, polimerase II e RNA polimerase III. As descobertas dos resultados acima ajudarão a identificar fatores de transcrição expressos diferencialmente durante o estresse pelo frio. Ele também fornece uma análise abrangente da regulação da atividade de transcrição de muitos genes. Portanto, este estudo fornece base molecular para melhorar a tolerância ao frio em cana-de-açúcar e outras gramíneas economicamente importantes.

Expression analysis of transcription factors in sugarcane during cold stress.

Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.

Optical characterization of non-thermal plasma jet energy carriers for effective catalytic processing of industrial wastewaters.

An argon plasma jet was sustained in open air and characterized for its chemical composition. The optically characterized plasma jet was used to treat industrial wastewater containing mixed textile dyes and heavy metals. Since plasma jet produces UV-radiations, the photocatalytic TiO2 was used to enhance plasma treatment efficiency especially for degradation of dyes. Mixed anatase and rutile phases of TiO2 (5.2-8.5 nm) were produced through surfactant assisted sol-gel approach. The emission spectrum confirmed the presence of excited argon, OH, excited nitrogen, excited oxygen, ozone and nitric oxide in the plasma jet. The spectral lines of excited Ar, NO, O3, OH-, N2, [Formula: see text], O, [Formula: see text] and O+ species were observed at wavelength of 695-740 nm, 254.3 nm, 307.9 nm, 302-310 nm, 330-380 nm, 390-415 nm, 715.6 nm, 500-600 nm and 400-500 nm. These reactive species decompose the organic pollutants and separate the heavy metals from the water samples. The conductivity of plasma exposed water samples increased while pH and hardness decreased. The atomic absorption spectrophotometry analysis confirmed the presence of heavy metals in the samples, which were effectively removed through plasma treatment. Finally, the effect of plasma treatment on Staphylococcus aureus strains was more pronounced than Escherichia coli strains.

Knowledge, attitude, practice and perceived barriers among healthcare workers regarding COVID-19: a cross-sectional survey from Pakistan.

A self-administered validated (Cronbach's alpha=0.077) questionnaire was used to assess knowledge, attitude and practice among healthcare workers (HCWs) in Pakistan regarding coronavirus disease 2019 (COVID-19). Findings showed that HCWs have good knowledge (93.2%, N=386), a positive attitude [mean 8.43 (standard deviation 1.78)] and good practice (88.7%, N=367) regarding COVID-19. HCWs perceived that limited infection control material (50.7%, N=210) and poor knowledge regarding transmission (40.6%, N=168) were the major barriers to infection control. Regression analysis indicated that pharmacists were more likely to demonstrate good practice than other HCWs (odds ratio 2.247, 95% confidence interval 1.11-4.55, P=0.025). This study found that HCWs in Pakistan have good knowledge, but there are gaps in specific aspects of knowledge and practice that warrant attention.

Descriptive sensory profile of cow and buffalo milk Cheddar cheese prepared using indigenous cultures.

The objective of the study was to compare the sensory profile of Cheddar cheese prepared from cow and buffalo milk using indigenous and commercial cultures. Commercially available and locally isolated, indigenous starter cultures were used to prepare cow and buffalo milk Cheddar cheese. The cheese was ripened at 4 and 12°C and analyzed for descriptive sensory profile by a panel of 10 assessors after 60 and 120 d of ripening. On evaluation, the mean scores for odor, flavor, and texture attributes obtained for buffalo milk cheese were significantly higher than those obtained for cow milk cheese. For most of the traits, cheese samples prepared from indigenous cultures and ripened at higher temperature received higher descriptive scores compared with those of commercial cultures and ripened at lower degrees. Milk sources highly significantly affected the "creamy" and "sour" traits of odor; the "creamy," "smoky," and "soapy" flavors; and all the texture attributes except "maturity." Starter cultures considerably influenced the production of "acidic," "bitter," "sweet," and "sour" characteristics. The use of elevated ripening temperature showed noticeable effect on all the characteristics except the "creamy" odor and flavor. Principal component analysis and hierarchical cluster analysis also showed that milk sources, starter cultures, and ripening temperatures significantly influenced the sensory characteristics.

Pulsed radiofrequency modulation for lingual neuralgia.

Pulsed radiofrequency modulation (PRM) is a minimally invasive procedure that has been used successfully to treat neuropathic pain. Its use to treat lingual neuralgia has not to our knowledge been described previously, and we report a case.

Advances in heart failure: natriuretic peptide testing.

Natriuretic peptide testing in the form of B-type natriuretic peptide (BNP) or NT-proBNP measurement has revolutionized modern heart failure (HF) diagnostics for those patients with acute symptoms, and promises to have similarly profound effects not only for the earlier recognition of those with HF, but also for the therapy of patients across the entire spectrum of HF. Future efforts are necessary to better understand the complex biology of the natriuretic peptides, to further optimize use of the assays for their measurement, and to gain clarity regarding the appropriate venue for their measurement. The ultimate goal is to recognize more readily and treat the syndrome that is HF, in order to reduce the considerable morbidity and mortality among those so afflicted.

Sampling methods as abundance indices for adult Diaprepes abbreviatus (Coleoptera: Curculionidae) in citrus.

Beat sampling and two type of traps, cup traps and Tedders traps, were evaluated as sampling methods to detect and estimate population densities of adult Diaprepes abbreviatus L. weevils newly colonizing young citrus trees. The study was conducted over a 65-wk period across a 0.25-ha area of 80 citrus trees [Citrus sinensis (L.) Osbeck] (1.2-1.5 m tall). Beat samples were taken weekly to determine the number of trees infested and number of new adult weevils per tree. Sixteen of the 80 trees studied were each monitored weekly using one of the following trapping methods: cup traps in trees, cup traps on a stake in the ground within the tree drip line, cup traps on a stake in the ground outside of the drip line, Tedders traps on the ground within the drip line, and Tedders traps on the ground outside of the drip line. Weevils collected each week from trees and traps were removed from the study site. Based on the coefficients associated with Taylor's power law, the optimum numbers of trees to sample for an SEM equal to 25% of the mean estimate decreased from 50 trees at a mean of 0.5 new weevils per tree to 30 trees at a mean of 0.8 new weevils per tree. A significant relationship was found between the weekly mean number of new weevils per tree and the proportion of trees infested, a binomial relationship that could be further explored in the search for a sampling program for adult D. abbreviatus. Regression analyses indicated that three of the trapping methods served at least as weak indices of the presence and abundance of new weevils: cup traps in trees, Tedders traps inside the dripline and Tedders traps outside the dripline. Cup traps in trees and Tedders traps inside the dripline captured the most weevils and most frequently detected weevils. Although relatively inefficient as abundance indices of populations of new weevils, these two trapping methods appeared to have some value with respect to signaling when weevils first appeared in trees during the spring.

Microbiological and biochemical characteristics of Canestrato Pugliese cheese made from raw milk, pasteurized milk or by heating the curd in hot whey.

Canestrato Pugliese cheeses were produced from raw ewes' milk (R and R(II) cheeses), pasteurized ewes' milk (P cheese) and by heating the curd in hot whey according to a traditional protocol (T cheese). R(II) differed from R cheese mainly by having been produced from raw milk with a higher number of somatic cells, 950.000 vs. 750.000 ml(-1), respectively. Compared to P and T cheeses, R and R(II) cheeses had a higher concentration (one or two orders of magnitude) of cheese-related bacteria such as adventitious mesophilic lactobacilli, enterococci and staphylococci. At the end of ripening, all cheeses contained less than 1.0 log cfu g(-1) of total and fecal coliforms, and Escherichia coli and Staphylococcus aureus were not detected. As shown by phenotypic identification and RAPD-PCR, R cheese contained the largest number of mesophilic lactobacilli species and the greatest diversity of strains within the Lactobacillus plantarum species. Primary proteolysis did not differ appreciably among the cheeses. On the contrary, both urea-PAGE and the RP-HPLC analyses of the water-soluble N fractions showed the more complex profiles in cheeses produced by raw milks. R and R(II) cheeses had the highest values of water-soluble N/total N (ca. 30%) and the highest concentration of total free amino acids (ca. 40 mg g(-1) which approached or exceeded those reported for Italian cheeses with very high level of proteolysis during ripening. The main differences between R-R(II) and P-T cheeses were the concentrations of aspartic acid, proline, alanine, isoleucine, histidine and lysine. The water-soluble extracts of R and R(II) cheeses contained levels of amino-, imino- and di-peptidase activities, which were about twice those found in P and T cheeses. Cheeses differed slightly in the concentration of total free fatty acids that ranged between 1673 and 1651 mg kg(-1) in R and R(II) cheeses, and 1397 and 1334 mg kg(-1) in P and T cheeses. Butyric, caproic, capric, palmitic, oleic and linoleic acids were found at the highest concentrations.

Hepatic resection at a community hospital.

Hepatic resection remains the "gold standard" in the primary management of primary and metastatic tumors to the liver. Advanced surgical techniques along with more modern and sophisticated equipment have led to an increasing number of hepatic resections being performed with a concomitant decrease in morbidity and mortality. We followed prospectively 18 consecutive hepatic resections performed over a period of approximately 2.5 years. The setting was a community teaching hospital with a low volume of referrals for hepatic resection. Sixteen (88%) had metastatic disease and two had primary liver disease. There were four trisegmentectomies, four lobectomies, four segmentectomies, and six large wedge re-sections. Average estimated blood loss was 608 ml. Seven patients required transfusions. Complications occurred in five patients (27%). In-hospital mortality was 0%. Our experience suggests that liver resections in a low-volume community hospital can be performed safely provided an experienced surgical team with familiarity of advanced surgical techniques and sophisticated equipment used in hepatic resection is readily available.

Diaphragmatic rupture: A complication of violent cough.

The cough is a complex physiologic response designed to protect airways from unwanted secretions and foreign materials. Violent and paroxysmal coughs are associated with many complications. In this article, we will discuss a patient who sustained diaphragmatic rupture as a result of violent coughing. The possible mechanisms of this rare complication are explained.

Intradialytic serial vascular access flow measurements.

Hemodialysis vascular access failure represents a major source of morbidity and mortality in chronic hemodialysis (CHD) patients. Serial vascular access blood flow (VABF) measurements are being used as a screening method at an increasing rate. There are limited data on the changes in VABF throughout the hemodialysis session, which may potentially affect the validity of VABF measurement. This study is performed to evaluate the trend in VABF during a given hemodialysis session by serial VABF measurements, along with potential factors that may affect VABF. Thirty-two CHD patients had serial VABF measurements performed during a hemodialysis session. Each patient had three serial VABF measurements during a hemodiaysis treatment (within 30, 90, and 150 minutes from the start of hemodialysis). Mean arterial blood pressure (MAP), ultrafiltration rate, and patient symptoms were recorded simultaneously. The mean VABF was 1,344 +/- 486 mL/min within 30 minutes of hemodialysis and decreased to 1,308 +/- 532 and 1,250 +/- 552 mL/min after 90 and 150 minutes, respectively. This trend was statistically significant (P = 0.03). There was a strong correlation between VABF measurements and MAP, which was more pronounced after 90 minutes of initiation of hemodialysis (r = 0.68; P < 0.001). Using multivariate analysis, it can be predicted that after 90 minutes of hemodialysis, each 10% decrease in MAP would result in an expected decrease of 8% in VABF. There was no effect of type of vascular access, baseline VABF, or amount of ultrafiltration on VABF changes. In conclusion, VABF measurements can be performed up to 2 to 2(1/2) hours from the start of hemodialysis in the majority of patients. The major determinant of VABF changes is MAP. In a subset of patients with a decrease MAP greater than 15%, it is advisable to perform VABF measurement either at the first 90 minutes of hemodialysis or postpone it to another treatment session, when MAP is more stable.