UBC and YWHAZ as suitable reference genes for accurate normalisation of gene expression using MCF7, HCT116 and HepG2 cell lines

Relative quantification of in vitro gene expression using real-time PCR requires stably expressed reference gene for normalisation. In this study, total RNA from MCF7, HCT116 and HepG2 cells were extracted and converted to cDNA using commercially available kit, and real-time PCR was then performed to analyse the expression levels of twelve reference genes to select the most ideal reference gene for accurate normalisation in gene expression study. geNorm and NormFinder software were used to analyse the stabilities of the reference genes, which showed a wide range of C_t values. The geNorm analysis showed the following ranking for stability of genes: UBC, YWHAZ > RPLP > TBP > ACTB > HPRT1 > PPIA > GAPDH > GUSB > B2M > TUBB > RRN18S. A similar ranking of reference genes was obtained by NormFinder, and the four most stable reference genes were identical using both approaches. UBC and YWHAZ were proposed to be the two most suitable reference genes based on the above analyses. To further assess the stabilities of the UBC and YWHAZ in a formal experiment, MCF7, HCT116 and HepG2 cell lines were subjected to treatments with 5-aza-dC and TSA. Both UBC and YWHAZ exhibited stable expression levels across control and treatment groups. Therefore, we propose that UBC and YWHAZ are the two most suitable reference genes for our gene expression studies using MCF7, HCT116 and HepG2 cell lines.     

Combination of all-stage and high-temperature adult-plant resistance QTL confers high-level,durable resistance to stripe rust in winter wheat cultivar Madsen

Key message

Wheat cultivar Madsen has a new gene on the short arm of chromosome 1A and two QTL for all-stage resistance and three QTL for high-temperature adult-plant resistance that in combination confer high-level, durable resistance to stripe rust.

Abstract

Wheat cultivar Madsen has maintained a high-level resistance to stripe rust over 30 years. To map quantitative trait loci (QTL) underlying the high-level, durable resistance, 156 recombinant inbred lines (RILs) developed from cross Avocet S?×?Madsen were phenotyped with selected races of Puccinia striiformis f. sp. tritici in the greenhouse seedling tests, and in naturally infected fields during 2015–2017. The RILs were genotyped by SSR and SNP markers from genotyping by sequencing and the 90 K wheat SNP chip. Three QTL for all-stage resistance were mapped on chromosomes 1AS, 1BS and 2AS, and two QTL for high-temperature adult-plant (HTAP) resistance were mapped on 3BS and 6BS. The most effective QTL on 2AS, explaining 8.97–23.10% of the phenotypic variation in seedling tests and 8.60–71.23% in field tests, contained Yr17 for all-stage resistance and an additional gene for HTAP resistance. The 6BS QTL, detected in all field tests, was identified as Yr78. The 1AS QTL, conferring all-stage resistance, was identified as a new gene, which explained 20.45 and 30.23% of variation in resistance to races PSTv-37 and PSTv-40, respectively, and contributed significantly to field resistance at Pullman in 2015-2017, but was not detected at Mount Vernon. The interactions among QTL were mostly additive, and RILs with all five QTL had the highest level of resistance in the field, similar to Madsen. Genotyping 148 US Pacific Northwest wheat cultivars with markers for the 1AS, 2AS and 6BS QTL validated the genes and markers, and indicated their usefulness for marker-assisted selection.

     

BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability

Ligands for the bromodomain and extra-terminal domain (BET) family of bromodomains have shown promise as useful therapeutic agents for treating a range of cancers and inflammation. Here we report that our previously developed 3,5-dimethylisoxazole-based BET bromodomain ligand (OXFBD02) inhibits interactions of BRD4(1) with the RelA subunit of NF-κB, in addition to histone H4. This ligand shows a promising profile in a screen of the NCI-60 panel but was rapidly metabolised (t_½?=?39.8?min). Structure-guided optimisation of compound properties led to the development of the 3-pyridyl-derived OXFBD04. Molecular dynamics simulations assisted our understanding of the role played by an internal hydrogen bond in altering the affinity of this series of molecules for BRD4(1). OXFBD04 shows improved BRD4(1) affinity (IC₅₀?=?166?nM), optimised physicochemical properties (LE?=?0.43; LLE?=?5.74; SFI?=?5.96), and greater metabolic stability (t_½?=?388?min).     

The temporal requirement for vitamin A in the developing eye: mechanism of action in optic fissure closure and new roles for the vitamin in regulating cell proliferation and adhesion in the embryonic retina

Mammalian eye development requires vitamin A (retinol, ROL). The role of vitamin A at specific times during eye development was studied in rat fetuses made vitamin A deficient (VAD) after embryonic day (E) 10.5 (late VAD). The optic fissure does not close in late VAD embryos, and severe folding and collapse of the retina is observed at E18.5. Pitx2, a gene required for normal optic fissure closure, is dramatically downregulated in the periocular mesenchyme in late VAD embryos, and dissolution of the basal lamina does not occur at the optic fissure margin. The addition of ROL to late VAD embryos by E12.5 restores Pitx2 expression, supports dissolution of the basal lamina, and prevents coloboma, whereas supplementation at E13.5 does not. Surprisingly, ROL given as late as E13.5 completely prevents folding of the retina despite the presence of an open fetal fissure, showing that coloboma and retinal folding represent distinct VAD-dependent defects. Retinal folding due to VAD is preceded by an overall reduction in the percentage of cyclin D1 positive cells in the developing retina, (initially resulting in retinal thinning), as well as a dramatic reduction in the cell adhesion-related molecules, N-cadherin and β-catenin. Reduction of retinal cell number combined with a loss of the normal cell-cell adhesion proteins may contribute to the collapse and folding of the retina that occurs in late VAD fetuses.     

Clinical Risk Factors for Life-Threatening Lower Respiratory Tract Infections in Children: A Retrospective Study in an Urban City in Malaysia

Aim

Lower respiratory tract infections (LRTIs) are an important cause of morbidity and mortality, especially in low income countries. The aim of this study was to determine risk factors of life-threatening LRTIs in hospitalised children in Malaysia.

Methods

This retrospective study included children aged less than 18 years admitted for LRTIs over 13 months in a tertiary referral centre in Kuala Lumpur, Malaysia. Neonates, children with asthma and those with either no or a normal chest radiograph were excluded. Life-threatening infection was defined as that needing non-invasive ventilation or admission to the paediatric intensive care unit. Routine blood investigations and nasopharyngeal secretion results (bacterial and viral) were obtained. Chest radiographs were reviewed by a designated radiologist. Environmental data (rainfall, particulate matter ≤10 µm [PM10] and air pollution index [API]) was obtained from the respective government departments.

Results

Three hundred and ninety-one episodes of LRTIs were included. Viruses were implicated in 48.5% of LRTIs, with respiratory syncytial virus (RSV) being detected in 44% of viral LRTIs. Forty-six (11.8%) children had life-threatening disease and the overall mortality rate was 1.3% (5 children). RSV was detected in 26% of children with life-threatening LRTIs. In multivariate logistic regression, chronic lung disease, presenting history of apnoea and signs of hypoxia, was associated with life threatening LRTIs. Increased LRTI admissions were associated with low rainfall but not PM10 nor API. Of those on follow-up, 39% had persistent respiratory symptoms.

Conclusion

One in nine children admitted with LRTI had a life-threatening LRTI. The aetiology was viral in almost half of admitted children. RSV was detected in a quarter of children with life-threatening LRTIs. Children who present with LRTIs and either have chronic lung disease, presenting history of apnoea or signs of hypoxia, should be observed carefully as the risk of deterioration to life-threatening illness is high.     

Effects of an insect‐mediated mental healthcare program for mentally disordered children

Insects are the most diverse groups of animals on the planet, representing more than one‐half of all known living organisms, and are found in nearly every environment. Recently, the importance of insects as food sources or as pets has increased in many countries, including Korea. In addition, several insects have been shown to exert a strong influence on people's emotions. Our insect‐mediated mental healthcare program is designed to help meet the physical, behavioral and developmental needs of people with mental disorders. Children with mental disorders, the experimental group, were provided with an insect‐mediated mental healthcare program for a total of eight sessions, one session per week, at 1–2 h per session, accompanied by a pre‐test and post‐test. The overall, gender, education level, and mental disease profiles of the participants in this study were balanced. Our results indicated that children who participated in the insect‐mediated healthcare program group once showed significant improvement in their emotional health and insect awareness. Additionally, paired education level's t‐tests showed that the outcomes of the participants in treatment group were significantly improved (α < 0.05). However, participants' satisfaction with their school life (middle school) was not influenced. These results suggest that insects positively influence children's emotional health through an insect‐mediated healthcare program. Further research on the basis of this study is expected to help children with emotional therapy in other areas.     

Enzymatic and nonenzymatic synthesis of glutathione conjugates: application to the understanding of a parasite's defense system and alternative to the discovery of potent glutathione S-transferase inhibitors

A primary pathway for metabolism of electrophilic compounds in Schistosoma japonicum involves glutathione S-transferase (SjGST)-catalyzed formation of glutathione (GSH) conjugates. As part of a program aimed at gaining a better understanding of the defense system of parasites, a series of aromatic halides (1-8), aliphatic halides (9, 10), epoxides (11-20), alpha,beta-unsaturated esters (21, 22), and alpha,beta-unsaturated amides (23, 24) were prepared, and their participation in glutathione conjugate formation was evaluated. Products from enzymatic and nonenzymatic reactions of these substances with glutathione were characterized and quantified by using reverse-phase high-performance liquid chromatography (HPLC), NMR, and fast atom bombardment mass spectrometry (FAB-MS) analysis. Mechanisms for formation of specific mono(glutathionyl) or bis(glutathionyl) conjugates are proposed. Although the results of this effort indicate that SjGST does not catalyze addition or substitution reactions of 1, 3, 4, 7-9, 11-13, 15-17, 19-21, and 24, they demonstrate that 2, 5, 6, 14, 18, and 23 undergo efficient enzyme-catalyzed conjugation reactions. The kcat values for SjGST with 23 and 18 are about 886-fold and 14-fold, respectively, larger than that for 5. This observation suggests that 23 is a good substrate in comparison to other electrophiles. Furthermore, the initially formed conjugation product, 23a, is also a substrate for SjGST in a process that forms the bis(glutathionyl) conjugate 23b. Products arising by enzymatic and nonenzymatic pathways are generated under the conditions of SjGST-activated GSH conjugation. Interestingly, production of nonenzymatic GSH conjugates with electrophilic substrates often overwhelms the activity of the enzyme. The nonenzymatic GSH conjugates, 9a-11a, 16a, 21a, and 22a, are inhibitors of SjGST with respective IC50 values of 1.95, 75.5, 0.96, 19.0, 152, and 0.36 microM, and they display moderate inhibitory activities against human GSTA2. Direct evidence has been gained for substrate inhibition by 10 toward SjGST and GSTA2 that is more potent than that of its GSH conjugate 10a. The significance of this work is found in the development of a convenient NMR-based technique that can be used to characterize glutathione conjugates derived from small molecule libraries as part of efforts aimed at uncovering specific potent SjGST and GSTA2 inhibitors. This method has potential in applications to the identification of novel inhibitors of other GST targets that are of chemotherapeutic interest.