Computational analysis of atpB gene promoter from different Pakistani apple varieties

Apple is the fourth most important fruit crop grown in temperate areas of the world belongs to the family Rosaceae. In the present study, the promoter (∼1000 bp) region of atpB gene was used to evaluate the genetic diversity and phylogeny of six local apple varieties. atpB gene is one of the large chloroplastic region which encodes β-subunit of ATP synthase and previously it had been used largely in phylogenetic studies. During the present study, atpB promoter was amplified, sequenced and analyzed using various bioinformatics tools including Place Signal Scan, MEGA6 and BLASTn. During the phylogenetic analysis, obtained phylogram divided the studied varieties into two clusters revealing the monophyletic origin of studied apple varieties. Pairwise distance revealed moderate genetic diversity that ranges from 0.047–0.170 with an average of 0.101. While identifying different cis-acting elements present in the atpB promoter region, results exhibited the occurrence of 56 common and 20 unique cis-regulatory elements among studied varieties. The identified cis-acting regulatory elements were mapped as well. It was observed that Kala Kulu has the highest unique features with reference to the availability of cis-acting elements. Moreover, the possible functions of all regulatory elements present on the promoter sequence of atpB gene were predicted based on already reported information regarding their in vivo role.     

Bipartite network analysis reveals metabolic gene expression profiles that are highly associated with the clinical outcomes of acute myeloid leukemia

Dysregulated and reprogrammed metabolism are one of the most important characteristics of cancer, and exploiting cancer cell metabolism can aid in understanding the diverse clinical outcomes for patients. To investigate the differences in metabolic pathways among patients with acute myeloid leukemia (AML) and differential survival outcomes, we systematically conducted microarray data analysis of the metabolic gene expression profiles from 384 patients available from the Gene Expression Omnibus and Cancer Genome Atlas databases. Pathway enrichment analysis of differentially expressed genes (DEGs) showed that the metabolic differences between low-risk and high-risk patients mainly existed in two pathways: biosynthesis of unsaturated fatty acids and oxidative phosphorylation. Using the gene-pathway bipartite network, 62 metabolic genes were identified from 272 DEGs involved in 88 metabolic pathways. Based on the expression patterns of the 62 genes, patients with shorter overall survival (OS) durations in the training set (hazard ratio (HR) = 1.58, p = 0.038) and in two test sets (HR = 1.69 and 1.56 and p = 0.089 and 0.029, respectively) were well discriminated by hierarchical clustering analysis. Notably, the expression profiles of ALAS2, BCAT1, BLVRB, and HK3 showed distinct differences between the low-risk and high-risk patients. In addition, models for predicting the OS outcome of AML from the 62 gene signatures achieved improved performance compared with previous studies. In conclusion, our findings reveal significant differences in metabolic processes of patients with AML with diverse survival durations and provide valuable information for clinical translation.     

Effects of low-dose gamma-irradiation on production of shikonin derivatives in callus cultures of Lithospermum erythrorhizon S.

The yield increase of secondary metabolite production was examined in plant cell cultures with the use of relatively low to high doses gamma irradiation. Suspension culture of Lithospermum erythrorhizon cells was irradiated to 2, 16, and 32 Gy. The gamma irradiation significantly stimulated the shikonin biosynthesis of the cells and increased the total shikonin yields (intracellular+extracellular shikonin yields) by 400% at 16 Gy and by only 240% and 180% at 2 and 32 Gy, respectively. One of the key enzymes for the shikonin biosynthesis of cells, p-hydroxylbenzoic acid (PHB) geranyltransferase, was found to be stimulated by the gamma-radiation treatments. The activity of PHB geranyltransferase was increased at 2 and 16 Gy with a negligible change at 32 Gy. In contrast, the activity of PHB glucosyltransferase was slightly changed at all doses of gamma radiation compared with the control cells. Therefore, the increase in PHB geranyltransferase activity leads to the accumulation of secondary metabolites such as a shikonin, which may contribute to plant defense against the stresses induced by gamma irradiation.     

Reactivity of chlorodeoxypseudoephedrines with oxo-, thio-, and selenocyanates

Herein, the reactivity of chlorodeoxypseudoephedrine hydrochlorides with oxo-, thio-, and selenocyanate nucleophiles is reported. 1,3-Heterazolidine-2-iminium or ammonium salts were obtained stereoselectively in most cases. The hard–soft nature of the calcogen atom determines the mechanistic pathway via an S_N2 (X = O), aziridine intermediate (X = Se), or both (X = S). A simple method to synthesize stereoselectively the trans-isomer of 3,4-dimethyl-5-phenyl-oxazolidine-2-iminium chloride and the cis-isomer of 4-methyl-5-phenyl-oxazoline-2-ammonium chloride, was also found. In addition, heterazolidine-2-imines or amines were liberated from the corresponding salts [Cl⁻ or XCN⁻ (X = O, S, Se)] with aqueous NaOH. Finally, cis-3,4-dimethyl-5-phenyl-oxazolidine-2-iminium chloride, cis-4-methyl-5-phenyl-oxazoline-2-amine, and trans-4-methyl-5-phenyl-selenazoline-2-amine compounds were studied by X-ray diffraction.     

(Vapour + liquid) equilibria for the binary mixtures (cis-pinane + α-pinene) and (cis-pinane + 1-butanol)

The isothermal and isobaric (vapour + liquid) equilibria for (cis-pinane + α-pinene) and (cis-pinane + 1-butanol) measured with an inclined ebulliometer are presented. The experimental results are analysed using the UNIQUAC equation with the temperature-dependence binary parameters with satisfactory results. Experimental vapour pressures of cis-pinane are also included.     

Spin-crossover in dimeric hydrogen-bonded iron(II) 2-(pyrazolyl)-pyridine and 2-(imidazolyl)-pyridine complexes

Five new hydrogen-bonded solvated iron(II) complexes of pyrazolyl- and imidazolyl-based N,N-chelating ligands have been synthesised. Water to ligand-NH hydrogen-bonded bridges occur in the pseudo-dimeric complexes {cis-[Fe(pypzH)₂(NCX)₂]₂(μ-OH₂)(H₂O)₂} · H₂O · MeOH (where X = S or Se), and in the chain complex {cis-[Fe(pypzH)₂(NCS)₂](μ-OH₂)}_n. A “half” spin-crossover (T_c = 125 K) was observed in the dimeric X = Se complex by means of magnetic measurements and no thermal hysteresis occurred between 4 and 300 K. The crystal structure at 123 K showed Fe–N distances consistent with the magnetism. Each Fe in the dimeric unit was structurally equivalent in the HS–LS state. Removal of the solvate molecules led to HS–HS behaviour over the temperature range 4–300 K. The pseudo-dimer with X = S also showed HS–HS behaviour as did the monomeric analogue cis-[Fe(pypzH)₂(NCS)₂]H₂O and a structurally different methanol-bridged dimer {cis-[Fe(pyimH)₂(NCS)₂]₂(μ-MeOH)₂} · 2MeOH (pypzH = 2-(1H-pyrazol-3-yl)-pyridine; pyimH = 2-(1H-imidazol-2-yl)-pyridine).     

Optochemical Control of mRNA Translation in Eukaryotes

A major stage in the expression of genes is the translation of messenger RNA (mRNA), and the regulation of this process is essential for protein production in cells. How tightly controlled gene expression can be spatially and temporally, is particularly evident in polar cells and embryonic development. We need tools to dissect these complex processes, if we wish to understand the underlying links, especially the difficulties brought on by malfunction. External bioorthogonal triggers are very helpful in this area, if they let us precisely control where and when a process is started. Equipping nucleic acids with light-responsive groups has proven to be an effective approach to examine the dynamic regulatory route of mRNA translation in living cells. In this review, we present an overview of the most recent methods for optochemically controlling translation, focusing on cis-acting technologies.     

Diterpenoids from the aerial parts of Leonurus macranthus

One cis clerodane-type (1) and three highly oxygenated labdane-type diterpenes (2-4) were isolated from the aerial parts of Leonurus macranthus. Compound 1 represents the first example of cis clerodane-type diterpene in the plants of Leonurus genus.     

Do lipases also catalyse the ring cleavage of inactivated cyclic trans-β-lactams?

Twelve-membered cyclic cis- and trans-β-lactams 1b and 2b and the corresponding cyclic cis- and trans-β-amino acid enantiomers, 1a, 1c and 2a, 2c were prepared through the CAL-B-catalysed enantioselective ring cleavage of racemic cis-13-azabicyclo[10.2.0]tetradecan-14-one, (±)-1, and trans-13-azabicyclo[10.2.0]tetradecan-14-one, (±)-2. High enantioselectivities (E >200) were observed for the ring opening of both the cis- and trans-β-lactams when the Lipolase-catalysed reactions were performed with 0.5 equiv of H₂O in i-Pr₂O at 70 °C. The resolved β-lactams 1b and 2b (yield ⩾47%) and β-amino acids 1a and 2a (yield ⩾32%) could be easily separated.     

Spectra and structure of silicon containing compounds: XXIX. Conformational studies of methyl vinyl difluorosilane from temperature dependent FT-IR spectra of xenon and krypton solutions

Variable temperature (−55 to −150°C) studies of the infrared spectra (3500–400 cm⁻¹) of methyl vinyl difluorosilane, CH₂CHSiF₂CH₃, dissolved in liquid xenon and krypton have been recorded. Utilizing three sets of conformer doublets due to the cis and gauche rotamers from the krypton solution and two pairs from the xenon solution, the enthalpy difference has been determined to be 67±7 cm⁻¹ (0.80±0.09 kJ/mol) and 83±11 cm⁻¹ (0.99±0.14 kJ/mol), respectively, with the gauche conformer the more stable form. However, in the crystalline solid only the cis conformer is present. Ab initio calculations have been carried out with several different basis sets up to MP2/6-311+G(2d,2p) with full electron correlation by the perturbation method from which the conformational stabilities have been determined. With the largest basis set MP2/6-311+G(2d,2p), the cis conformer is predicted to be the more stable conformer by 10 cm⁻¹ which is inconsistent with the experimental results; however, this value is so small that the ab initio prediction cannot be relied on to give the correct conformer stability. The spectroscopic and theoretical results are compared to the corresponding quantities for some similar molecules.