Breakpoint determination of 15 large deletions in Peutz–Jeghers subjects

The Peutz–Jeghers Syndrome (PJS) is an autosomal dominant polyposis disorder with increased risk of multiple cancers. STK11/LKB1 (hereafter named STK11) germline mutations account for the large majority of PJS cases whereas large deletions account for about 30% of the cases. We report here the first thorough molecular characterization of 15 large deletions identified in a cohort of 51 clinically well-characterized PJS patients. The deletions were identified by MLPA analysis and characterized by custom CGH-array and quantitative PCR to define their boundaries. The deletions, ranging from 2.9 to 180 kb, removed one or more loci contiguous to the STK11 gene in six patients, while partial STK11 gene deletions were present in the remaining nine cases. By means of DNA sequencing, we were able to precisely characterize the breakpoints in each case. Of the 30 breakpoints, 16 were located in Alu elements, revealing non-allelic homologous recombination (NAHR) as the putative mechanism for the deletions of the STK11 gene, which lays in a region with high Alu density. In the remaining cases, other mechanisms could be hypothesized, such as microhomology-mediated end-joining (MMEJ) or non-homologous end-joining (NHEJ). In conclusion we here demonstrated the non-random occurrence of large deletions associated with PJS. All our patients had a classical PJS phenotype, which shows that haploinsufficiency for SBNO2, C19orf26, ATP5D, MIDN, C19orf23, CIRBP, C19orf24,and EFNA2, does not apparently affect their clinical phenotype.     

Secondary ion mass spectrometry imaging and multivariate data analysis reveal co‐aggregation patterns of Populus trichocarpa leaf surface compounds on a micrometer scale

Spatially resolved analysis of a multitude of compound classes has become feasible with the rapid advancement in mass spectrometry imaging strategies. In this study, we present a protocol that combines high lateral resolution time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) imaging with a multivariate data analysis (MVA) approach to probe the complex leaf surface chemistry of Populus trichocarpa. Here, epicuticular waxes (EWs) found on the adaxial leaf surface of P. trichocarpa were blotted on silicon wafers and imaged using TOF‐SIMS at 10 μm and 1 μm lateral resolution. Intense M^+● and M^?● molecular ions were clearly visible, which made it possible to resolve the individual compound classes present in EWs. Series of long‐chain aliphatic saturated alcohols (C₂₁–C₃₀), hydrocarbons (C₂₅–C₃₃) and wax esters (WEs; C₄₄–C₄₈) were clearly observed. These data correlated with the ⁷Li‐chelation matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) analysis, which yielded mostly molecular adduct ions of the analyzed compounds. Subsequently, MVA was used to interrogate the TOF‐SIMS dataset for identifying hidden patterns on the leaf's surface based on its chemical profile. After the application of principal component analysis (PCA), a small number of principal components (PCs) were found to be sufficient to explain maximum variance in the data. To further confirm the contributions from pure components, a five‐factor multivariate curve resolution (MCR) model was applied. Two distinct patterns of small islets, here termed ‘crystals’, were apparent from the resulting score plots. Based on PCA and MCR results, the crystals were found to be formed by C₂₃ or C₂₉ alcohols. Other less obvious patterns observed in the PCs revealed that the adaxial leaf surface is coated with a relatively homogenous layer of alcohols, hydrocarbons and WEs. The ultra‐high‐resolution TOF‐SIMS imaging combined with the MVA approach helped to highlight the diverse patterns underlying the leaf's surface. Currently, the methods available to analyze the surface chemistry of waxes in conjunction with the spatial information related to the distribution of compounds are limited. This study uses tools that may provide important biological insights into the composition of the wax layer, how this layer is repaired after mechanical damage or insect feeding, and which transport mechanisms are involved in deploying wax constituents to specific regions on the leaf surface.     

Oxidative stability of polyunsaturated fatty acid in phosphatidylcholine liposomes

Synthesized PCs containing docosahexaenoic acid (DHA), arachidonic acid (AA), linoleic acid (LA), and palmitic acid (PA) at known positions in the glycerol moiety were oxidized in liposomes, bulk, and organic solvent. In bulk and organic solvent, the oxidative stability of PC decreased with increasing degrees of unsaturation. However, the degree of unsaturation had little effect on the stability of PC in liposomes. The oxidative stability of PC in liposomes would be affected by the chemical reactivity based on the degree of unsaturation and by the conformation of fatty acyl component in PC bilayers. When the oxidative stability of 1-PA-2-LA-PC or 1-PA-2-AA-PC was compared with that of a 1:1 (mol ratio) mixture of 1,2-diPA-PC + 1,2-diLA-PC, or 1,2-diPA-PC + 1,2-diAA-PC, respectively, the former PC was more oxidatively stable than that of the latter PC mixture in all oxidation systems, although the degree of unsaturation of 1-PA-2-PUFA-PC was the same as that of the corresponding mixture of diPA-PC + diPUFA-PC. The higher oxidative stability of 1-PA-2-PUFA-PC than that of a corresponding mixture of diPA-PC + diPUFA-PC in liposomes was suggested to be due to the different conformation of PC bilayers and the different rate of hydrogen abstraction by free radicals from intermolecular and intramolecular acyl groups.     

Altered mitochondrial apoptotic pathway in placentas from undernourished rat gestations

Maternal undernutrition (MUN) during pregnancy results in intrauterine growth-restricted (IUGR) fetuses and small placentas. Although reduced fetal nutrient supply has been presumed to be etiologic in IUGR, MUN-induced placental dysfunction may occur prior to detectable fetal growth restriction. Placental growth impairment may result from apoptosis signaled by mitochondria in response to reduced energy substrate. Therefore, we sought to determine the presence of mitochondrial-induced apoptosis under MUN and ad libitum diet (AdLib) pregnancies. Pregnant rats were fed an AdLib or a 50% MUN diet from embryonic day 10 (E10) to E20. At E20, fetuses and placentas from proximal- and mid-horns (extremes of nutrient/oxygen supply) were collected. Right-horn placentas were used to quantify apoptosis. Corresponding left-horn placentas were separated into basal (hormone production) and labyrinth (feto-maternal exchange) zones, and protein expression of the mitochondrial pathway was determined. Our results show that the MUN placentas had significantly increased apoptosis, with lower expression of cytosolic and mitochondrial anti-apoptotic Bcl2 and Bcl-X(L), and significantly higher expression of pro-apoptotic Bax and Bak especially in the labyrinth zone. This was paralleled by higher coimmunostaining with the mitochondrial marker manganese superoxide dismutase (MnSOD), indicating transition of pro-apoptotic factors to the mitochondrial membrane. Also, cytosolic cytochrome c and activated caspases-9 and -3 were significantly higher in all MUN. Conversely, peroxisome proliferator-activator receptor-γ (PPARγ), a member of the nuclear receptor family with anti-apoptotic properties, was significantly downregulated in both zones and horns. Our results suggest that MUN during rat pregnancy enhances mitochondria-dependent apoptosis in the placenta, probably due to the downregulation of PPARγ expression.     

Serum levels of IL-32 in patients with coronary artery disease and its relationship with the serum levels of IL-6 and TNF-α

Molecular Biology Reports - The coronary artery disease (CAD) is a chronic inflammatory disease caused by atherosclerosis, in which arteries become clogged due to plaque formation, fat...     

Genetic Background of Hirschsprung Disease: A Bridge Between Basic Science and Clinical Application

Hirschsprung's disease (HSCR) is a congenital disorder, defined by partial or complete loss of the neuronal ganglion cells in the intestinal tract, which is caused by the failure of neural crest cells to migrate completely during intestinal development during fetal life. HSCR has a multifactorial etiology, and genetic factors play a key role in its pathogenesis; these include mutations within several gene loci. These have been identified by screening candidate genes, or by conducting genome wide association (GWAS) studies. However, only a small portion of them have been proposed as major genetic risk factors for the HSCR. In this review, we focus on those genes that have been identified as either low penetrant or high penetrant variants that determine the risk of Hirschsprung's disease. J. Cell. Biochem. 119: 28–33, 2018. © 2017 Wiley Periodicals, Inc.     

The fungal phytochrome FphA from Aspergillus nidulans

The red light-sensing photoreceptor FphA from Aspergillus nidulans is involved in the regulation of developmental processes in response to light. Here we present extended biochemical and spectroscopic characterization of recombinant FphA using a synthetic gene with host-adapted codon usage. The recombinant photosensory domain FphAN753 was shown to display all features of a bona fide phytochrome. It covalently binds biliverdin as chromophore and undergoes red/far-red light-inducible photoconversion with both parent states being protonated. The large N-terminal variable extension of FphA exerts a stabilizing effect on the active Pfr state. Upon substitution of the highly conserved histidine 504, involved in the hydrogen-bonding network of the protein moiety and the chromophore, chromophore attachment and photoreversibility were completely impaired. FphA is a functional sensor histidine kinase with a strong red-light-dependent autophosphorylation activity. Furthermore, intermolecular trans-phosphorylation to the response regulator domain of a second monomer could be demonstrated. Interestingly, co-incubation of FphA and FphA variants led to enhanced autophosphorylation, including the "inactive" Pr form. The latter observed phenomenon might suggest that auto- and trans-phosphorylation activity is modulated by additional interaction partners leading to variable phosphorylation events that trigger a specific output response.     

Changes in secondary metabolites and fiber quality of cotton (Gossypium hirsutum) seed under consecutive water stress and in silico analysis of cellulose synthase and xyloglucan endotransglucosylase

Global warming has led to severe drought conditions. The selection of plant varieties that can withstand drought and produce increased yields are of utmost importance. In the current study, secondary metabolites, seed trait and fiber characteristic of cottonseeds (Gossypium hirsutum) exposed to double and third water stress exposure was investigated. Total phenol and tannin content in W₁S₃₃ increased significantly after third water stress exposure. Accumulation of wax was enhanced in seeds of W₃S₃₃ and W₃S₃₄ that were subjected to third water stress. Fiber quality parameters decreased when cottonseeds were rainfed. High irrigation resulted in fragile and delicate fiber. Seeds grown under 66% FC irrigation saved water and produced seeds that had the potential of producing high quality fibers. In silico analysis was performed on cellulose synthase A (CesA) and xyloglucan endotransglycosylase (XET) enzymes present in Gossypium hirsutum. The intracellular locations of the CesA and XET1 enzymes are the plasma membrane and cell wall, respectively. Proline is conserved in the C-terminal of the CesA enzyme and plays an important role in enzyme functionality. This study provides a better understanding as to the mechanisms by which the plant can tolerate and combat water stress conditions as well as reduce water consumption. In order to grow cotton seeds with desirable morphometric characteristics and optimal fibers under water stress exposure and in dry areas, it is better to use seeds that are irrigated under optimal irrigation conditions, ie 66% FC.