The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.     

Inactivation of TNF signaling by rationally designed dominant-negative TNF variants

Tumor necrosis factor (TNF) is a key regulator of inflammatory responses and has been implicated in many pathological conditions. We used structure-based design to engineer variant TNF proteins that rapidly form heterotrimers with native TNF to give complexes that neither bind to nor stimulate signaling through TNF receptors. Thus, TNF is inactivated by sequestration. Dominant-negative TNFs represent a possible approach to anti-inflammatory biotherapeutics, and experiments in animal models show that the strategy can attenuate TNF-mediated pathology. Similar rational design could be used to engineer inhibitors of additional TNF superfamily cytokines as well as other multimeric ligands.     

Evidence of a pluripotent human embryonic stem cell line derived from a cloned blastocyst

Somatic cell nuclear transfer (SCNT) technology has recently been used to generate animals with a common genetic composition. In this study, we report the derivation of a pluripotent embryonic stem (ES) cell line (SCNT-hES-1) from a cloned human blastocyst. The SCNT-hES-1 cells displayed typical ES cell morphology and cell surface markers and were capable of differentiating into embryoid bodies in vitro and of forming teratomas in vivo containing cell derivatives from all three embryonic germ layers in severe combined immunodeficient mice. After continuous proliferation for more than 70 passages, SCNT-hES-1 cells maintained normal karyotypes and were genetically identical to the somatic nuclear donor cells. Although we cannot completely exclude the possibility that the cells had a parthenogenetic origin, imprinting analyses support a SCNT origin of the derived human ES cells.     

Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase

Silent information regulator 2 (Sir2) proteins (sirtuins) are nicotinamide adenine dinucleotide-dependent deacetylases that regulate important biological processes. Mammals have seven sirtuins, Sirt1 to Sirt7. Four of them (Sirt4 to Sirt7) have no detectable or very weak deacetylase activity. We found that Sirt5 is an efficient protein lysine desuccinylase and demalonylase in vitro. The preference for succinyl and malonyl groups was explained by the presence of an arginine residue (Arg(105)) and tyrosine residue (Tyr(102)) in the acyl pocket of Sirt5. Several mammalian proteins were identified with mass spectrometry to have succinyl or malonyl lysine modifications. Deletion of Sirt5 in mice appeared to increase the level of succinylation on carbamoyl phosphate synthase 1, which is a known target of Sirt5. Thus, protein lysine succinylation may represent a posttranslational modification that can be reversed by Sirt5 in vivo.     

Endocannabinoid hydrolysis generates brain prostaglandins that promote neuroinflammation

Phospholipase A(2)(PLA(2)) enzymes are considered the primary source of arachidonic acid for cyclooxygenase (COX)-mediated biosynthesis of prostaglandins. Here, we show that a distinct pathway exists in brain, where monoacylglycerol lipase (MAGL) hydrolyzes the endocannabinoid 2-arachidonoylglycerol to generate a major arachidonate precursor pool for neuroinflammatory prostaglandins. MAGL-disrupted animals show neuroprotection in a parkinsonian mouse model. These animals are spared the hemorrhaging caused by COX inhibitors in the gut, where prostaglandins are instead regulated by cytosolic PLA(2). These findings identify MAGL as a distinct metabolic node that couples endocannabinoid to prostaglandin signaling networks in the nervous system and suggest that inhibition of this enzyme may be a new and potentially safer way to suppress the proinflammatory cascades that underlie neurodegenerative disorders.     

Synthesis of zeolite as ordered multicrystal arrays

Zeolites are crystalline nanoporous aluminosilicates widely used in industry. In order for zeolites to find applications as innovative materials, they need to be organized into large two- and three-dimensional (2D and 3D) arrays. We report that uniformly aligned polyurethane films can serve as templates for the synthesis of uniformly aligned 2D and possibly 3D arrays of silicalite-1 crystals, in which the orientations of the crystals are controlled by the nature of the polymers. We propose that the supramolecularly organized organic-inorganic composites that consist of the hydrolyzed organic products and the seed crystals are responsible for this phenomenon.     

Confirmation of hybrid origin in Arisaema (Araceae) using molecular markers

A population of hybrids between Arisaema triphyllum subsp. stewardsonii and A. dracontium was investigated using molecular markers to document the hybrid origin. Total genomic DNA was extracted from A. triphyllum, A. dracontium, and the hybrids, and subjected to sequence analysis of various regions of intergenic spacer and genes of chloroplast or intergenic spacer and genes of nuclear ribosome for single nucleotide polymorphisms (SNPs). Clustering was performed using the unweighted pair group method with averages (UPGMA) tested by bootstrap (BS). Hybrid origin could not be easily confirmed in some regions. However, dendrograms constructed with a combined sequence analysis of A. triphyllum 26S ribosomal RNA gene [sequence identification (SI) 467] plus A. tortuosum phytochrome C-like (phyC) gene (SI 468) were very similar to dendrograms constructed from sequences of all regions. This suggests that selecting SI 467 and SI 468 would be practical to identify hybrid origins involving two parental species. Clustering of hybrids together with the female parent in most target regions suggests that, in Arisaema, cpDNA is considered maternally inherited.     

Effect of microfluidization on in vitro micellization and intestinal cell uptake of lutein from Chlorella vulgaris

Chlorella is a nutrient-rich microalga that contains protein, lipid, minerals, vitamins, and high levels of lutein. This study evaluated the bioavailability of lutein from Chlorella vulgaris using a coupled in vitro digestion and human intestinal Caco-2 cell model. Lutein bioaccessibility was low, and approximately 75% of total C. vulgaris lutein was not micellized during the digestion process but remained in the insoluble digestate. Microfluidization improved lutein micellization efficiency during C. vulgaris digestion. C. vulgaris was microfluidized at a pressure exceeding 10000 psi, and the cell surface disruption was visualized by scanning electron microscopy. The mean C. vulgaris particle size was reduced from 3.56 to 0.35 μm with the microfluidization treatment. C. vulgaris microfluidization at 20000 psi was three times more efficient for aqueous lutein micelles production as compared with untreated C. vulgaris, and the final lutein content accumulated by intestinal Caco-2 cells was also higher with microfluidization. C. vulgaris lutein stability was not affected by microfluidization. These results indicate that microfluidization may be useful for improving lutein bioaccessibility from C. vulgaris during food processing.     

Identification and structure elucidation of a p-phenoxybenzaldehyde in bamboo shoots by HPLC-ESI/MS/MS and NMR

In this study, a derivative of p-phenoxybenzaldehyde in bamboo shoots was investigated. Bamboo shoots were ground and extracted with water, and an aqueous suspension was purified by SPE using Oasis HLB cartridges. After the SPE procedure, the analytes were analyzed by HPLC with refractive index detection (HPLC-RI). In the HPLC-RI analysis for sucralose, a putative sucralose was detected. In the subsequent HPLC-PDA analysis, the suspicious peak showed a unique UV absorption spectrum with the maximum wavelength at 285 nm indicating the existence of an aromatic ring. The contents of the unknown compound in bamboo shoot products ranged from 0.01 to 0.15 mg/g. The identity of the unknown compound was further confirmed by HPLC-ESI/MS/MS. The molecular weight of the unknown compound was determined to be 244. The chemical structure of the unknown compound was elucidated on the basis of NMR spectroscopic analyses ((1)H, (13)C, DEPT, COSY, HMQC, and HMBC). Finally, the structure of the unknown compound was characterized as 4-(4-dihydroxymethylphenoxy)benzaldehyde.