Schmeissneria: A missing link to angiosperms?

BACKGROUND: The origin of angiosperms has been under debate since the time of Darwin. While there has been much speculation in past decades about pre-Cretaceous angiosperms, including Archaefructus, these reports are controversial. The earliest reliable fossil record of angiosperms remains restricted to the Cretaceous, even though recent molecular phylogenetic studies suggest an origin for angiosperms much earlier than the current fossil record. RESULTS: In this paper, after careful SEM and light microscopic work, we report fossils with angiospermous traits of the Jurassic age. The fossils were collected from the Haifanggou Formation (middle Jurassic) in western Liaoning, northeast China. They include two female structures and an associated leaf on the same slab. One of the female structures is physically connected to the apex of a short shoot. The female organs are borne in pairs on short peduncles that are arranged along the axis of the female structure. Each of the female organs has a central unit that is surrounded by an envelope with characteristic longitudinal ribs. Each central unit has two locules completely separated by a vertical septum. The apex of the central unit is completely closed. The general morphology places these fossils into the scope of Schmeissneria, an early Jurassic genus that was previously attributed to Ginkgoales. CONCLUSION: Because the closed carpel is a character only found in angiosperms, the closed apex of the central unit suggests the presence of angiospermy in Schmeissneria. This angiospermous trait implies either a Jurassic angiosperm or a new seed plant group parallel to angiosperms and other known seed plants. As an angiosperm, the Liassic age (earliest Jurassic) of Schmeissneria microstachys would suggest an origin of angiosperms during the Triassic. Although still uncertain, this could have a great impact on our perspective of the history, diversity and systematics of seed plants and angiosperms

MSIsensor-ct: Microsatellite instability detection using cfDNA sequencing data

MOTIVATION: Microsatellite instability (MSI) is a promising biomarker for cancer prognosis and chemosensitivity. Techniques are rapidly evolving for the detection of MSI from tumor-normal paired or tumor-only sequencing data. However, tumor tissues are often insufficient, unavailable, or otherwise difficult to procure. Increasing clinical evidence indicates the enormous potential of plasma circulating cell-free DNA (cfNDA) technology as a noninvasive MSI detection approach. RESULTS: We developed MSIsensor-ct, a bioinformatics tool based on a machine learning protocol, dedicated to detecting MSI status using cfDNA sequencing data with a potential stable MSIscore threshold of 20%. Evaluation of MSIsensor-ct on independent testing datasets with various levels of circulating tumor DNA (ctDNA) and sequencing depth showed 100% accuracy within the limit of detection (LOD) of 0.05% ctDNA content. MSIsensor-ct requires only BAM files as input, rendering it user-friendly and readily integrated into next generation sequencing (NGS) analysis pipelines. AVAILABILITY: MSIsensor-ct is freely available at https://github.com/niu-lab/MSIsensor-ct. SUPPLEMENTARY INFORMATION: Supplementary data are available at Briefings in Bioinformatics online

Dietary Sphingomyelin Inhibits Colonic Tumorigenesis with an Up-regulation of Alkaline Sphingomyelinase Expression in ICR Mice

Background: Sphingomyelin (SM) hydrolysis generates biologically active products regulating cell growth, differentiation and apoptosis. Dietary SM has been found to inhibit colonic tumorigenesis. Alkaline sphingomyelinase (alk-SMase) is the key enzyme responsible for sphingomyelin digestion in the gut. Whether or not dietary sphingomyelin affects alk-SMase expression was examined in a colon cancer animal model. Materials and Methods: Imprinting control region (ICR) mice were injected with 1,2-dimethylhydrazine (DMH) and then fed a diet with or without SM (0.5 g/kg in diet) for 22 weeks. The colonic tumorigenesis and alk-SMase activity were determined and alk-SMase expression was examined by Western blot and PCR. Results: Dietary SM inhibited the tumorigenesis and increased the alk-SMase activity in the colon by 65%. The increased activity was associated with increased enzyme protein and mRNA expression. No changes of acid and neutral sphingomyelinase activities were found. Conclusion: Long-term supplementation with dietary sphingomyelin up-regulates colonic alk-SMase expression, which may contribute to the inhibitory effects of sphingomyelin against colonic carcinogenesis

A New Organic-Inorganic Compound Fertilizer for Improving Growth, Yield, and 2-Acetyl-1-Pyrroline Biosynthesis of Fragrant Rice

Fragrant rice (Oryza sativa L.) is a high-valued rice type and possesses a unique aroma with 2-acetyl-1-pyrroline (2-AP) as the critical component. However, the cultivation measures in fragrant rice production are far from perfect. In this study, a new organic-inorganic compound fertilizer was made with organic matter, urea, superphosphate, potassium chloride, zinc sulfate, and lanthanum chloride. A four-year field experiment was conducted to investigate its effects on fragrant rice growth, yield formation, and 2-acetyl-1-pyrroline biosynthesis. Three treatments, i.e., (CK) no fertilizer was applied, (IF) the urea, superphosphate, and potassium chloride were applied at 234 kg ha−1, 450 kg ha−1 and 108 kg ha−1, and (OICF) this new fertilizer composed of 10% organic matter, 26% urea, 50% superphosphate, 12% potassium chloride, 1.9% zinc sulfate, and 0.1% lanthanum chloride, was applied at 900 kg ha−1, were adopted in the present study. Across four experimental years, the results showed that the grain yield in OICF treatment ranged between 5.86–8.29 t ha−1, and was significantly (p < 0.05) higher than that in IF treatment and CK. The improvement in grain yield due to OICF treatment was explained by increased effective panicle number per m2 and seed-setting rate. The highest or equally highest chlorophyll content and the net photosynthetic rate at 20, 40, 60, and 80 days after transplanting were recorded in OICF treatment among three treatments. OICF treatment also increased the aboveground biomass of fragrant rice compared with IF treatment and CK. Moreover, compared with CK and IF treatment, OICF treatment significantly (p < 0.05) increased grain 2-AP content by 30–38% and 10–21%, respectively. The contents of 2-AP related precursors, including proline and 1-pyrroline, also increased due to OICF treatment. This study provided a new organic-inorganic compound fertilizer and suggested that it could be used to achieve the goals of high yield and high grain 2-AP content in fragrant rice production

Preparation and Antibiofilm Properties of Zinc Oxide/Porous Anodic Alumina Composite Films

Abstract The PAA (porous anodic alumina) films were prepared by two-step anodic oxidation after different times, and then the ZnO/PAA composite films were prepared by sol-gel method on their surface. Meanwhile, the ZnO/PAA composite films were characterized by X-ray diffraction (XRD), thermogravimetric/differential thermal analyzer (TG/DTA), Fourier transform infrared spectrometer (FT-IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), selected area electron diffraction (SAED), and water contact angle (CA). The antibiofilm properties of ZnO/PAA composite films on Shewanella putrefaciens were measured simultaneously. The results show that the micromorphologies of PAA and ZnO/PAA composite films are affected by second anodization time. ZnO is a hexagonal wurtzite structure, and ZnO particles with a diameter of 10–30 nm attach to the inner or outer surfaces of PAA. After being modified by Si69, the ZnO films translate from hydrophilia to hydrophobicity. The ZnO/PAA film with the optimal antibiofilm properties is prepared on the PAA surface by two-step anodization for 40 min. The adherence of Shewanella putrefaciens is restrained by its super-hydrophobicity, and the growth of biofilm bacteria is inhibited by its abundant ZnO particles

Batf3-dependent CD8α+ Dendritic Cells Aggravates Atherosclerosis via Th1 Cell Induction and Enhanced CCL5 Expression in Plaque Macrophages

Dendritic cells (DCs) play an important role in controlling T cell-mediated adaptive immunity in atherogenesis. However, the role of the basic leucine zipper transcription factor, ATF-like 3 (Batf3)-dependent CD8α+ DC subset in atherogenesis remains unclear. Here we show that Batf3−/−Apoe−/− mice, lacking CD8α+ DCs, exhibited a significant reduction in atherogenesis and T help 1 (Th1) cells compared with Apoe−/− controls. Then, we found that CD8α+ DCs preferentially induce Th1 cells via secreting interleukin-12 (IL-12), and that the expression of interferon-gamma (IFN-γ)or chemokine (C-C motif) ligand 5 (CCL5) in aorta were significantly decreased in Batf3−/−Apoe−/− mice. We further demonstrated that macrophages were the major CCL5-expressing cells in the plaque, which was significantly reduced in Batf3−/−Apoe−/− mice. Furthermore, we found CCL5 expression in macrophages was promoted by IFN-γ. Finally, we showed that Batf3−/−Apoe−/− mice displayed decreased infiltration of leukocytes in the plaque. Thus, CD8α+ DCs aggravated atherosclerosis, likely by inducing Th1 cell response, which promoted CCL5 expression in macrophages and increased infiltration of leukocytes and lesion inflammation