An Improved FPT Algorithm for the Flip Distance Problem

Given a set cal P of points in the Euclidean plane and two triangulations of cal P, the flip distance between these two triangulations is the minimum number of flips required to transform one triangulation into the other. The Parameterized Flip Distance problem is to decide if the flip distance between two given triangulations is equal to a given integer k. The previous best FPT algorithm runs in time O^*(kcdot c^k) (cleq 2times 14^11), where each step has fourteen possible choices, and the length of the action sequence is bounded by 11k. By applying the backtracking strategy and analyzing the underlying property of the flip sequence, each step of our algorithm has only five possible choices. Based on an auxiliary graph G, we prove that the length of the action sequence for our algorithm is bounded by 2|G|. As a result, we present an FPT algorithm running in time O^*(kcdot 32^k)

Summer moisture changes in the Lake Qinghai area on the northeastern Tibetan Plateau recorded from a meadow section over the past 8400 yrs

Holocene climatic and environmental changes on the northeastern Tibetan Plateau (TP) have been widely discussed based on the climatic records from sedimentary cores. However, differences in the reconstructed climatic history from various studies in this region still exist, probably due to influence of climatic proxies from multiple factors and the chronological uncertainties in lacustrine sediments. Here we present records of terrestrial plant delta C-13, soil color and total organic carbon content over the past 8400 years from a well-dated meadow section on the northeastern TP. The terrestrial plant delta C-13 value serves as a good summer precipitation/moisture indicator in the studied region. Soil color property and TOC content are also able to disentangle the moisture evolution history. All the data show much wet climates at 8400-7400 cal yr BP, dry climates at 7400-6000 cal yr BP and then wet conditions with fluctuation at 6000-3200 cal yr BP. Late Holocene moisture appears to be comparable with moist conditions from 6000 to 3200 cal yr BP. By further comparing the climatic variations in the Lake Qinghai area with records of the reconstructed summer temperature and the Asian Monsoon precipitation, we believe that the pattern of moisture/precipitation evolution in the Lake Qinghai area was not completely consistent with regions around Lake Qinghai, probably due to complicated interaction between the East Asian Summer Monsoon and the Indian Summer Monsoon

A conserved circadian function for the Neurofibromatosis 1 gene

Summary: Loss of the Neurofibromatosis 1 (Nf1) protein, neurofibromin, in Drosophila disrupts circadian rhythms of locomotor activity without impairing central clock function, suggesting effects downstream of the clock. However, the relevant cellular mechanisms are not known. Leveraging the discovery of output circuits for locomotor rhythms, we dissected cellular actions of neurofibromin in recently identified substrates. Herein, we show that neurofibromin affects the levels and cycling of calcium in multiple circadian peptidergic neurons. A prominent site of action is the pars intercerebralis (PI), the fly equivalent of the hypothalamus, with cell-autonomous effects of Nf1 in PI cells that secrete DH44. Nf1 interacts genetically with peptide signaling to affect circadian behavior. We extended these studies to mammals to demonstrate that mouse astrocytes exhibit a 24-hr rhythm of calcium levels, which is also attenuated by lack of neurofibromin. These findings establish a conserved role for neurofibromin in intracellular signaling rhythms within the nervous system. : Bai et al. show that the gene mutated in the disease Neurofibromatosis 1 is required for maintaining levels or cycling of calcium in circadian neurons in Drosophila and in mammalian cells. These effects likely account for effects of Nf1 on circadian behavior in Drosophila and may be relevant in explaining sleep phenotypes in patients. Keywords: circadian rhythms, neurofibromatosis 1, Drosophila, peptide signaling, cycling of calcium, mouse astrocyte

Hypoxia-Regulated miR-146a Targets Cell Adhesion Molecule 2 to Promote Proliferation, Migration, and Invasion of Clear Cell Renal Cell Carcinoma

Background/Aims: miR-146a has recently been shown to promote cell proliferation, migration, and invasion in many cancers, but the role of miR-146a in clear cell renal cell carcinoma (ccRCC) remains unclear. Methods: Reverse transcription quantitative PCR (RT-qPCR) was performed to investigate the mRNA expression of miR-146a and CADM2 in ccRCC tissues. The luciferase reporter assay, Western blotting, and ChIP assay were carried out to explore the promoter and the transcription factor of miR-146a. Moreover, the effect of miR-146a and CADM2 on ccRCC cells was explored using methyl thiazolyl tetrazolium, colony formation, and migration and invasion assays. The luciferase reporter assay, RT-qPCR, western blotting, and immunofluorescence assay were carried out to investigate whether CADM2 is directly regulated by miR-146a. A tumor xenograft model and immunohistochemical staining were used to examine the carcinogenic effect of miR-146a and CADM2 in vivo. Results: miR-146a has been shown to promote cell proliferation, migration, and invasion. Here, we found that miR-146a is highly expressed in ccRCC tissues, whereas CADM2 is down-regulated. Hypoxia can induce the expression of miR-146a by stimulating its promoter. In addition, we demonstrated that miR-146a promoted and CADM2 inhibited proliferation, migration, and invasion of ccRCC cells. The 3’ untranslated region (UTR) luciferase reporter assay identified that miR-146a targeted the 3’ UTR of CADM2 and negatively regulated its expression. Ectopic expression of CADM2 counteracted the promoting effect of miR-146a on cell proliferation, migration, invasion, and the epithelial–mesenchymal transition process. Conclusion: Together, the finding of down-regulation of CADM2 by miR-146a can provide new insights into ccRCC pathogenesis and might contribute to the development of novel therapeutic strategies

Characterization of a Novel Megabirnavirus from \u3cem\u3eSclerotinia sclerotiorum\u3c/em\u3e Reveals Horizontal Gene Transfer from Single-Stranded RNA Virus to Double-Stranded RNA Virus

Mycoviruses have been detected in all major groups of filamentous fungi, and their study represents an important branch of virology. Here, we characterized a novel double-stranded RNA (dsRNA) mycovirus, Sclerotinia sclerotiorum megabirnavirus 1 (SsMBV1), in an apparently hypovirulent strain (SX466) of Sclerotinia sclerotiorum. Two similarly sized dsRNA segments (L1- and L2-dsRNA), the genome of SsMBV1, are packaged in rigid spherical particles purified from strain SX466. The full-length cDNA sequence of L1-dsRNA/SsMBV1 comprises two large open reading frames (ORF1 and ORF2), which encode a putative coat protein and an RNA-dependent RNA polymerase (RdRp), respectively. Phylogenetic analysis of the RdRp domain clearly indicates that SsMBV1 is related to Rosellinia necatrix megabirnavirus 1 (RnMBV1). L2-dsRNA/SsMBV1 comprises two nonoverlapping ORFs (ORFA and ORFB) encoding two hypothetical proteins with unknown functions. The 5′-terminal regions of L1- and L2-dsRNA/SsMBV1 share strictly conserved sequences and form stable stem-loop structures. Although L2-dsRNA/SsMBV1 is dispensable for replication, genome packaging, and pathogenicity of SsMBV1, it enhances transcript accumulation of L1-dsRNA/SsMBV1 and stability of virus-like particles (VLPs). Interestingly, a conserved papain-like protease domain similar to a multifunctional protein (p29) of Cryphonectria hypovirus 1 was detected in the ORFA-encoded protein of L2-dsRNA/SsMBV1. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer may have occurred from a single-stranded RNA (ssRNA) virus (hypovirus) to a dsRNA virus, SsMBV1. Our results reveal that SsMBV1 has a slight impact on the fundamental biological characteristics of its host regardless of the presence or absence of L2-dsRNA/SsMBV1. IMPORTANCE Mycoviruses are widespread in all major fungal groups, and they possess diverse genomes of mostly ssRNA and dsRNA and, recently, circular ssDNA. Here, we have characterized a novel dsRNA virus (Sclerotinia sclerotiorum megabirnavirus 1 [SsMBV1]) that was isolated from an apparently hypovirulent strain, SX466, of Sclerotinia sclerotiorum. Although SsMBV1 is phylogenetically related to RnMBV1, SsMBV1 is markedly distinct from other reported megabirnaviruses with two features of VLPs and conserved domains. Our results convincingly showed that SsMBV1 is viable in the absence of L2-dsRNA/SsMBV1 (a potential large satellite-like RNA or genuine genomic virus component). More interestingly, we detected a conserved papain-like protease domain that commonly exists in ssRNA viruses, including members of the families Potyviridae and Hypoviridae. Phylogenetic analysis based on the protease domain suggests that horizontal gene transfer might have occurred from an ssRNA virus to a dsRNA virus, which may provide new insights into the evolutionary history of dsRNA and ssRNA viruses

New Insight Into the Structure-Activity Relationship of Sweet-Tasting Proteins: Protein Sector and Its Role for Sweet Properties

Sweet-tasting protein is a kind of biomacromolecule that has remarkable sweetening power and is regarded as the promising sugar replacer in the future. Some sweet-tasting proteins has been used in foods and beverages. However, the structure and function relationship of these proteins is still elusive, and guidelines for their protein engineering is limited. It is well-known that the sweet-tasting proteins bind to and activate the sweet taste receptor T1R2/T1R3, thus eliciting their sweetness. The “wedge-model” for describing the interaction between sweet-tasting proteins and sweet taste receptor to elucidate their sweetness has been reported. In this perspective article, we revealed that the intramolecular interaction forces in sweet-tasting proteins is directly correlated to their properties (sweetness and stability). This intramolecular interaction pattern, named as “protein sector,” refers to a small subset of residues forming physically connections, which cooperatively affect the function of the proteins. Based on the analysis of previous experimental data, we suggest that “protein sector” of sweet-tasting proteins is pivotal for their sweet properties, which are meaningful guidelines for the future protein engineering

The enhancement of electrochemical capacitance of biomass-carbon by pyrolysis of extracted nanofibers

Biomass-derived carbons have been extensively researched as electrode material for energy storage and conversion recently. However, most of the previous works convert crude biomass directly into carbon and the electrochemical capacitances for the resultant carbons are quite often underestimated as well as large variations in capacitances exist in literatures due to the complex nature of biomass, which practically hinder their applications. In this work, polysaccharide nanofibers were extracted from an inexpensive natural fungus using a hydrothermal method and were converted to porous carbon nanofibers (CNFs) by potassium hydroxide activation. The porous carbons were assembled into symmetric supercapacitors using both potassium hydroxide and an ionic liquid (IL) as electrolytes. Solid state nuclear magnetic resonance characterization showed that the micropores of the as-prepared carbons are accessible to the IL electrolyte when uncharged and thus high capacitance is expected. It is found in both electrolytes the electrochemical capacitances of CNFs are significantly higher than those of the porous carbon derived directly from the crude fungus. Furthermore, the CNFs delivered an extraordinary energy density of 92.3 Wh kg−1 in the IL electrolyte, making it a promising candidate for electrode materials for supercapacitors.<br/