Habitat associations and seasonal activity of carabid beetles (Coleoptera: Carabidae) in Dongling Mountain, North China

Habitat distribution and seasonal occurrence of carabid beetles were determined using pitfall traps in 1999 and 2000 in the temperate forest zone of the Dongling Mountain, North China. Eight sites differing in vegetation and moisture were selected so as to represent four habitat types. Carabid assemblages of the six forested habitats (lowland, upland and coppice) weremore similar to each other than to the two shrub assemblages. Lowland forest had the highest species richness, and coppice forest had the highest diversity (H’) and equitability (J). Of the 41 species caught, the 18 most abundant species were divided into four distribution types: habitat generalists, forest generalists, forest specialists, and shrub (or coppice) specialists. Mean catches of all beetles showed clear peaks from May to August in nearly all habitats. The catches of the six most abundant species were more or less positively correlated during the two study years, suggesting their similar habitat preferences

Carabus (Coleoptera: Carabidae) assemblages of native forests and non-native plantations in Northern China

The effects of non-native plantation established after clear-cutting were studied in Dongling Mountain region, Northern China. Pitfall catches of Carabus beetles from a non-native larch plantation were compared with those from two native forests, an oak forest and a mixed broad-leaved forest. More individuals were captured from the mixed broad-leaved forest and the larch plantation than from the oak forest. For the threemost abundant species in this area, C. crassesculptus peaked in abundance in the mixed broad-leaved forest; C. manifestus peaked in the larch plantation, and C. sculptipennis in the oak forest. Measured by PcoAusing Bray-Curtis index of dissimilarity, species composition of the larch plantation was different from the two native forests, but overlapped remarkably with them. All the three abundant species showed a similar positive relationship between local distribution and abundance. Captures of abundant species were clumped within the forest, but the extent of aggregation among forests was different. Monthly catches of total Carabus, and C. crassesculptus alone, peaked in June–August in all the three forests, but C. manifestus peaked in June and again in August. Our results suggest that the planting of non-native larch does not have a detrimental effect on Carabus assemblages in general, but it changes the spatial distribution and abundance compared to the native forests

9-{[4-(Dimethyl­amino)­benzyl]amino}-5-(4-hy­droxy-3,5-dimeth­oxy­phenyl)-5,5a,8a,9-tetra­hydro­furo[3′,4′:6,7]naphtho­[2,3-d][1,3]dioxol-6(8H)-one methanol monosolvate

In the title compound, C30H32N2O7·CH4O, the tetra­hydro­furan ring and the six-membered ring fused to it both display envelope conformations, with the ring C atom opposite the carbonyl group and the adjacent bridgehead C atom as the flaps, respectively. In the crystal structure, inter­molecular O—H⋯O hydrogen bonds link all moieties into ribbons along [010]. Weak inter­molecular C—H⋯O inter­actions consolidate the crystal packing further

9-[(Furan-2-ylmeth­yl)amino]-5-(3,4,5-trimeth­oxy­phen­yl)-5,5a,8a,9-tetra­hydro­furo[3′,4′:6,7]naphtho­[2,3-d][1,3]dioxol-6(8H)-one

In title compound, C27H27NO8, the dihydrofuran-2(3H)-one ring and the six-membered ring fused to it both display envelope conformations. The dihedral angle between the benzene ring of the benzo[d][1,3]dioxole group and the other benzene ring is 60.59 (2)°. In the crystal, weak inter­molecular C—H⋯O hydrogen bonds link the mol­ecules into a three-dimensional network. The furan ring is disordered over two sets of sites with occupancies of 0.722 (7) and 0.278 (7

Integrative transcriptomic analysis reveals a multiphasic epithelial–mesenchymal spectrum in cancer and non-tumorigenic cells

Epithelial–mesenchymal transition (EMT), the conversion between rigid epithelial cells and motile mesenchymal cells, is a reversible cellular process involved in tumorigenesis, metastasis, and chemoresistance. Numerous studies have found that several types of tumor cells show a high degree of cell-to-cell heterogeneity in terms of their gene expression signatures and cellular phenotypes related to EMT. Recently, the prevalence and importance of partial or intermediate EMT states have been reported. It is unclear, however, whether there is a general pattern of cancer cell distribution in terms of the overall expression of epithelial-related genes and mesenchymal-related genes, and how this distribution is related to EMT process in normal cells. In this study, we performed integrative transcriptomic analysis that combines cancer cell transcriptomes, time course data of EMT in non-tumorigenic epithelial cells, and epithelial cells with perturbations of key EMT factors. Our statistical analysis shows that cancer cells are widely distributed in the EMT spectrum, and the majority of these cells can be described by an EMT path that connects the epithelial and the mesenchymal states via a hybrid expression region in which both epithelial genes and mesenchymal genes are highly expressed overall. We found that key patterns of this EMT path are observed in EMT progression in non-tumorigenic cells and that transcription factor ZEB1 plays a key role in defining this EMT path via diverse gene regulatory circuits connecting to epithelial genes. We performed Gene Set Variation Analysis to show that the cancer cells at hybrid EMT states also possess hybrid cellular phenotypes with both high migratory and high proliferative potentials. Our results reveal critical patterns of cancer cells in the EMT spectrum and their relationship to the EMT process in normal cells, and provide insights into the mechanistic basis of cancer cell heterogeneity and plasticity

Sequencing bias: comparison of different protocols of MicroRNA library construction

<p>Abstract</p> <p>Background</p> <p>MicroRNAs(miRNAs) are 18-25 nt small RNAs playing critical roles in many biological processes. The majority of known miRNAs were discovered by conventional cloning and a Sanger sequencing approach. The next-generation sequencing (NGS) technologies enable in-depth characterization of the global repertoire of miRNAs, and different protocols for miRNA library construction have been developed. However, the possible bias between the relative expression levels and sequences introduced by different protocols of library preparation have rarely been explored.</p> <p>Results</p> <p>We assessed three different miRNA library preparation protocols, SOLiD, Illumina versions 1 and 1.5, using cloning or SBS sequencing of total RNA samples extracted from skeletal muscles from Hu sheep and Dorper sheep, and then validated 9 miRNAs by qRT-PCR. Our results show that SBS sequencing data highly correlate with Illumina cloning data. The SOLiD data, when compared to Illumina's, indicate more dispersed distribution of length, higher frequency variation for nucleotides near the 3'- and 5'-ends, higher frequency occurrence for reads containing end secondary structure (ESS), and higher frequency for reads that do not map to known miRNAs. qRT-PCR results showed the best correlation with SOLiD cloning data. Fold difference of Hu sheep and Dorper sheep between qRT-PCR result and SBS sequencing data correlated well (r = 0.937), and fold difference of miR-1 and miR-206 among SOLiD cloning data, qRT-PCR and SBS sequencing data was similar.</p> <p>Conclusions</p> <p>The sequencing depth can influence the quantitative measurement of miRNA abundance, but the discrepancy caused by it was not statistically significant as high correlation was observed between Illumina cloning and SBS sequencing data. Bias of length distribution, sequence variation, and ESS was observed between data obtained with the different protocols. SOLiD cloning data differ from Illumina cloning data mainly because of distinct methods of adapter ligation. The good correlation between qRT-PCR result and SOLiD data might be due to the similarities of the hybridization-based methods. The fold difference analysis indicated that methods based on hybridization may be superior for quantitative measurement of miRNA abundance. Because of the genome sequence of the sheep is not available, our data may not explain how the entire miRNA bias in the natural miRNAs in sheep or other mammal miRNA expression, unbiased artificially synthesized miRNA will help on evaluating the methodology of miRNA library preparation.</p

3-Isopropyl-2-(4-methoxy­phen­oxy)-1-benzo­furo[3,2-d]pyrimidin-4(3H)-one

In the title compound, C20H18N2O4, all non-H atoms of the three fused rings of the benzofuro[3,2-d]pyrimidine system are almost coplanar (r.m.s. deviation 0.021 Å). The dihedral angle between the fused ring system and the benzene ring is 1.47 (12)°. Intra­molecular and inter­molecular C—H⋯O hydrogen bonds together with weak C—H⋯π inter­actions stabilize the structure

Parallax correction in collocating CloudSat and Moderate Resolution Imaging Spectroradiometer (MODIS) observations: Method and application to convection study

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95467/1/jgrd17318.pd