New Bioactive Steroids from <i>Melia volkensii</i>

New Bioactive Steroids from Melia volkensii</i

Apoptosis induced by DICO, a novel non-aromatic B-ring flavonoid <i>via</i> a ROS-dependent mechanism in human colon cancer cells

5,7-Dihydroxy-2-(1,2-isopropyldioxy-4-oxo-cyclohex-5-enyl)-chromen-4-one (DICO) is a novel non-aromatic B-ring flavonoid, isolated mainly from Macrothelypteris viridifrons and has anti-tumour properties. In this study, we investigated the cytotoxicity and underlying biochemical pathways leading to cell death, in response to DICO treatment of a human colon cancer cell line HT-29. Our results indicated that DICO induced apoptosis by elevating the generation of reactive oxygen species, which could be quenched by the antioxidants N-acetyl cysteine. In addition, activation of signal transducer and activator of transcription 3 and suppression of nuclear factor kappa B played a crucial role in DICO-induced apoptosis. Overall, our results provide mechanistic insights into the apoptotic action of a potential anti-tumour drug, DICO.</p

Middle Triassic back-arc rifting in central China: Evidence from geochronology, geochemistry and Hf isotopes of basic–intermediate dykes in the Gonghe basin

In this paper, we present an integrated study of petrology, zircon U–Pb geochronology, whole-rock geochemistry, and zircon Lu–Hf isotopes for the basic–intermediate dykes in the western Gonghe basin, northeastern Qinghai–Tibetan Plateau. LA–MC–ICP–MS zircon U–Pb dating indicates that these dykes were emplaced in the Middle Triassic (240 ± 1.6 Ma). Geochemically, these basic–intermediate dykes are characterized by enrichments in light rare earth elements (LREEs) and large-ion lithophile elements (LILEs; e.g. K, Rb, and Pb), coupled with depletions in high-field-strength elements (HFSEs; e.g. Nb, Ta, and Ti). These geochemical features, along with the relatively low zircon εHf values (−7.2 to 1.6), suggest that these mafic dykes were originated from enriched mantle metasomatized by subduction-related fluids in a back-arc extensional environment. Literature investigations indicate that Middle Triassic mafic dykes are widespread in central China and are geochemically of arc affinities. Therefore, a regional back-arc extensional event occurred in central China during Middle Triassic time, which was likely caused by rollback of the subducting Kunlun–Animaqin Paleo-Tethyan slab.</p

Comparison of repeat annotation for CARP and RMD.

Summary of specific repeat content from CENSOR output, using a combined library of Repbase ‘Vertebrate’ with CARP or RMD consensus libraries. IR = Interspersed Repeats SD = Segmental Duplications.</p

Phylogenetic analysis of L2 elements in the platypus genome.

<p>Figure shows the dendrograms of full-length L2 elements in the platypus genome. Panel A) long L2 sequences from the platypus genome. Panel B) Long L2 CARP consensus sequences from platypus. Panel C) Long L2 RMD consensus sequences from platypus. Sequences were aligned with MUSCLE, trees inferred with FastTree and visualized with Archaeopteryx. ORF2-instact L2s are shown with a red dot at the tip of the branch.</p

Coverage plot of the top 5 high hit copy number CARP unclassified consensus sequences from the bearded dragon.

<p>A) CENSOR and BLASTN annotation of the peak coverage region in unclassified family 015220; B) CENSOR and BLASTN annotation of the peak coverage region in unclassified family 0309690; C) CENSOR and BLASTN annotation of the peak coverage region in unclassified family 127805; D) CENSOR and BLASTN annotation of the peak coverage region in unclassified family 137078; E) CENSOR and BLASTN annotation of the peak coverage region in unclassified family 187168. The number of family members identified by krishna/igor used for consensus sequence generation is shown in the upper left corner of each panel.</p

Superior <i>ab initio</i> identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

<div><p>Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate <i>ab initio</i> because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive <i>ab initio</i> Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for <i>ab initio</i> repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our <i>ab initio</i> repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.</p></div

Comparison of the total number of specific TE types in each method.

<p>Comparison of the total number of specific TE types in each method.</p

Comprehensive <i>ab initio</i> Repeat Pipeline (CARP).

<p>Figure shows the detailed steps for CARP. Repetitive DNA is identified by all vs all pairwise alignment using krishna. Single linkage clustering is then carried out to produce families of repetitive sequences that are globally aligned to generate a consensus sequence for each family. Consensus sequences are filtered for non-TE protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. The annotated consensus sequences are then used to annotate the genome. This is required to identify repeats with less than the threshold identity used for alignment that are overlooked during the initial pairwise alignment step.</p

Scatter plot of unclassified sequence copy number <i>versus</i> length.

<p>Plots show the copy number of hits of unclassified sequences annotated using CENSOR and combined libraries, with respect to their length. Both copy number and length were <i>log</i>₁₀-transformed. Red regions on the plot indicate high density, while blue regions indicate low density. Linear regression lines are plotted in red, with STANDARD ERROR represented by the gray shadow around the lines.</p