Single-cell transcriptional regulation and genetic evolution of neuroendocrine prostate cancer

Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer, with a 10% five-year survival rate. However, little is known about its origin and the mechanisms governing its emergence. Our study characterized ADPC and NEPC in prostate tumors from 7 patients using scRNA-seq. First, we identified two NEPC gene expression signatures representing different phases o

Potato virus Y HC-Pro reduces the ATPase activity of NtMinD, which results in enlarged chloroplasts in HC-Pro transgenic tobacco

Potato virus Y (PVY) is an important plant virus and causes great losses every year. Viral infection often leads to abnormal chloroplasts. The first step of chloroplast division is the formation of FtsZ ring (Z-ring), and the placement of Z-ring is coordinated by the Min system in both bacteria and plants. In our lab, the helper-component proteinase (HC-Pro) of PVY was previously found to interact with the chloroplast division protein NtMinD through a yeast two-hybrid screening assay and a bimolecular fluorescence complementation (BiFC) assay in vivo. Here, we further investigated the biological significance of the NtMinD/HC-Pro interaction. We purified the NtMinD and HC-Pro proteins using a prokaryotic protein purification system and tested the effect of HC-Pro on the ATPase activity of NtMinD in vitro. We found that the ATPase activity of NtMinD was reduced in the presence of HC-Pro. In addition, another important chloroplast division related protein, NtMinE, was cloned from the cDNA of Nicotiana tabacum. And the NtMinD/NtMinE interaction site was mapped to the C-terminus of NtMinD, which overlaps the NtMinD/HC-Pro interaction site. Yeast three-hybrid assay demonstrated that HC-Pro competes with NtMinE for binding to NtMinD. HC-Pro was previously reported to accumulate in the chloroplasts of PVY-infected tobacco and we confirmed this result in our present work. The NtMinD/NtMinE interaction is very important in the regulation of chloroplast division. To demonstrate the influence of HC-Pro on chloroplast division, we generated HC-Pro transgenic tobacco with a transit peptide to retarget HC-Pro to the chloroplasts. The HC-Pro transgenic plants showed enlarged chloroplasts. Our present study demonstrated that the interaction between HC-Pro and NtMinD interfered with the function of NtMinD in chloroplast division, which results in enlarged chloroplasts in HC-Pro transgenic tobacco. The HC-Pro/NtMinD interaction may cause the formation of abnormal chloroplasts in PVY-infected plants

Selecting and Testing of Cement-Bonded Magnetite and Chalcopyrite as Oxygen Carrier for Chemical-Looping Combustion

Combining iron and copper ores can generate an oxygen carrier that has a synergic effect of high temperature resistance and high reactivity. In this work, typical cements available in the market were studied as binders to bind magnetite and chalcopyrite to develop a suitable oxygen carrier for chemical-looping combustion (CLC). A first selection step suggested that an aluminate cement, namely CA70, could favor the generation of oxygen carrier particles having good crushing strength, good particle yield, and high reactivity. The CA70-bonded oxygen carrier was then subjected to cyclic tests with CH4, CO, and H-2 in reduction and in air oxidation at temperatures of 850, 900, and 950 degrees C with gas concentrations of 5, 10, 15, and 20% in a batch-fluidized bed reactor. The increase in temperature promoted the fuel conversion. At 950 degrees C, the conversions of CH4 and CO reached up to 80.4% and 99.2%, respectively. During more than 30 cycles, the oxygen carrier kept a similar reactivity to the fresh carrier and maintained its composition and physical properties. The oxygen transport capacity was maintained at 21-23%, and the phases were CuO, Fe2O3, Al2O3, and minor CaS. In the used sample, some grains were observed, but the morphology was not greatly changed. Agglomeration was absent during all the cycles, except for the deep reduction with H-2

Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

<p>Abstract</p> <p>Background</p> <p><it>Medicago truncatula </it>has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual <it>M. truncatula </it>transporters in several databases, until now there has been no available systematic database that includes all transporters in <it>M. truncatula</it>.</p> <p>Description</p> <p>The <it>M. truncatula </it>transporter database (MTDB) contains comprehensive information on the transporters in <it>M. truncatula</it>. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG) V3.5 V3 and the <it>M. truncatula </it>Gene Index (MTGI) V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST) mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created. In addition, we have provided a way to explore the expression of putative <it>M. truncatula </it>transporter genes under stress treatments.</p> <p>Conclusions</p> <p>In summary, the MTDB enables the exploration and comparative analysis of putative transporters in <it>M. truncatula</it>. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at <url>http://bioinformatics.cau.edu.cn/MtTransporter/</url>.</p

Epigenomic differences in the human and chimpanzee genomes are associated with structural variation

Structural variation (SV), including insertions and deletions (indels), is a primary mechanism of genome evolution. However, the mechanism by which SV contributes to epigenome evolution is poorly understood. In this study, we characterized the association between lineage-specific indels and epigenome differences between human and chimpanzee to investigate how SVs might have shaped the epigenetic landscape. By intersecting medium-to-large human-chimpanzee indels (20bp-50kb) with putative promoters and enhancers in cranial neural crest cells (CNCC) and repressed regions in induced pluripotent cells (iPSC), we found that ~12% indels overlap putative regulatory and repressed regions (RRRs), and 15% of these indels are associated with lineage-biased RRRs. Indel-associated putative enhancer and repressive regions are ~1.3 and ~3 times as likely to be lineage-biased, respectively, as those not associated with indels. We found a 2-fold enrichment of medium-sized indels (20bp to 50bp) in CpG island (CGI)-containing promoters than expected by chance. Lastly, from human-specific transposable element insertions, we identified putative regulatory elements, including NR2F1-bound putative CNCC enhancers derived from SVAs and putative iPSC promoters derived from LTR5s. Our results demonstrate that different types of indels are associated with specific epigenomic diversity between human and chimpanzee

The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Abstract Here, we introduce the 3D Genome Browser, http://3dgenome.org, which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure

Collision Attacks on NaSHA-384/512

NaSHA is a family of hash functions submitted by Markovski and Mileva as a SHA-3 candidate. In this paper, we present a collision attack on the hash function NaSHA for the output sizes 384-bit and 512-bit. This attack is based on the the weakness in the generate course of the state words and the fact that the quasigroup operation used in the compression function is only determined by partial state words. Its time complexity is about $2^{128}$ with negligible memory and its probability is more than $(1- \frac{2}{{2^{64} - 1}})^2$ ($\gg \frac{1}{2}$). This is currently by far the best known cryptanalysis result on this SHA-3 candidate

Conserved and divergent gene regulatory programs of the mammalian neocortex

Divergence of cis-regulatory elements drives species-specific trait