Although serum prostate specific antigen (PSA) is a well-established diagnostic tool for prostate cancer (PCa) detection, the definitive diagnosis of PCa is based on the information contained in prostate needle biopsy (PNBX) specimens. To define the proteomic features of PNBX specimens to identify candidate biomarkers for PCa, PNBX specimens from patients with PCa or benign prostatic hyperplasia (BPH) were subjected to comparative proteomic analysis. 2-DE revealed that 52 protein spots exhibited statistically significantly changes among PCa and BPH groups. Interesting spots were identified by MALDI-TOF-MS/MS. The 2 most notable groups of proteins identified included latent androgen receptor coregulators and FKBP4] and enzymes involved in mitochondrial fatty acid b-oxidation (DCI and ECHS1). An imbalance in the expression of peroxiredoxin subtypes was noted in PCa specimens. Furthermore, different post-translationally modified isoforms of HSP27 and HSP70.1 were identified. Importantly, changes in FLNA(7-15), FKBP4, and PRDX4 expression were confirmed by immunoblot analyses. Our results suggest that a proteomics-based approach is useful for developing a more complete picture of the protein profile of PNBX specimen. The proteins identified by this approach may be useful molecular targets for PCa diagnostics and therapeutics. ' 2007 Wiley-Liss, Inc.

Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp . Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg 2+ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3′-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.

Dear Editor, CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) systems are RNA-guided adaptive immune systems in prokaryotes. 1,2 Class 2 CRISPR-Cas systems (including type II, V, and VI) involve large single effector proteins in complex with crRNA for interference. 3,4 The type II and V effectors, such as Cas9 and Cas12a, have been engineered into powerful tools for genome editing. The type VI system encompasses RNA-guided RNases. Its effectors Cas13a, Cas13b and Cas13d are capable of both precursor CRISPR RNA (pre-crRNA) processing and target RNA cleavage, which protect the host from phage attacks. 5-7 Once bound to a target RNA, they are activated, switching on a non-specific RNase activity. Moreover, they have been utilized to target and edit RNA as programmable RNAbinding modules. 6,[8][9][10][11][12] Although related to Cas13a and Cas13d, Cas13b possesses many distinctive features. These include the lack of significant sequence similarity with Cas13a and Cas13d, disparate crRNA repeat region, double-sided protospacer flanking sequence (PFS)-dependent target RNA cleavage. [5][6][7][8]13 To investigate how Cas13b processes pre-crRNA, recognizes crRNA and settles the spacer nucleotides for target recognition, we solved the crystal structure of Bergeyella zoohelcum Cas13b (BzCas13b) in complex with its crRNA at 2.79 Å resolution (Supplementary information, Table S1). The binary complex was obtained by the SeMet-derived BzCas13b R1177A mutant co-expressed with CRISPR template in vivo. The architecture of BzCas13b assumes a triangular domain distribution around the central L-shaped crRNA ( Fig. 1a-e; Supplementary information, Movie S1). In the binary complex, Helical-1, HEPN-1 and HEPN-2 domains together form one side of the triangular structure. Helical-1 domain comprises six α-helices connected with random loops (Supplementary information, Fig. S1). The second side of the triangle is formed by RRI-1 (the repeat region interacting domain-1), RRI-2 domains and the linker region. RRI-1 domain can be subdivided into two separate motifs (RRI-1 I and II) that stack onto each other. Both motifs contain a short twostranded, antiparallel β-sheet flanked by five α-helices. RRI-2 domain includes a long central two-stranded, antiparallel β-sheet flanked by two α-helices, and a short central two-stranded, antiparallel β-sheet flanked by three α-helices. The linker region consists of random loops that connect two short α-helices, which shows multiple interactions with RRI-2 domain. Helical-2 domain is composed of nine α-helices and its rather long helix-23 extends in parallel with crRNA, thereby forming the third side of the triangle. Helix-8 of Helical-1 domain and helix-23 of Helical-2 domain protrude out of the complex in a crab claw-like manner to clamp the spacer region of crRNA (Supplementary information, Fig. S1). In addition, HEPN-1 domain bridges Helical-1 and Helical-2 domains.A mature 52-nt crRNA, originated from a co-expressed CRISPR encoding sequence and bein...

Although the formation of metal–carbon σ bonds is a fundamental principle in organometallic chemistry, the direct bonding of one organic molecule with one metal center to generate more than two metal–carbon σ bonds remains a challenge. Herein, we report an aromaticity-driven method whereby multiyne chains are used to construct three metal–carbon σ bonds in a one-pot reaction under mild conditions. In this method, multiyne chains act as ligand precursors capable of chelating an osmium center to yield planar metallapolycycles, which exhibit aromaticity and good stability. The direct assembly of various multiyne chains with commercially available metal complexes or even simple metal salts provides a convenient and efficient strategy for constructing all carbon-ligated chelates on the gram scale.

The first incorporation of a second-row transition metal carbyne unit into a ring is realized by virtue of aromaticity.

With the explosive growth of images containing faces, scalable face image retrieval has attracted increasing attention. Due to the amazing effectiveness, deep hashing has become a popular hashing method recently. In this work, we propose a new Discriminative Deep Hashing (DDH) network to learn discriminative and compact hash codes for large-scale face image retrieval. The proposed network incorporates the end-to-end learning, the divide-and-encode module and the desired discrete code learning into a unified framework. Specifically, a network with a stack of convolution-pooling layers is proposed to extract multi-scale and robust features by merging the outputs of the third max pooling layer and the fourth convolutional layer. To reduce the redundancy among hash codes and the network parameters simultaneously, a divide-andencode module to generate compact hash codes. Moreover, a loss function is introduced to minimize the prediction errors of the learned hash codes, which can lead to discriminative hash codes. Extensive experiments on two datasets demonstrate that the proposed method achieves superior performance compared with some state-of-the-art hashing methods.

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BackgroundVascular endothelial apoptosis is significantly associated with atherosclerosis and cardiovascular diseases, for which oxidized low-density lipoprotein (ox-LDL) is a major risk factor. Allicin, the primary active ingredient of garlic, has been found to have cardiovascular protective effect by changing the fatty-acid composition, but its effect on ox-LDL-induced vascular endothelial injury remains unclear. We investigated the protective effect of allicin on cell viability, LDH release, apoptosis and apoptotic signaling in human umbilical vein endothelial cells (HUVECs).MethodsIn cultured HUVEC cell line, ox-LDL induced injury was investigated. The cell viability and injury were evaluated by using cell proliferation Assay kit and LDH release assay. The apoptosis was evaluated by the Annexin V-FITC kit. The activity of caspase-3 was assessed using a colorimetric caspase-3 assay kit. The ROS production was evaluated by fluorometric assay and NADPH oxidase activity was assessed with a GENMED kit.ResultsExposure of HUVECs to ox-LDL (150 μg/ml) reduced cell viability, induced apoptosis and increased activity of caspase-3, NADPH oxidase, and reactive oxygen species (ROS) production. The pretreatment with allicin (30 and 100 μM) significantly rescued the cell viability, inhibited ox-LDL-induced apoptosis and activity of caspase-3, NADPH oxidase and ROS production in HUVECs, and the protective effect is concentration-dependent. The allicin (100 μM) alone did not show significant difference from control. Our study demonstrated that allicin protected HUVECs from ox-LDL-induced endothelial injury by reducing the apoptosis, mediated by inhibition of caspase-3 and NADPH oxidase related apoptotic signaling.ConclusionsAllicin prevents ox-LDL-induced endothelial cell injury by inhibiting apoptosis and oxidative stress pathway.