The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters

Blin, Kai,Medema, Marnix H.,Kottmann, Renzo,Lee, Sang Yup,Weber, Tilmann Oxford University Press 2017 Nucleic acids research Vol.45 No.d1

<P>Secondary metabolites produced by microorganisms are the main source of bioactive compounds that are in use as antimicrobial and anticancer drugs, fungicides, herbicides and pesticides. In the last decade, the increasing availability of microbial genomes has established genome mining as a very important method for the identification of their biosynthetic gene clusters (BGCs). One of the most popular tools for this task is antiSMASH. However, so far, antiSMASH is limited to <I>de novo</I> computing results for user-submitted genomes and only partially connects these with BGCs from other organisms. Therefore, we developed the antiSMASH database, a simple but highly useful new resource to browse antiSMASH-annotated BGCs in the currently 3907 bacterial genomes in the database and perform advanced search queries combining multiple search criteria. antiSMASH-DB is available at http://antismash-db.secondarymetabolites.org/.</P>

Wireless Communication at 310 GHz using GaAs High-Electron-Mobility Transistors for Detection

Blin, Stephane,Tohme, Lucie,Coquillat, Dominique,Horiguchi, Shogo,Minamikata, Yusuke,Hisatake, Shintaro,Nouvel, Philippe,Cohen, Thomas,Penarier, Annick,Cano, Fabrice,Varani, Luca,Knap, Wojciech,Nagats The Korea Institute of Information and Commucation 2013 Journal of communications and networks Vol.15 No.6

We report on the first error-free terahertz (THz) wireless communication at 0.310 THz for data rates up to 8.2 Gbps using a 18-GHz-bandwidth GaAs/AlGaAs field-effect transistor as a detector. This result demonstrates that low-cost commercially-available plasma-wave transistors whose cut-off frequency is far below THz frequencies can be employed in THz communication. Wireless communication over 50 cm is presented at 1.4 Gbps using a uni-travelling-carrier photodiode as a source. Transistor integration is detailed, as it is essential to avoid any deleterious signals that would prevent successful communication. We observed an improvement of the bit error rate with increasing input THz power, followed by a degradation at high input power. Such a degradation appears at lower powers if the photodiode bias is smaller. Higher-data-rate communication is demonstrated using a frequency-multiplied source thanks to higher output power. Bit-error-rate measurements at data rates up to 10 Gbps are performed for different input THz powers. As expected, bit error rates degrade as data rate increases. However, degraded communication is observed at some specific data rates. This effect is probably due to deleterious cavity effects and/or impedance mismatches. Using such a system, realtime uncompressed high-definition video signal is successfully and robustly transmitted.

Mixing and matching TREK/TRAAK subunits generate heterodimeric K_2P channels with unique properties

Blin, Sandy,Ben Soussia, Ismail,Kim, Eun-Jin,Brau, Fré,dé,é,ric,Kang, Dawon,Lesage, Florian,Bichet, Delphine National Academy of Sciences 2016 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.113 No.15

<P>The tandem of pore domain in a weak inwardly rectifying K+ channel (Twik)-related acid-arachidonic activated K+ channel (TRAAK) and Twik-related K+ channels (TREK) 1 and TREK2 are active as homodimers gated by stretch, fatty acids, pH, and G protein-coupled receptors. These two-pore domain potassium (K-2P) channels are broadly expressed in the nervous system where they control excitability. TREK/TRAAK KO mice display altered phenotypes related to nociception, neuroprotection afforded by polyunsaturated fatty acids, learning and memory, mood control, and sensitivity to general anesthetics. These channels have emerged as promising targets for the development of new classes of anesthetics, analgesics, antidepressants, neuroprotective agents, and drugs against addiction. Here, we show that the TREK1, TREK2, and TRAAK subunits assemble and form active heterodimeric channels with electrophysiological, regulatory, and pharmacological properties different from those of homodimeric channels. Heteromerization occurs between all TREK variants produced by alternative splicing and alternative translation initiation. These results unveil a previously unexpected diversity of K-2P channels that will be challenging to analyze in vivo, but which opens new perspectives for the development of clinically relevant drugs.</P>

Estradiol Testing in the Exploration of Early Onset Puberty: Comparison of RIA and Chemiluminescence Immunoassay

Blin Justine,Hochman Clarisse,Graveline Nolwenn,Masson Damien,Baron Sabine,Bach-Ngohou Kalyane 대한진단검사의학회 2023 Annals of Laboratory Medicine Vol.43 No.6

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

Blin, Kai,Wolf, Thomas,Chevrette, Marc G.,Lu, Xiaowen,Schwalen, Christopher J.,Kautsar, Satria A.,Suarez ,Duran, Hernando G.,de ,los ,Santos, Emmanuel ,L. ,C.,Kim, Hyun Uk,Nave, Ma Oxford University Press 2017 Nucleic acids research Vol.45 No.w1

<P><B>Abstract</B></P><P>Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of <I>trans</I>-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.</P>

Wireless Communication at 310 GHz Using GaAs High-Electron-Mobility Transistors for Detection

Stéphane Blin,Lucie Tohme,Dominique Coquillat,Shogo Horiguchi,Yusuke Minamikata,Shintaro Hisatake,Philippe Nouvel,Thomas Cohen,Annick Pénarier,Fabrice Cano,Luca Varani,Wojciech Knap,Tadao Nagatsuma 한국통신학회 2013 Journal of communications and networks Vol.15 No.6

We report on the first error-free terahertz (THz) wirelesscommunication at 0.310 THz for data rates up to 8.2 Gbps using a18-GHz-bandwidth GaAs/AlGaAs field-effect transistor as a detector. This result demonstrates that low-cost commercially-availableplasma-wave transistors whose cut-off frequency is far below THzfrequencies can be employed in THz communication. Wirelesscommunication over 50 cm is presented at 1.4 Gbps using a unitravelling-carrier photodiode as a source. Transistor integration isdetailed, as it is essential to avoid any deleterious signals that wouldprevent successful communication. We observed an improvementof the bit error rate with increasing input THz power, followed bya degradation at high input power. Such a degradation appearsat lower powers if the photodiode bias is smaller. Higher-dataratecommunication is demonstrated using a frequency-multipliedsource thanks to higher output power. Bit-error-ratemeasurementsat data rates up to 10 Gbps are performed for different inputTHz powers. As expected, bit error rates degrade as data rate increases. However, degraded communication is observed at somespecific data rates. This effect is probably due to deleterious cavityeffects and/or impedance mismatches. Using such a system, realtimeuncompressed high-definition video signal is successfully androbustly transmitted.

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Weber, Tilmann,Blin, Kai,Duddela, Srikanth,Krug, Daniel,Kim, Hyun Uk,Bruccoleri, Robert,Lee, Sang Yup,Fischbach, Michael A,Mü,ller, Rolf,Wohlleben, Wolfgang,Breitling, Rainer,Takano, Eriko,Medema, Oxford University Press 2015 Nucleic acids research Vol.43 No.w1

<P><B>Abstract</B></P><P>Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.</P>

Target sequences for microRNAs within the Tff gene cluster

A.A. Shah,N. Blin 한국바이오칩학회 2010 BioChip Journal Vol.4 No.4

Despite the increasing interest focusing on control of gene activity by microRNAs this abundant class of thousands of regulatory transcripts still requires elucidation of open questions concerning selection of targets and mechanisms of complementarity, multiplicity and cooperativity of microRNAs, to name some immediate issues. In silico microRNA target prediction is often the first line of approaching the complex system and helping in setting search priorities for experimental validation of such mechanisms of gene control. We now used a well studied gene cluster coding for the trefoil peptide family (Tff1, Tff2, Tff3) with all its sequence data and information on factors driving gene expression and a combined computer-based set of target prediction programs to collect microRNAs involved in Tff gene regulation. The sequence preference of specific microRNAs was mapped and their multiplicity and cooperativity were denoted to establish an interactive regulatory profile. This computational venue will subsequently allow enhanced and specific in vitro confirmation of the regulatory networks in cellular systems and possibly later on in transgenic animal models

Antagonistic Effect of a Cytoplasmic Domain on the Basal Activity of Polymodal Potassium Channels

Soussia, Ismail Ben,Choveau, Frank S.,Blin, Sandy,Kim, Eun-Jin,Feliciangeli, Sylvain,Chatelain, Franck C.,Kang, Dawon,Bichet, Delphine,Lesage, Florian Frontiers Media S.A. 2018 Frontiers in molecular neuroscience Vol.11 No.-

<P>TREK/TRAAK channels are polymodal K<SUP>+</SUP> channels that convert very diverse stimuli, including bioactive lipids, mechanical stretch and temperature, into electrical signals. The nature of the structural changes that regulate their activity remains an open question. Here, we show that a cytoplasmic domain (the proximal C-ter domain, pCt) exerts antagonistic effects in TREK1 and TRAAK. In basal conditions, pCt favors activity in TREK1 whereas it impairs TRAAK activity. Using the conformation-dependent binding of fluoxetine, we show that TREK1 and TRAAK conformations at rest are different, and under the influence of pCt. Finally, we show that depleting PIP<SUB>2</SUB> in live cells has a more pronounced inhibitory effect on TREK1 than on TRAAK. This differential regulation of TREK1 and TRAAK is related to a previously unrecognized PIP<SUB>2</SUB>-binding site (R329, R330, and R331) present within TREK1 pCt, but not in TRAAK pCt. Collectively, these new data point out pCt as a major regulatory domain of these channels and suggest that the binding of PIP<SUB>2</SUB> to the pCt of TREK1 results in the stabilization of the conductive conformation in basal conditions.</P>

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST

Tong, Yaojun,Whitford, Christopher M.,Robertsen, Helene L.,Blin, Kai,Jørgensen, Tue S.,Klitgaard, Andreas K.,Gren, Tetiana,Jiang, Xinglin,Weber, Tilmann,Lee, Sang Yup National Academy of Sciences 2019 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.116 No.41

<P><B>Significance</B></P><P>Although CRISPR-Cas9 tools dramatically simplified the genetic manipulation of actinomycetes, significant concerns of genome instability caused by the DNA double-strand breaks (DSBs) and common off-target effects remain. To address these concerns, we developed CRISPR-BEST, a DSB-free and high-fidelity single-nucleotide–resolution base editing system for streptomycetes and validated its use by determining editing properties and genome-wide off-target effects. Furthermore, our CRISPR-BEST toolkit supports Csy4-based multiplexing to target multiple genes of interest in parallel. We believe that our CRISPR-BEST approach is a significant improvement over existing genetic manipulation methods to engineer streptomycetes, especially for those strains that cannot be genome-edited using normal DSB-based genome editing systems, such as CRISPR-Cas9.</P><P>Streptomycetes serve as major producers of various pharmacologically and industrially important natural products. Although CRISPR-Cas9 systems have been developed for more robust genetic manipulations, concerns of genome instability caused by the DNA double-strand breaks (DSBs) and the toxicity of Cas9 remain. To overcome these limitations, here we report development of the DSB-free, single-nucleotide–resolution genome editing system CRISPR-BEST (CRISPR-Base Editing SysTem), which comprises a cytidine (CRISPR-cBEST) and an adenosine (CRISPR-aBEST) deaminase-based base editor. Specifically targeted by an sgRNA, CRISPR-cBEST can efficiently convert a C:G base pair to a T:A base pair and CRISPR-aBEST can convert an A:T base pair to a G:C base pair within a window of approximately 7 and 6 nucleotides, respectively. CRISPR-BEST was validated and successfully used in different <I>Streptomyces</I> species. Particularly in nonmodel actinomycete <I>Streptomyces collinus</I> Tu¨365, CRISPR-cBEST efficiently inactivated the 2 copies of <I>kirN</I> gene that are in the duplicated kirromycin biosynthetic pathways simultaneously by STOP codon introduction. Generating such a knockout mutant repeatedly failed using the conventional DSB-based CRISPR-Cas9. An unbiased, genome-wide off-target evaluation indicates the high fidelity and applicability of CRISPR-BEST. Furthermore, the system supports multiplexed editing with a single plasmid by providing a Csy4-based sgRNA processing machinery. To simplify the protospacer identification process, we also updated the CRISPy-web (https://crispy.secondarymetabolites.org), and now it allows designing sgRNAs specifically for CRISPR-BEST applications.</P>