...improve your next manuscript 1. Be consistent with your figures The figures of a manuscript are the result...introduce the reader to the manuscript and engage them in the material. So the manuscript should be able to be... When Publishing a Scientific Manuscript Writing Scientific Manuscripts: Literature Searching, Reading... a publication. There is an art to composing manuscripts and the ASM Scientific Writing and Publishing...the do’s and don’ts of that week’s piece of a manuscript. The webinars were my favorite part due to the...consisted of reading that class’s section of a manuscript and critiquing it, were not too laborious, but...helped build my understanding of how to generate a manuscript. At the end of the online course, we were given...

...help the editor handling your manuscript decide on whether your manuscript fits the scope and the interest...proofread your manuscript and help you correct any language- and spelling mistakes. A manuscript that is well...journal. Publishing via open access means that your manuscript will be available to anyone who wishes to read...read it, without them needing a subscription to the journal. An increasing number of funding bodies insist...style and the things you need to include in your manuscript. What information do I need to include in my ...in the Materials and methods section of their manuscript to make resources easier to identify, find back...back, and share. Depending on the type of manuscript you are writing, it may be useful to consult the ...

...Beginner’s Guide to Writing Scientific Manuscripts. Any scientific manuscript will require numerous other references...Scientific Manuscripts by Johnna Roose Dos & Don'ts When Publishing a Scientific Manuscript by Maaike...in ‘writing-mode’ for a grant or a scientific manuscript, the reading will likely be more intense, but...need to be on a network with an institutional subscription), archived on PubMed Central, or in preprint...down your own results; are they the same as the description the authors give? Ask yourself if the results...of the Beginner’s Guide to Writing Scientific Manuscripts series on Johnna's blog. Thank you to our guest...  scientific manuscript...

...type VI-D enzymes are the latest tools in the transcriptome engineering toolbox. How were Cas13d enzymes...small hairpin RNA interference, dCas9-mediated transcriptional inhibition (CRISPRi), and Cas13a/Cas13b RNA...only time will tell how large the genome and transcriptome engineering toolbox will be. It is, however,...community. References Konermann, Silvana, et al. “Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR...Editing with REPAIR Get tips for using Cas9 Transcriptional Activators Learn about Cas13a (C2c2) Characterization...

...expressing a novel reverse transcriptase (RT), MarathonRT. Reverse transcriptases are critical tools for ...!  MarathonRT: A highly processive reverse transcriptase Article contributed by Will Arnold  Listen ... are dependent on long, error-free, reverse transcription of RNA such as long-read cDNA sequencing and...unbiased discovery of proteins involved in transcriptional regulation and chromatin structure at your ...

...initiation step of gene transcription; today we'll provide an overview on how transcription stops, or termination...generally serves to promote transcript longevity in eukaryotes and promote transcript degradation in prokaryotes...thought to destabilize the transcription complex, initiating cleavage of the transcript.   Figure 1: ...expression levels. Transcription Termination Rho-dependent termination DNA transcription Polyadenylation...sequence-based element, is to define the end of a transcriptional unit (such as a gene) and initiate the process...releasing the newly synthesized RNA from the transcription machinery. Terminators are found downstream ...gene-expression. Polyadenylation is the post-transcriptional additional of multiple adenine (A) nucleotides...

... polymerase and transcription factors. Since the promoter region drives transcription of a target gene...promoter to induce transcription of the phage repressor cI. Repressor cI inhibits transcription from phage promoter... the promoter, turning it ON and initiating transcription.     Negative inducible In the OFF state, the...a bound repressor protein actively prevents transcription. Once an inducer binds the repressor protein...the DNA. With the repressor protein absent, transcription is turned ON. Types of inducible promoters Chemical...induction of a promoter. Below, you’ll find a short description of these three types of inducible promoters, ...removal of the lac repressor (lacI protein) for transcription to be activated. In the presence of lactose ...

...Promoter   Primarily used for RNA     transcript     Description Expression Additional considerations ...Primarily used for Description Expression Additional considerations T7 in vitro transcription/ general expression...for in vitro transcription, the promoter drives either the sense OR antisense transcript depending on ...This element is responsible for initiating the transcription of your insert into RNA. In practice, the term...controls the binding of the RNA polymerase and transcription factors, therefore promoters play a large role...

... a strong transcriptional activation domain. Guided by dCas9, VP64 recruits transcriptional machinery ...Mediator (SAM) Description SAM uses specially engineered sgRNAs to increase transcription. This is done...cells. VPR Description VPR fuses a tripartite complex with dCas9 to activate transcription. This complex...as two other potent transcriptional activators (p65 and Rta). These transcriptional activators work in ...interest. Upon binding, CRISPRa systems recruit transcription factors to increase gene expression. CRISPRa...CRISPRa methods vary in their transcriptional activators: some methods rely on fusion proteins while others...genes across diverse cell lines.   dCas9-VP64 Description CRISPR activation can occur through fusing dCas9...

... polymerase and transcription factors. Since the promoter region drives transcription of a target gene...repressor then prevents transcription from occurring, which means that transcription is now OFF.   We’ll...other. For example, the GAL4 transcription factor cannot drive transcription from the QUAS promoter, and...and the QF transcription factor cannot drive transcription from the UAS promoter. This is important because...Repressible: An activator protein is bound, turning transcription ON. When a repressor binds the activator protein...cannot bind the promoter sequence anymore and transcription is turned OFF. Negative Repressible: A repressor..., but cannot bind the promoter sequence and transcription is ON. Once a co-repressor protein binds the...

...gene transcription (6). The EBOV genome contains seven viral genes, each flanked by a transcription start...start signal sequence (gene start) and a transcription termination/polyadenylation signal sequence (gene...genome which are required for replication and transcription (Figure 1). All viral genes are removed and ...direct minigenome replication and reporter gene transcription by the EBOV polymerase (reviewed in 2, 5). The...are required for viral genome replication and transcription: NP, VP35, VP30, and L (reviewed in 5). The ...catalytic protein and its cofactor VP35. VP30 is a transcription enhancement factor. When used to study minigenomes...minigenome as a template for replication and transcription, as it would for a full-length viral genome ...

...light-dependent activity to transcription, they fused BldD to the transcriptional activators p65 and VP64 ...readily found at Addgene. Shining light on transcriptional activation using dCas9 Initial photoactivatable...early 2015 focused on using light to control transcription. Two separate labs, Moritoshi Sato’s lab at ...photolyase homology region (CRY2PHR) fused to a transcriptional activator domain (VP64 or p65). Upon expression...the activator into position to activate gene transcription. The researchers tested a variety of combinations...CRY2FL-VP64, a fusion of full-length CRY2 and the transcriptional activator domain VP64. Using this system in...expresses the C-terminal fragment of Cas9 while transcription of the N-terminus is light-dependent (Yu et ...

...copying and pasting pieces from our existing script into the script block of the Nextflow process.  Next, we...possible solutions for each in the form of one-off scripts or programs, our goal was to find a suitable software...sequential computational tasks for which existing script(s) have been developed for a singular purpose (...sequence assembly), but the order and usage of the scripts needs to be customized in the pipeline for the ...In Nextflow, a process defines which command or script will run and can be thought of as a particular ...Prior to using Nextflow, we routinely wrote Python scripts, queried our database with SQL or Django, and executed...channels. Since a Nextflow process can utilize any scripting language that can be executed on Linux, we created...

...recent paper, "Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds." Adam has...visualize the concepts discussed in the paper. The transcriptional control of multiple loci is deftly coordinated...CRISPR-based RNA scaffolds to mimic natural transcriptional programs on multiple genes. Modifying the ...synthetic RNA scaffolds that can recruit various transcriptional regulators (Zalatan et al. 2015).  These scaffolds...nucleotide sequence then subsequently recruit a transcriptional regulator to modulate expression at that locus...expression levels dependent upon the type of transcriptional regulator or the number of designed scaffold...unprecedented level of flexible tunability of transcription is possible. From a design perspective, this...

...estradiol controlled transcription factor and a ZIF268/progesterone controlled transcription factor as well ... levels. That is, if transcription factor 1 controls expression of transcription factor 2, which directly...Tyler J. Ford Listen to the Synthetic Yeast Transcription Factors Podcast Segment Researchers from the...deposited plasmids encoding synthetic yeast transcription factors that can independently control expression...expression of your genes of interest. These transcription factors consist of the GAL4 or ZIF268 DNA binding...domains and the MSN2 transactivation domain. Transcription factor activation via the appropriate ligand...addition to plasmids encoding these synthetic transcription factors, the El-Samad lab has deposited plasmids...

... pair has focused considerable attention on transcription factors, starting with an established method... relies on antibodies to recognize and bind transcription factors directly, but that’s a slow-going process...ENCODE project is to look at all 1,500 or 1,600 transcription factors and figure out where they bind to the... ChIP-seq, but it’s really hard for lots of transcription factors. Our groups got together to adapt CRISPR...big difference. We can now look at many more transcription factors. Addgene: How does the system work? ...second plasmid to target an epitope tag onto the transcription factors. By the way, you can actually use this... in all kinds of different assays, not just transcription factors. The second vector is a homology directed...

...signal downstream of the transcription start site will terminate transcription of most of the ncRNA (Figure...lncRNA regulatory elements that are crucial for transcription and downstream function. Rather than attempting...the lncRNA locus, scientists can mutate the transcription start site, splice sites, exons, and/or promoters...the removal of exons. Disrupting promoter or transcription start site function would also help to reveal...stop elements can be inserted to disrupt the transcription of the ncRNA (Hazan and Bester 2021). For example.../Cas9-based approaches to study ncRNAs. (A) Transcription start site (TSS) deletion. (B) Mutations of ...dCas9) and a sgRNA to temporarily block the transcription machinery of a target gene or DNA that codes...

...Fusing dCas9 to a transcriptional activator like VP64 or VPR activates transcription, whereas dCas9-KRAB...domain, could mediate demethylation and induce transcription at CpG regions of various promoters. Other researchers...TALEN-based LITE system, which uses light to regulate transcription, also includes light-regulated histone methyltransferases...check out our CRISPR Epigenetics resource. Transcriptional activation p300 acetyltransferase dCas9 fused...enhancer regions. These marks are associated with transcriptional activation. Created with BioRender.com. ...Tet1-CD to decrease methylation and activate transcription. A lentiviral vector with the same modifier,... demethylation is associated with increased transcription. Created with BioRender.com. Tet1 initiates...

...will dissociate when gene transcription is complete. However, transcription of thousands of genes is constantly...Transcription, translation, and prone to degradation – those are the words that describe RNA! Double ...thought to be associated with bidirectional transcription. In an uninfected cell, dsRNA rarely circulates...short, dsRNA molecules designed to degrade mRNA transcripts. RNAi activates the RNA-induced silencing complexes...elements can generate dsRNA by bidirectional transcription or as inverted repeats. These elements are almost... produce dsRNA as a result of bidirectional transcription of their circularized DNA. These dsRNAs are ...structure produced is known as an R-loop. During transcription, RNA is synthesized from a DNA template, inherently...

... to create a complete transcription factor, activating luciferase transcription. Tang et al. coined this...Connie Cepko’s lab allow researchers to activate transcription or Cre recombinase activity only in the presence...Using nanobodies to create GFP scaffolds for transcriptional activation The project began with a frustration...GFP-labeled cells. Once Tang and Cepko found a description of GFP-binding nanobodies, the project really...this system T-DDOG (Transcriptional Devices Dependent On GFP). In testing the specificity of their system... dsRed, mCherry, and TdTomato do not induce transcription. Thus, T-DDOGs can be used in combination with...T-DDOG results showed that GFP could regulate transcription in a cell-type specific manner, and Tang and...