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Mashup Score: 2Flawed machine-learning confounds coding sequence annotation - 2 hour(s) ago
Detecting protein coding genes in genomic sequences is a significant challenge for understanding genome functionality, yet the reliability of bioinformatic tools for this task remains largely unverified. This is despite some of these tools having been available for several decades, and being widely used for genome and transcriptome annotation. We perform an assessment of nucleotide sequence and alignment-based de novo protein-coding detection tools. The controls we use exclude any previous training dataset and include coding exons as a positive set and length-matched intergenic and shuffled sequences as negative sets. Our work demonstrates that several widely used tools are neither accurate nor computationally efficient for the protein-coding sequence detection problem. In fact, just three of nine tools significantly outperformed a naive scoring scheme. Furthermore, we note a high discrepancy between self-reported accuracies and the accuracy achieved in our study. Our results show that
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Mashup Score: 1
In-solution hybridisation enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmarked the commercial “Twist Ancient DNA” reagent from Twist Biosciences using sequencing libraries from ancestrally diverse ancient human samples with low to high endogenous DNA content (0.1-44%). For each library, we tested one and two rounds of enrichment, and assessed performance compared to deep shotgun sequencing. We find that the “Twist Ancient DNA” assay provides robust enrichment of ~1.2M target SNPs without introducing allelic bias that may interfere with downstream population genetics analyses. Additionally, we show that pooling up to 4 sequencing libraries and performing two rounds of enrichment is both reliable and cost-effective for libraries with less than 27% endogenous DN
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Mashup Score: 0
Contrary to the common belief, the most commonly used laboratory mouse inbred strains are shaped by a distinctive genetic and phenotypic diversity. In the past 10 years next generation sequencing unveiled a wide spectrum of genetic variants in different mouse inbred strains and the meticulous observation of researchers pointed to a variegate intra-and inter-strain phenotypic diversity. Although a genotype-phenotype correlation has been described for some traits, the relationship between several endophenotypes and causative genetic variability remains still unknown. Recently, we characterized the brain collateral plasticity in two brain ischemia C57BL/6J mouse models (i.e bilateral common carotid artery stenosis [BCCAS] and 60-min transient unilateral middle cerebral artery occlusion [MCAO]) and observed a Mendelian-like fashion of inheritance of the posterior communicating artery (PcomA) plasticity. Interestingly, a copy number variant (CNV) spanning Ide locus was reported to segregate
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Mashup Score: 0A phosphate-binding pocket in cyclin B3 is essential for XErp1/Emi2 degradation in meiosis I - 2 hour(s) ago
To ensure the correct euploid state of embryos, it is essential that vertebrate oocytes await fertilization arrested at metaphase of meiosis II. This MII arrest is mediated by XErp1/Emi2, which inhibits the ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome). Cyclin B3 in complex with Cdk1 (cyclin-dependent kinase 1) is essential to prevent an untimely arrest of vertebrate oocytes in meiosis I by targeting XErp1/Emi2 for degradation. Yet, the molecular mechanism of XErp1/Emi2 degradation in MI is not well understood. Here, by combining TRIM-Away in oocytes with egg extract and in vitro studies, we demonstrate that a hitherto unknown phosphate-binding pocket in cyclin B3 is essential for efficient XErp1/Emi2 degradation in meiosis I. This pocket enables Cdk1/cyclin B3 to bind pre-phosphorylated XErp1/Emi2 facilitating further phosphorylation events, which ultimately target XErp1/Emi2 for degradation in a Plk1 (Polo-like kinase 1) dependent manner. Key elements of this degradat
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Mashup Score: 0Development and Characterization of Recombinant ADP-Ribose Binding Reagents that Allow Simultaneous Detection of Mono and Poly ADP-Ribose - 2 hour(s) ago
ADP-ribosylation (ADPRylation) is a post-translational modification (PTM) of proteins mediated by the activity of a variety of ADP-ribosyltransferase (ART) enzymes, such as the Poly(ADP-ribose) Polymerase (PARP) family of proteins. This PTM is diverse in both form and biological functions, which makes it a highly interesting modification, but difficult to study due to limitations in reagents available to detect the diversity of ADP-ribosylation. Recently we developed a set of recombinant antibody-like ADP-ribose binding proteins, using naturally occurring ADPR binding domains (ARBDs) that include macrodomains and WWE domains, that have been functionalized by fusion to the constant Fc region of rabbit immunoglobulin. Herein, we present an expansion of this biological toolkit, where we have replaced the rabbit Fc sequence with two other species, the Fc for mouse and goat immunogloblulin. Characterization of the new reagents indicates that they can be detected in a species-dependent manne
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Mashup Score: 0Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae - 2 hour(s) ago
Rhodopsin with the NTQ motif and heliorhodopsins, both discovered for the first time in actinomycetes of the family Geodermatophilaceae were characterized, along with characterization of the DTEW, DTEF and NDQ rhodopsins reported in members of this family previously. The identified absorption maxima ranged from 513 to 559 nm, of which the blue-shifted rhodopsin contained the NTQ motif and the red-shifted one were heliorhodopsin. An assessment of the pumping activity of the NTQ rhodopsin and heliorhodopsin showed that the former functioned as inward Cl–, Br–, I–pump with much weaker activity towards NO3-, while no any activity was detected for the later. The DTEW and DTEF rhodopsins had the outward H+-transport activity which was dependent on the presence of Ca2+ ions and on the particular E. coli expression strain. The outward pumping of H+ was also detected for NDQ rhodopsin both in NaCl and KCl solutions at pH 5 and 6, but not at pH 7. Weak Na+-efflux activity for this rhodopsin w
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Mashup Score: 2Efficient DNA base editing via an optimized DYW-like deaminase - 2 hour(s) ago
CRISPR-based cytosine base editors enable precise genome editing without inducing double-stranded DNA breaks, yet traditionally depend on a limited selection of deaminases from the APOBEC/AID or TadA families. Here, we introduce SsCBE, a novel CRISPR-based cytosine base editor utilizing SsdAtox, a DYW-like deaminase derived from the toxin of Pseudomonas syringae. Strategic engineering of SsdAtox has led to remarkable improvements in the base editing efficiency (by up to 8.4-fold) and specificity for SsCBE, while concurrently reducing cytotoxicity. Exhibiting exceptional versatility, SsCBE was delivered and efficiently applied using diverse delivery methods, including the engineered virus-like particles (eVLPs). Its application has enabled targeted cytosine base editing in mouse zygotes and pioneering edits in mitochondrial DNA. The advent of SsCBE marks a significant advancement in the CRISPR toolkit, providing a versatile tool for advanced research and therapeutic strategies. ### Comp
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Mashup Score: 0TRIM52 is a primate-specific player in the DNA repair process under tight proteolytic control by a triad of giant E3 ligases - 2 hour(s) ago
Tripartite motif 52 (TRIM52) exhibits strong positive selection in humans, yet is lost in many other mammals. In contrast to what one would expect for such a non-conserved factor, TRIM52 loss compromises cell fitness. We set out to determine the cellular function of TRIM52. Genetic and proteomic analyses revealed TRIM52’s involvement in resolving topoisomerase 2 (TOP2)-DNA cross-links, mitigating DNA damage and preventing cell-cycle arrest. Consistent with a fitness-promoting function, TRIM52 is upregulated in various cancers, prompting us to investigate its regulatory pathways. We found TRIM52 to be targeted for ultra-rapid proteasomal degradation by the giant E3 ubiquitin ligases BIRC6, HUWE1, and UBR4/KCMF1. BIRC6 mono-ubiquitinates TRIM52, with subsequent extension by UBR4/KCMF1. These findings underscore TRIM52’s pivotal role in DNA damage repair and regulation of its own abundance through multi-ligase degradation. ### Competing Interest Statement The authors have declared no comp
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Mashup Score: 0
Streptococcus pyogenes is a human-specific bacterial pathogen that produces several proteins that exploit the plasminogen (PLG)-plasmin (PLM) fibrinolysis system to dismantle blood clots and to facilitate spread and survival within the host. In this study, we explored the interactions between streptolysin O (SLO), a key cytolytic toxin produced by S. pyogenes , and human plasma proteins using affinity-enrichment mass spectrometry. SLO binds specifically to PLG, and this interaction accelerates the conversion of PLG to PLM by tissue-type plasminogen activator (tPA). To further investigate the molecular detail of the PLG-SLO interaction, we employed hydrogen/deuterium exchange mass spectrometry combined with targeted cross-linking mass spectrometry, uncovering that SLO binding induces local conformational shifts in PLG. These changes lead to the formation of a stabilized intermediate PLG-SLO complex that becomes significantly more sensitive to proteolytic processing by tPA. Our findings
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Mashup Score: 1
Extracellular RNA (exRNA) mediates intercellular communication in plants and lower animals; whether it serves a signalling function in mammals is controversial. Reductionist experiments, in which a single RNA is over-expressed or tagged, have shown RNA transfer between tissues but these may not be relevant to normal physiology. For example, the microRNA miR-122 is released from injured hepatocytes and is taken up by kidney cells. We sought to determine the scale of RNA transfer between liver and kidney through the metabolic labelling of RNA in mice. We used 4-thiouracil to specifically label RNA in hepatocytes then detected labelled (thiolated) RNA in the kidney using SLAMseq: SH-Linked Alkylation for the Metabolic sequencing of RNA. In the kidney, mRNA labelling was detected in 5% of all kidney transcripts under healthy conditions and was increased to 34% of kidney transcripts after acute hepatocellular injury. Labelling was evident in kidney transcripts mapping to known hepatocyte ma
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Flawed machine-learning confounds coding sequence annotation https://t.co/jUWwmdLjba #bioRxiv