bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simple Method to Dual Site-Specifically Label a Protein Using Tryptophan Auxotrophic Escherichia coli
Authors: Wu Ti , Joseph Simpson 
Published: November 2021

AbstractSite-specifically labeling proteins with multiple dyes or molecular moieties is an important yet non-trivial task for many research, such as when using Föster resonance energy transfer (FRET) to study dynamics of protein conformational change. Many strategies have been devised, but usually done on a case-by-case basis. Expanded genetic code provided a general platform to incorporate non-canonical amino acids (ncAA), which can also enable multiple site-specific labeling, but it’s technically complicated and not suitable for some applications. Here we present a streamlined method that could enable dual site-specific protein labeling by using a tryptophan auxotroph of Escherichia coli to incorporate a naturally found tryptophan analog, 5-hydroxytryptophan into a recombinant protein. As a demonstration, we incorporated 5-hydroxytryptophan into E. coli release factor 1 (RF1), a protein known to possess two different conformations, and site-specifically attached two different fluorophores, one on 5-hydroxytryptophan and another on a cysteine residue. This method is simple, generally applicable, efficient, and can serve as an alternative way for researchers who want to install an additional labeling site in their proteins.
Chromosome splitting of Plasmodium berghei using the CRISPR/Cas9 system
Authors: Addo-Gyan Daniel , Matsushita Haruka , Sora Enya , Nishi Tsubasa , Yuda Masao , Shinzawa Naoaki , Iwanaga Shiroh 
Published: November 2021

ABSTRACTSpatial arrangement of chromosomes is responsible for gene expression in Plasmodium parasites. However, methods for rearranging chromosomes have not been established, which makes it difficult to investigate its role in detail. Here, we report a method for splitting chromosome in rodent malaria parasite by CRISPR/Cas9 system using fragments in which a telomere and a centromere were incorporated. The resultant split chromosomes segregated accurately into daughter parasites by the centromere. In addition, elongation of de novo telomeres were observed, indicating its proper function. Furthermore, chromosome splitting had no effect on development of parasites. Splitting of the chromosome is expected to alter its spatial arrangement, and our method will thus be useful for investigating its biological role related with gene expression.
Toward optimal fingerprint indexing for large scale genomics
Authors: Agret Clément , Cazaux Bastien , Limasset Antoine 
Published: November 2021

AbstractMotivationTo keep up with the scale of genomic databases, several methods rely on local sensitive hashing methods to efficiently find potential matches within large genome collections. Existing solutions rely on Minhash or Hyperloglog fingerprints and require reading the whole index to perform a query. Such solutions can not be considered scalable with the growing amount of documents to index.ResultsWe present NIQKI, a novel structure with well-designed fingerprints that lead to theoretical and practical query time improvements, outperforming state-of-the-art by orders of magnitude. Our contribution is threefold. First, we generalize the concept of Hyperminhash fingerprints in (h,m)-HMH fingerprints that can be tuned to present the lowest false positive rate given the expected sub-sampling applied. Second, we provide a structure able to index any kind of fingerprints based on inverted indexes that provide optimal queries, namely linear with the size of the output. Third, we implemented these approaches in a tool dubbed NIQKI that can index and calculate pairwise distances for over one million bacterial genomes from GenBank in a few days on a small cluster. We show that our approach can be orders of magnitude faster than state-of-the-art with comparable precision. We believe this approach can lead to tremendous improvements, allowing fast queries and scaling on extensive genomic databases.Availability and implementationWe wrote the NIQKI index as an open-source C++ library under the AGPL3 license available at https://github.com/Malfoy/NIQKI. It is designed as a user-friendly tool and comes along with usage samples.2012 ACM Subject ClassificationApplied computing → BioinformaticsDigital Object Identifier10.4230/LIPIcs.WABI.2022.25
USPNet: unbiased organism-agnostic signal peptide predictor with deep protein language model
Authors: Chen Shenyang , Tan Qingxiong , Li Jingchen , Li Yu 
Published: November 2021

AbstractSignal peptide is a short peptide located in the N-terminus of proteins. It plays an important role in targeting and transferring transmembrane proteins and secreted proteins to correct positions. Compared with traditional experimental methods to identify and discover signal peptides, the computational methods are faster and more efficient, which are more practical for the analysis of thousands or even millions of protein sequences in reality, especially for the metagenomic data. Therefore, computational tools are recently proposed to classify signal peptides and predict cleavage site positions, but most of them disregard the extreme data imbalance problem in these tasks. In addition, almost all these methods rely on additional group information of proteins to boost their performances, which, however, may not always be available. To deal with these issues, in this paper, we present Unbiased Organism-agnostic Signal Peptide Network (USPNet), a signal peptide prediction and cleavage site prediction model based on deep protein language model. We propose to use label distribution-aware margin (LDAM) loss and evolutionary scale modeling (ESM) embedding to handle data imbalance and object-dependence problems. Extensive experimental results demonstrate that the proposed method significantly outperforms all the previous methods on the classification performance. Additional study on the simulated metagenomic data further indicates that our model is a more universal and robust tool without dependency on additional group information of proteins, with the Matthews correlation coefficient improved by up to 17.5%. The proposed method will be potentially useful to discover new signal peptides from the abundant metagenomic data.
Genome Mining Uncovers Clustered Biosynthetic Pathways for Defense-Related Molecules in Bread Wheat
Authors: Polturak Guy , Dippe Martin , Stephenson Michael J , Misra Rajesh Chandra , Owen Charlotte , Ramirez-Gonzalez Ricardo , Haidioulis John , Schoonbeek Henk-Jan , Chartrain Laetitia , Borrill Philippa , Nelson David R , Brown James , Nicholson Paul , Uauy Cristobal , Osbourn Anne 
Published: November 2021

ABSTRACTWheat is one of the most widely grown food crops in the world. However, it succumbs to numerous pests and pathogens that cause substantial yield losses. A better understanding of biotic stress responses in wheat is thus of major importance. Here we identify previously unknown pathogen-induced biosynthetic pathways that produce a diverse set of molecules, including flavonoids, diterpenes and triterpenes. These pathways are encoded by six biosynthetic gene clusters and share a common regulatory network. We further identify associations with known or novel phytoalexin clusters in other cereals and grasses. Our results significantly advance the understanding of chemical defenses in wheat and open up new avenues for enhancing disease resistance in this agriculturally important crop.
Genotype-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline
Authors: Pinseel Eveline , Nakov Teofil , Van den Berge Koen , Downey Kala M. , Judy Kathryn J. , Kourtchenko Olga , Kremp Anke , Ruck Elizabeth C. , Sjöqvist Conny , Töpel Mats , Godhe Anna , Alverson Andrew J. 
Published: November 2021

AbstractThe salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of S. marinoi grown in a common garden. Our experiment included eight genotypes from source populations spanning the Baltic Sea salinity cline. Changes in gene expression revealed a shared response to salinity across genotypes, where low salinities induced profound changes in cellular metabolism, including upregulation of carbon fixation and storage compound biosynthesis, and increased nutrient demand and oxidative stress. Nevertheless, the genotype effect overshadowed the salinity effect, as genotypes differed significantly in their response, both in the magnitude and direction of gene expression. Intraspecific differences included regulation of transcription and translation, nitrogen metabolism, cell signaling, and aerobic respiration. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond and adapt to environmental change.
WITHDRAWN: KMT5C encodes robust heterochromatin retention and liquid-like behavior using limited sequence features
Authors: Strickfaden Hilmar , Missiaen Kristal , Knechtel Justin W. , Hendzel Michael J. , Underhill D. Alan 
Published: November 2021

Withdrawal StatementThe authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2019/776625. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi:10.1101/776625.
Sketching and sampling approaches for fast and accurate long read classification
Authors: Das Arun , Schatz Michael C. 
Published: November 2021

AbstractBackgroundIn modern sequencing experiments, quickly and accurately identifying the sources of the reads is a crucial need. In metagenomics, where each read comes from one of potentially many members of a community, it can be important to identify the exact species the read is from. In other settings, it is important to distinguish which reads are from the targeted sample and which are from potential contaminants. In both cases, identification of the correct source of a read enables further investigation of relevant reads, while minimizing wasted work. This task is particularly challenging for long reads, which can have a substantial error rate that obscures the origins of each read.ResultsExisting tools for the read classification problem are often alignment or index-based, but such methods can have large time and/or space overheads. In this work, we investigate the effectiveness of several sampling and sketching-based approaches for read classification. In these approaches, a chosen sampling or sketching algorithm is used to generate a reduced representation (a “screen”) of potential source genomes for a query readset before reads are streamed in and compared against this screen. Using a query read’s similarity to the elements of the screen, the methods predict the source of the read. Such an approach requires limited pre-processing, stores and works with only a subset of the input data, and is able to perform classification with a high degree of accuracy.ConclusionsThe sampling and sketching approaches investigated include uniform sampling, methods based on MinHash and its weighted and order variants, a minimizer-based technique, and a novel clustering-based sketching approach. We demonstrate the effectiveness of these techniques both in identifying the source microbial genomes for reads from a metagenomic long read sequencing experiment, and in distinguishing between long reads from organisms of interest and potential contaminant reads. We then compare these approaches to existing alignment, index and sketching-based tools for read classification, and demonstrate how such a method is a viable alternative for determining the source of query reads. Finally, we present a reference implementation of these approaches at https://github.com/arun96/sketching.
Multi-site phosphorylation of yeast Mif2/CENP-C promotes inner kinetochore assembly
Authors: Hinshaw Stephen M. , Quan Yun , Cai Jiaxi , Zhou Ann L. , Zhou Huilin 
Published: November 2021

AbstractKinetochores control eukaryotic chromosome segregation by connecting chromosomal centromeres to spindle microtubules. Duplication of centromeric DNA necessitates kinetochore disassembly and subsequent reassembly on the nascent sisters. To search for a regulatory mechanism that controls the earliest steps of kinetochore assembly, we studied Mif2/CENP-C, an essential basal component. We found that Polo-like kinase (Cdc5) and Dbf4-dependent kinase (DDK) phosphorylate the conserved PEST region of Mif2/CENP-C and that this phosphorylation directs inner kinetochore assembly. Mif2 phosphorylation promotes kinetochore assembly in a reconstituted biochemical system, and it strengthens Mif2 localization at centromeres in cells. Disrupting one or more phosphorylation sites in the Mif2-PEST region progressively impairs cellular fitness and sensitizes cells to microtubule poisons. The most severe Mif2-PEST mutations are lethal in cells lacking otherwise non-essential Ctf19 complex factors. These data suggest that multi-site phosphorylation of Mif2/CENP-C is a robust switch that controls inner kinetochore assembly, ensuring accurate chromosome segregation.
Transmission of Acute Respiratory Infections during Aerosol Generating Medical Procedures (AGMPs): An updated review
Authors: Leal Jenine , Hofmeister Mark , Mastikhina Liza , Taplin John , Li Joyce , Farkas Brenlea , Dowsett Laura , Noseworthy Tom , Clement Fiona 
Published: November 2021

1ABSTRACTObjectivesTo review the literature from 2011 until March 31st, 2020 to identify the risk of transmission of ARIs to healthcare workers caring for patients undergoing AGMPs compared with the risk of transmission when caring for patients not undergoing AGMPs.ResultsOnly two prospective cohort studies were identified meeting inclusion criteria. One found that performance or assistance with AGMP during the previous week was significantly associated with symptomatic influenza (adjusted OR: 2.29, 95% CI: 1.3 to 4.2). The second study found that performance of AGMP was significantly associated with clinical respiratory infections (RR 2.9, 95% CI 1.42-5.87, p<0.01), laboratory-confirmed virus or bacteria (RR 2.9, 95% CI 1.37-6.22, p=0.01), and laboratory-confirmed virus (RR 3.3, 95% CI 1.01-11.02, p=0.05). Further evidence is needed regarding what constitutes an AGMP and the risk of ARI transmission during presumed AGMPs. Organizations need to interpret these findings with caution when establishing AGMP lists requiring airborne precautions.
The Anaphase Promoting Complex/ cyclosome co-activator, Cdh1, is a novel target of human Papillomavirus 16 E7 oncoprotein in cervical oncogenesis
Authors: Jaiswal Neha , Nandi Deeptashree , Cheema Pradeep Singh , Nag Alo 
Published: November 2021

ABSTRACTThe transforming properties of the high risk human papillomavirus E7 oncoprotein are indispensable for driving the virus life cycle and pathogenesis. Besides inactivation of retinoblastoma (Rb) family of tumor suppressors as part of its oncogenic endeavors, E7-mediated perturbations of eminent cell cycle regulators, checkpoint proteins and proto-oncogenes are considered to be the tricks of its transformative traits. However, many such critical interactions are still unknown. In the present study, we have identified the anaphase promoting complex/ cyclosome (APC/C) co-activator, Cdh1, as a novel interacting partner and a degradation target of E7. We found that HPV16 E7-induced inactivation of Cdh1 promoted abnormal accumulation of multiple Cdh1 substrates. Such a mode of deregulation possibly contributes to HPV-mediated cervical oncogenesis. Our mapping studies recognized the carboxyl-terminal zinc finger motif of E7 to associate with Cdh1 and interfere with the timely degradation of FoxM1, a bona fide Cdh1 substrate and a potent oncogene. Importantly, the E7 mutant with impaired interaction with Cdh1 exhibited defects in its ability for overriding typical cell cycle transition and oncogenic transformation, thereby validating the functional and pathological significance of the E7-Cdh1 axis during cervical carcinoma progression. Altogether, the findings from our study discover a unique nexus between E7 and APC/C-Cdh1, thereby adding to our understanding of the mechanism of E7-induced carcinogenesis and provide a promising target for the management of cervical carcinoma.
Prediction of broad chemical toxicities using induced pluripotent stem cells and gene networks by transfer learning from embryonic stem cell data
Authors: Yamane Junko , Wada Takumi , Otsuki Hironori , Inomata Koji , Suzuki Mutsumi , Hisaki Tomoka , Sekine Shuichi , Kouzuki Hirokazu , Kobayashi Kenta , Sone Hideko , Yamashita Jun K. , Osawa Mitsujiro , Saito Megumu K. , Fujibuchi Wataru 
Published: November 2021

SUMMARYThe assessment of toxic chemicals using animals has limited applicability to humans. Moreover, from the perspective of animal protection, effective alternatives are also desired. Previously, we developed a method that combines developmental toxicity testing based on undifferentiated human embryonic stem (ES) cells (KhES-3) and gene networks. We showed that ≥ 95% accurate predictions could be achieved for neurotoxins, genotoxic carcinogens, and non-genotoxic carcinogens. Here, we expanded this method to predict broad toxicities and predicted the toxicity of 24 chemicals in six categories (neurotoxins, cardiotoxins, hepatotoxins, nephrotoxins [glomerular nephrotoxins/tubular nephrotoxins], and non-genotoxic carcinogens) and achieved high prediction accuracy (AUC = 0.90–1.00) in all categories. Moreover, to develop a testing system with fewer ethical issues, we screened for an induced pluripotent stem (iPS) cell line on the basis of cytotoxic sensitivity and used this line to predict toxicity in the six categories based on the gene networks of iPS cells using transfer learning from the ES cell gene networks. We successfully predicted toxicities in four toxin categories (neurotoxins, hepatotoxins, glomerular nephrotoxins, and non-genotoxic carcinogens) at high accuracy (AUC = 0.82–0.99). These results demonstrate that the prediction of chemical toxicity is possible even with iPS cells by transfer learning once a gene expression database has been developed from an ES cell line. This method holds promise for tailor-made safety evaluations using individual iPS cells.
De novo assembly of 20 chickens reveals the undetectable phenomenon for thousands of core genes on sub-telomeric regions
Authors: Li Ming , Sun Congjiao , Xu Naiyi , Bian Peipei , Tian Xiaomeng , Wang Xihong , Wang Yuzhe , Jia Xinzheng , Heller Rasmus , Wang Mingshan , Wang Fei , Dai Xuelei , Luo Rongsong , Guo Yingwei , Wang Xiangnan , Yang Peng , Zhang Shunjin , Li Xiaochang , Wen Chaoliang , Lan Fangren , Zonaed Siddiki AMAM , Suwannapoom Chatmongkon , Zhao Xin , Nie Qinghua , Hu Xiaoxiang , Jiang Yu , Yang Ning 
Published: November 2021

AbstractThe gene numbers and evolutionary rates of birds were assumed to be much lower than that of mammals, which in sharp contrast to the huge species number and morphological diversity of birds. It is very necessary to construct a complete avian genome and analyze its evolution.We constructed a chicken pan-genome from 20 de novo genome assemblies with high sequencing depth, newly identified 1,335 protein-coding genes and 3,011 long noncoding RNAs. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were accidentally measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal sub-telomeric regions, surrounded with extremely high proportions of tandem repeats, and strongly blocked DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had three-fold elevated substitution rates than known ones, updating the evolutionary rates of birds. Our study provides a framework for constructing a better chicken genome, which will contribute towards the understanding of avian evolution and improvement of poultry breeding.
The β-lactam Ticarcillin is a Staphylococcus aureus UDP-N-acetylglucosamine 2-epimerase binder
Authors: de Azevedo Erika Chang , Nascimento Alessandro S. 
Published: November 2021

AbstractInfectious diseases account for 25% of the causes of death worldwide and this rate is expected to increase due to antibiotic resistance. Among the bacteria associated with healthcare infections, Staphylococcus aureus is a prevalent pathogen and about 50% of the isolates are found to be methicillin-resistant. Here we describe the identification of ticarcillin as a weak binder of the S. aureus UDP-N-acetylglucosamine 2-epimerase. After a docking screening, ticarcillin was identified as a ligand in using the recently proposed isothermal analysis of differential scanning fluorimetry data. Finally, an equilibrium MD simulation confirmed the docking binding mode as a stable pose, with large contributions to the binding energy coming from interactions between Arg206 and Arg207 and the carboxylate groups in ticarcillin.
An astrocytic signaling loop for frequency-dependent control of dendritic integration and spatial learning
Authors: Bohmbach Kirsten , Masala Nicola , Schönhense Eva M. , Hill Katharina , Haubrich André N. , Zimmer Andreas , Opitz Thoralf , Beck Heinz , Henneberger Christian 
Published: November 2021

AbstractDendrites of hippocampal CA1 pyramidal cells amplify clustered glutamatergic input by activation of voltage-gated sodium channels and N-methyl-D-aspartate receptors (NMDARs). NMDAR activity depends on the presence of NMDAR co-agonists such as D-serine, but how co-agonists influence dendritic integration is not well understood. Using combinations of whole-cell patch clamp, iontophoretic glutamate application, two-photon excitation fluorescence microscopy and glutamate uncaging we found that exogenous D-serine reduces the threshold of dendritic spikes and increases their amplitude. Triggering an astrocytic mechanism controlling endogenous D-serine supply via endocannabinoid receptors (CBRs) also increased dendritic spiking. Unexpectedly, this pathway was activated by pyramidal cell activity primarily in the theta range, which required HCN channels and astrocytic CB1Rs. Therefore, astrocytes close a positive and frequency-dependent feedback loop between pyramidal cell activity and their integration of dendritic input. Its disruption led to an impairment of spatial memory, which demonstrates its behavioral relevance.