bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Sofosbuvir, Daclatasvir and Ribavirin combination therapy in treatment naïve hepatitis C patients at tertiary care hospital of South Punjab
Authors: Umar Qasim , Gul Muhammad Asif , Din Chaudhary Farooq Mohyud , Kanju Shehryar , Hameed Rizwan , Shahwar Dure 
Published: November 2021

AbstractIntroductionHepatitis C has gradually become endemic in Pakistan, with infectivity rates one of the highest in the world. The emergence of direct acting antivirals (DAAs) has become a ray of sunshine in eradicating this menace from this region. The combination of sofosbuvir, daclatasvir and ribavirin (SOF/DACLA/RIBA) has had phenomenal success all over the world in eradicating this virus. Our study aims to see the effectiveness of this regime in this part of the world.MethodsAfter approval from the institutional review board (IRB), retrospective analysis of data of treatment naïve patients who have been treated with the above mentioned regimen was collected to assess the efficacy by calculating the sustained virological response (SVR) at 12 weeks after completion of therapy.ResultsData of 300 patients (172 females, 128 males) was collected. Mean age was 39.66 years. Majority (almost 90%) of patients were from District Multan Age range was from 18 years to 60 years. Eighty-three percent of the patients were non-cirrhotics, 15.7% had compensated cirrhosis, while only 1 % had decompensated cirrhosis. Out of the 300 patients, 291 patients had undetectable HCV RNA on polymerase chain reaction (PCR) at 12 weeks after completion of treatment, achieving SVR rates of 97%. There was no significant association of SVR rates with gender and age of patients.ConclusionThe combination of SOF/DACA/RIBA is highly efficacious for treatment of hepatitis C patients.
amica: an interactive and user-friendly web-platform for the analysis of proteomics data
Authors: Didusch Sebastian , Madern Moritz , Hartl Markus , Baccarini Manuela 
Published: November 2021

AbstractSummaryQuantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high throughput data analysis. In order to facilitate this task for users with limited background knowledge, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources and provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica interactively to compare proteins across multiple groups, create customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators.Availability and ImplementationThe code for the application, input data and documentation can be accessed online at https://github.com/tbaccata/amica and is also incorporated in the web application. A freely available version of amica is available at https://bioapps.maxperutzlabs.ac.at/app/amica.
A chromosome-level reference genome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae
Authors: Wang Ziwei , Rouard Mathieu , Biswas Manosh Kumar , Droc Gaetan , Cui Dongli , Roux Nicolas , Baurens Franc-Christophe , Ge Xue-Jun , Schwarzacher Trude , Heslop-Harrison Pat (J.S.) , Liu Qing 
Published: November 2021

AbstractBackgroundEnsete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence of E. glaucum offers a vital genomic resource for functional and evolutionary studies of Ensete, the Musaceae, and more widely in the Zingiberales.FindingsUsing a combination of Illumina and Oxford Nanopore Technologies (ONT) sequencing, genome-wide chromosome conformation capture (Hi-C), and RNA survey sequence, we report a high-quality assembly of the 481.5Mb genome with 9 pseudochromosomes and 36,836 genes (BUSCO 94.7%). A total of 55% of the genome is composed of repetitive sequences with LTR-retroelements (37%) and DNA transposons (7%) predominant. The 5S and 45S rDNA were each present at one locus, and the 5S rDNA had an exceptionally long monomer length of c.1,056 bp, contrasting with the c. 450 bp monomer at multiple loci in Musa. A tandemly repeated c. 134 bp satellite, 1.1% of the genome (with no similar sequence in Musa), was present around all nine centromeres, with a LINE retroelement also found at Musa centromeres. The assembly, including centromeric positions, enabled us to characterize in detail the chromosomal rearrangements occurring between the x = 9 species and x = 11 species of Musa. Only one chromosome has the same gene content as M. acuminata (ma). Three ma chromosomes represent part of only one E. glaucum (eg) chromosome, while the remaining seven ma chromosomes are fusions of parts of two, three, or four eg chromosomes, demonstrating complex and multiple evolutionary rearrangements in the change between x = 9 and x = 11.ConclusionsThe advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly show how chromosome number evolves, and features of the rapid evolution of repetitive sequences.
A bioactive phlebovirus-like envelope protein in a hookworm endogenous retrovirus
Authors: Merchant Monique , Mata Carlos P. , Liu Yangci , Zhai Haoming , Protasio Anna V. , Modis Yorgo 
Published: November 2021

AbstractEndogenous retroviruses (ERVs), accounting for 14% of our genome, serve as a genetic reservoir from which new genes can emerge. Nematode ERVs are particularly diverse and informative of retrovirus evolution. We identify Atlas virus – a novel, intact ERV in the human hookworm Ancylostoma ceylanicum with an envelope protein genetically related to GN-GC glycoproteins from phleboviruses. A cryo-EM structure of Atlas GC reveals a class II viral membrane fusion protein fold not previously seen in retroviruses. Atlas GC has the structural hallmarks of an active fusogen. Atlas GC trimers insert into membranes with endosomal lipid compositions and low pH. When expressed on the plasma membrane, Atlas GC has cell-cell fusion activity. Atlas virus is transcriptionally active at specific stages of hookworm development. The preserved activities and expression pattern of Atlas GC suggest it has acquired a cellular function. Our work reveals an unexpected degree of structural and genetic plasticity in retroviruses.
Inferring kinetic rate constants from single-molecule FRET trajectories – a blind benchmark of kinetic analysis tools
Authors: Götz Markus , Barth Anders , Bohr Søren S.-R. , Börner Richard , Chen Jixin , Cordes Thorben , Erie Dorothy A. , Gebhardt Christian , Hadzic Mélodie C.A.S. , Hamilton George L. , Hatzakis Nikos S. , Hugel Thorsten , Kisley Lydia , Lamb Don C. , de Lannoy Carlos , Mahn Chelsea , Dunukara Dushani , de Ridder Dick , Sanabria Hugo , Schimpf Julia , Seidel Claus A.M. , Sigel Roland K.O. , Sletfjerding Magnus Berg , Thomsen Johannes , Vollmar Leonie , Wanninger Simon , Weninger Keith R. , Xu Pengning , Schmid Sonja 
Published: November 2021

ABSTRACTSingle-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals. The powerful ability to infer quantitative kinetic information from smFRET data is, however, complicated by experimental limitations. Diverse analysis tools have been developed to overcome these hurdles but a systematic comparison is lacking. Here, we report the results of a blind benchmark study assessing eleven analysis tools used to infer kinetic rate constants from smFRET trajectories. We tested them against simulated and experimental data containing the most prominent difficulties encountered in analyzing smFRET experiments: different noise levels, varied model complexity, non-equilibrium dynamics, and kinetic heterogeneity. Our results highlight the current strengths and limitations in inferring kinetic information from smFRET trajectories. In addition, we formulate concrete recommendations and identify key targets for future developments, aimed to advance our understanding of biomolecular dynamics through quantitative experiment-derived models.
Improved peptide backbone fragmentation is the primary advantage of MS-cleavable crosslinkers
Authors: Kolbowski Lars , Lenz Swantje , Fischer Lutz , Sinn Ludwig R , O’Reilly Francis J , Rappsilber Juri 
Published: November 2021

AbstractProteome-wide crosslinking mass spectrometry studies have coincided with the advent of MS-cleavable crosslinkers that can reveal the individual masses of the two crosslinked peptides. However, recently such studies have also been published with non-cleavable crosslinkers suggesting that MS-cleavability is not essential. We therefore examined in detail the advantages and disadvantages of using the most popular MS-cleavable crosslinker, DSSO. Indeed, DSSO gave rise to signature peptide fragments with a distinct mass difference (doublet) for nearly all identified crosslinked peptides. Surprisingly, we could show that it was not these peptide masses that proved the main advantage of MS-cleavability of the crosslinker, but improved peptide backbone fragmentation that allowed for more confident peptide identification. We also show that the more intricate MS3-based data acquisition approaches lack sensitivity and specificity, causing them to be outperformed by the simpler and faster stepped HCD method. This understanding will guide future developments and applications of proteome-wide crosslinking mass spectrometry.
Circular RNA signatures of human healing and non-healing wounds
Authors: Toma Maria A. , Liu Zhuang , Wang Qizhang , Zhang Letian , Li Dongqing , Sommar Pehr , Landén Ning Xu 
Published: November 2021

AbstractBackgroundAlthough the widespread expression of circular RNAs (circRNAs) has only been recognized recently, increasing evidence has suggested their important roles in health and disease. To identify clinically relevant circRNAs with potential for wound diagnosis and therapy, an in-depth characterization of circRNA expression in human healing and non-healing wounds is a prerequisite that has not been attained yet.MethodsWe collected wound-edge biopsies through the healing process of healthy donors and in chronic non-healing venous ulcers (VU). Paired total RNA- and small RNA-sequencing were performed to profile circRNAs, protein-coding mRNAs, and microRNA expression. We analyzed the co-expression relationship between circRNAs and mRNAs with weighted correlation network analysis (WGCNA) and constructed circRNA-microRNA-mRNA networks. For the circRNAs surfaced in the in-silico analysis, after validating their expression with RT-PCR and sequencing, we silenced hsa-CHST15_0003 and hsa-TNFRSF21_0001 expression in keratinocytes with siRNAs and studied their function with transcriptomic profiling and live-cell monitoring.ResultsOur study unravels the dynamically changed expression patterns of circRNAs during human skin wound healing and their abnormal expression signature in VU, which are presented as a searchable web resource (http://130.229.28.87/shiny/circRNA_wholebiopsy-shinyApp/).In silicoanalysis deciphers the circRNA-miRNAs-mRNA networks specific to the inflammatory and proliferative phases of wound repair and VU, the biological processes that circRNAs are involved, and the circRNAs that could act as miRNAs sponge in human wounds. Importantly, we found that hsa-CHST15_0003 and hsa-TNFRSF21_0001, two circRNAs upregulated in VU, hampered keratinocyte migration while promoting proliferation through modulating gene networks underpinning these cellular processes.ConclusionBy integrating circRNA, mRNA, and miRNA expression profiles in a unique collection of clinical samples, we identify the circRNAs that are relevant to human wound healing physiology and pathology. This study paves the way to decipher the functional significance of circRNAs in tissue repair.
RNA-binding protein Orb2 causes microcephaly and supports centrosome asymmetry inDrosophilaneural stem cells
Authors: Robinson Beverly V. , Buehler Joseph , Hailstock Taylor , Adebambo Temitope H. , Fang Junnan , Mehta Dipen S. , Lerit Dorothy A. 
Published: November 2021

AbstractTo maintain a balance of self-renewal versus neurogenesis, neural stem cells (NSCs) undergo asymmetric cell division along an invariant polarity axis instructed by centrosomes. In the NSCs of the third instarDrosophilalarval brain, the interphase centrosomes are defined by marked asymmetries in protein composition and functional activity as microtubule-organizing centers. Here we show that a conserved RNA-binding protein, Orb2, supports NSC centrosome asymmetry by localizing to the cytoplasm, where it promotes robust apical centrosome maturation and transient basal centrosome inactivation, required for centrosome segregation and spindle morphogenesis. Orb2 is required cell autonomously within NSCs to support centrosome asymmetry and maintenance of the stem cell pool. We suggest Orb2 plays opposing roles in centrosome activation and inactivation at the apical versus basal centrosomes respectively, possibly through the translational regulation of multiple mRNAs. Conversely, loss oforb2manifests in microcephaly independent of Orb2 function in NSCs. Bioinformatics uncovers a significant overlap among RNA targets betweenDrosophilaOrb2 and human CPEB4, consistent with a conserved role for CPEB proteins in centrosome regulation and neurodevelopment.
A drug discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screening
Authors: Bellini Dom 
Published: November 2021

AbstractIn X-ray macromolecular crystallography, cryoprotection of crystals mounted on harvesting loops is achieved when the water in the sample solvent transitions to vitreous ice before crystalline ice forms. This is achieved by rapid cooling in liquid nitrogen or propane. Protocols for protein crystal cryoprotection are based on either increasing environmental pressure or reducing the water fraction in the solvent. This study presents a new protocol for cryoprotecting crystals. It is based on vapour diffusion dehydration of the crystal drop to reduce the water fraction in the solvent by adding a highly concentrated salt solution, 13 M potassium formate (KF13), directly to the reservoir. Cryoprotection by the KF13 protocol is non-invasive to the crystal, high throughput, not labour intensive, can benefit diffraction resolution and ligand binding, and is very useful in cases with high redundancy such as drug discovery projects which utilize very large compound or fragment libraries. Moreover, an application of KF13 to discover new crystal hits from clear drops of equilibrated crystallization screening plates is also shown.
Plants species’ influence on rhizosphere microbial communities depends on N availability
Authors: Potter Teal S. , Anacker Brian L. , Churchill Amber C. , Bowman William D. 
Published: November 2021

AbstractPurposePlants and soil microbes both influence how ecosystems respond to environmental change. Yet, we lack the ability to generalize how plants and soil microbes influence each other in the same or varying soil conditions. This limitation thwarts ecologists’ ability to understand and predict effects of environmental changes such and elevated anthropogenic nitrogen (N) deposition. Accordingly, we examined the specificity of plant species’ influence on soil microbial community composition.MethodsWe tested (1) whether congeneric grass species have unique effects on soil microbial communities, (2) how relative abundances of microbial taxa can be explained by Poa phylogeny, plant traits, and range-wide traits (annual temperature and soil pH), and (3) whether N addition alters associations between Poa species and soil microbes, and (4) whether the magnitude of microbial community change in response to elevated N can be explained by plant growth responses to N. We conducted a greenhouse experiment with seven Poa species and native soils.ResultsWe found that individual Poa species were associated with different soil fungi but similar soil bacteria. Differences in microbial composition were not attributable to Poa phylogeny, plant traits, or range-wide traits. Nitrogen addition enhanced the unique effects of Poa species on fungal and bacterial community compositions.ConclusionThese results demonstrate how ecological interactions of related plant species vary depending on resource supply, revealing important context dependency for accurately predicting microbially-mediated nutrient cycling and ecosystem responses to changes in nutrient availability.
Molecular Basis of Antibiotic Self-Resistance in a Bee Larvae Pathogen
Authors: Dang Tam , Loll Bernhard , Müller Sebastian , Skobalj Ranko , Ebeling Julia , Bulatov Timur , Gensel Sebastian , Göbel Josefine , Wahl Markus C. , Genersch Elke , Mainz Andi , Süssmuth Roderich D. 
Published: November 2021

AbstractPaenibacillus larvae, the causative agent of the devastating honey-bee disease American Foulbrood, produces the cationic polyketide-peptide hybrid paenilamicin that displays high antibacterial and antifungal activity. Its biosynthetic gene cluster contains a gene coding for theN-acetyltransferase PamZ. We show that PamZ acts as self-resistance factor inP. larvaeby deactivation of paenilamicin. Using tandem MS, NMR spectroscopy and synthetic diastereomers, we identified the N-terminal amino group of the agmatinamic acid as theN-acetylation site. These findings highlight the pharmacophore region of paenilamicin, which we very recently identified as a new ribosome inhibitor. Here, we further elucidated the crystal structure of PamZ:acetyl-CoA complex at 1.34 Å resolution. An unusual tandem-domain architecture provides a well-defined substrate-binding groove decorated with negatively-charged residues to specifically attract the cationic paenilamicin. Our results will help to understand the mode of action of paenilamicin and its role in pathogenicity ofP. larvaeto fight American Foulbrood.
Protonation-Dependent Sequencing of 5-Formylcytidine in RNA
Authors: Link Courtney N. , Gamage Supuni Thalalla , Gallimore Diamond A. , Kopajtich Robert , Evans Christine N. , Nance Samantha R. , Fox Stephen D. , Andresson Thorkell , Chari Raj , Ivanic Joseph , Prokisch Holger , Meier Jordan L. 
Published: November 2021

AbstractChemical modification of cytidine in non-coding RNAs plays a key role in regulating translation and disease. However, the distribution and dynamics of many of these modifications remains unknown due to a lack of sensitive site-specific sequencing technologies. Here we report a protonation-dependent sequencing reaction for detection of 5-formylcytidine (5fC) and 5-carboxycytidine (5caC) in RNA. First, we evaluate how protonation combined with electron-withdrawing substituents alters the molecular orbital energies and reduction of modified cytidine nucleosides, highlighting 5fC and 5caC as reactive species. Next, we apply this reaction to detect these modifications in synthetic oligonucleotides as well as endogenous human tRNA. Finally, we demonstrate the utility of our method to characterize a patient-derived model of 5fC-deficiency, where it enables facile monitoring of both pathogenic loss and exogenous rescue of NSUN3-dependent 5fC within the wobble base of human mitochondrial tRNAMet. These studies showcase the ability of protonation to enhance the reactivity and sensitive detection of 5fC in RNA, and provide a molecular foundation for applying optimized sequencing reactions to better understand the role of oxidized RNA cytidine nucleobases in disease.
Treatment of infection-induced vascular pathologies is protective against persistent rough morphotype Mycobacterium abscessus infection in zebrafish
Authors: Kam Julia Y , Wright Kathryn , Britton Warwick J , Oehlers Stefan H 
Published: November 2021

AbstractMycobacterium abscessus infections are of increasing global prevalence and are often difficult to treat due to complex antibiotic resistance profiles. While there are similarities between the pathogenesis of M. abscessus and tuberculous mycobacteria, including granuloma formation and stromal remodeling, there are distinct molecular differences at the host-pathogen interface. Here we have used a zebrafish-M. abscessus model and host-directed therapies that were previously identified in the zebrafish-M. marinum model to identify potential host-directed therapies against M. abscessus infection. We find efficacy of anti-angiogenic and vascular normalizing therapies against rough M. abscessus infection, but no effect of anti-platelet drugs.
TFAP2 paralogs facilitate chromatin access for MITF at pigmentation genes but inhibit expression of cell-cell adhesion genes independently of MITF
Authors: Kenny Colin , Dilshat Ramile , Seberg Hannah , Otterloo Eric Van , Bonde Gregory , Helverson Annika , Franke Christopher M. , Steingrímsson Eiríkur , Cornell Robert A. 
Published: November 2021

AbstractIn developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that Tfap2 facilitates MITF’s ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa- expressing cells that also express Tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the latter necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.