Top 6 Biorxiv Papers Today in Molecular Biology


2.003 Mikeys
#1. Streamlined production, purification, and comparison of recombinant extracellular polyhydroxybutyrate depolymerases
Diana Isabel Martínez-Tobón, Brennan Waters, Anastasia L. Elias, Dominic Sauvageau
Heterologous production of extracellular polyhydroxybutyrate (PHB) depolymerases (PhaZs) has been of interest for over 30 years, but implementation is sometimes difficult and can limit the scope of research. With the constant development of tools to improve recombinant protein production in Escherichia coli, we propose a method that takes characteristics of PhaZs from different bacterial strains into account. Recombinant His-tagged versions of PhaZs (rPhaZ) from Comamonas testosteroni 31A, Cupriavidus sp., Marinobacter algicola DG893, Pseudomonas stutzeri, and Ralstonia sp. were successfully produced with varying expression, solubility, and purity levels. PhaZs from C. testosteroni and P. stutzeri were more amenable to heterologous expression in all aspects; however, strategies were developed to circumvent low expression and purity for the other PhaZs. Degradation activity of the rPhaZs was compared using a simple PHB plate-based method, adapted to test for various pH and temperatures. rPhaZ from M. algicola presented the highest...
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biorxivpreprint: Streamlined production, purification, and comparison of recombinant extracellular polyhydroxybutyrate depolymerases https://t.co/ht6oDWYpH0 #bioRxiv
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Authors: 4
Total Words: 0
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2.003 Mikeys
#2. Exosome-mediated crosstalk stimulated by liver fluke granulin promotes a microenvironment conducive to cholangiocarcinoma
Patpicha Arunsan, Apisit Chaidee, Christina J Cochan, Victoria H Mann, Toshihiko Tanno, chutima kumkhaek, Michael Smout, Shannon Karinshak, Rutchanee Rodpai, Javier Sotillo, Alex Loukas, THEWARACH LAHA, Paul J Brindley, Wannaporn Ittiprasert
Crosstalk between malignant and neighboring cells contributes to tumor growth. In East Asia, infection with fish-borne liver flukes is a major risk factor for cholangiocarcinoma (CCA). The liver fluke Opisthorchis viverrini secretes a growth factor, termed liver fluke granulin (Ov-GRN-1), a homologue of the human progranulin (huPGRN). Secreted Ov-GRN-1 contributes significantly to biliary tract fibrosis and morbidity during infection. Here, exosome-mediated transfer of mRNAs from a human cholangiocyte cell line following exposure to Ov-GRN-1 to na ïve recipient cells was investigated. In addition, aiming to minimize the effects of endogenous human GRN, the gene encoding human granulin was inactivated in H69 line cholangiocytes by genome editing, and several huPGRN-depleted cell lines, termed ΔhuPGRN-H69 cells, were established. These mutant H69 cell lines, termed ΔhuPGRN-H69, exhibited >80% reduction in huPGRN transcription and protein expression, both within cells and within secreted exosomes. Profiles of exosomal RNAs (exRNA)...
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biorxivpreprint: Exosome-mediated crosstalk stimulated by liver fluke granulin promotes a microenvironment conducive to cholangiocarcinoma https://t.co/dANxske1oB #bioRxiv
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Authors: 14
Total Words: 12728
Unqiue Words: 4923

2.002 Mikeys
#3. Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele
RNA profiling has emerged as a powerful tool to investigate the biomarker potential of human biofluids. However, despite enormous interest in extracellular nucleic acids, RNA sequencing methods to quantify the total RNA content outside cells are rare. Here, we evaluate the performance of the SMARTer Stranded Total RNA-Seq method in human platelet-rich plasma, platelet-free plasma, urine, conditioned medium, and extracellular vesicles (EVs) from these biofluids. We found the method to be accurate, precise, compatible with low-input volumes and able to quantify a few thousand genes. We picked up distinct classes of RNA molecules, including mRNA, lncRNA, circRNA, miscRNA and pseudogenes. Notably, the read distribution and gene content drastically differ among biofluids. In conclusion, we are the first to show that the SMARTer method can be used for unbiased unraveling of the complete transcriptome of a wide range of biofluids and their extracellular vesicles.
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jvdesomp: "Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles", our latest study in bioRxiv by @celine_everaert and @hHetty https://t.co/bJDYfs4REg https://t.co/wimka3ACM1
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1.996 Mikeys
#4. Unveiling The Worldwide UV-Metaresistome: Metagenomic Analysis of Microbiomes Exposed to Different UV-B Regimes
Daniel Gonzalo Alonso-Reyes, Maria Eugenia Farias, Virginia Helena Albarracin
During evolution, microorganisms exposed to high UV doses have developed a complex battery of physiological and molecular mechanisms to cope with UV stress and damage recently called as the UV-resistome. As a precedent, the UV-resistome was analyzed at the genomic and proteomic level in poly-extremophiles bacteria isolated from High-Altitude Andean Lakes. In this work, we go further by exploring the impact of UV-B radiation on microbiomes in different geographic regions across the globe. The abundance of photoprotection and DNA repair pathways in each microbiome was use to configure the world-wide UV-metaresistome. Metagenomics combined with georeferenced climate data indicated that the higher the UV-B dose suffered by the microbiome the higher the abundance and diversity of the UV-metaresistome genes. In contrast, a substantial depletion on microbial diversity was observed in higher irradiated environments. A positive correlation between CPF abundance and radiation intensity/photoperiod was detected. CPF genes were investigated...
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Authors: 3
Total Words: 11686
Unqiue Words: 4237

1.995 Mikeys
#5. Isothermal Digital Detection Of MicroRNA Using Background-Free Molecular Circuit
Guillaume Gines, Roberta Menezes, Kaori Nara, Anne-Sophie Kirstetter, Valerie Taly, Yannick Rondelez
MicroRNA, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design DNA circuit that converts, threshold, amplifies and report the presence of a specific microRNA, down to the femtomolar concentration. Using a leak-absorption mechanism, we were able to suppress non-specific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNA: by partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The...
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Authors: 6
Total Words: 6257
Unqiue Words: 2409

1.995 Mikeys
#6. LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay
Anna MATTOUT, Dimos Gaidatzis, Jan Padeken, Christoph Schmid, Florian Aeschlimann, Veronique Kalck, Susan M Gasser
In fission yeast and plants, RNA-processing pathways contribute to constitutive and facultative heterochromatin silencing, complementing well-characterized pathways of transcriptional repression. However, it was unclear whether this additional level of regulation occurs in metazoans. Here we describe a pathway of silencing in C. elegans somatic cells, in which the highly conserved, RNA binding complex LSM2-8 selectively silences heterochromatic reporters and endogenous genes bearing the Polycomb mark H3K27me3. Importantly, the LSM2-8 complex works cooperatively with XRN-2, a 5'-3' exoribonuclease, and disruption of the pathway leads to mRNA stabilization. This selective LSM2-8-mediated RNA degradation does not target nor depend on H3K9me2/me3, unlike previously described pathways of heterochromatic RNA degradation. Intriguingly, the loss of LSM2-8 coincides with a localized drop in H3K27me3 levels on lsm-8-sensitive loci only. Together this defines a mechanism of RNA degradation that selectively targets a subset of H3K27me3-marked...
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