Top 10 Biorxiv Papers Today in Molecular Biology


2.25 Mikeys
#1. Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers and Nanopore sequencing
Søren M. Karst, Ryan Ziels, Rasmus H. Kirkegaard, Mads Albertsen
High-throughput amplicon sequencing of large genomic regions represents a challenge for existing short-read technologies. Long-read technologies can in theory sequence large genomic regions, but they currently suffer from high error rates. Here, we report a high-throughput amplicon sequencing approach that combines unique molecular identifiers (UMIs) with Oxford Nanopore sequencing to generate single-molecule consensus sequences of large genomic regions. We demonstrate the approach by generating more than 10,000 full-length ribosomal RNA (rRNA) operons of roughly 4,400 bp in length from a mock microbial community consisting of eight bacterial species using a single Oxford Nanopore MinION flowcell. The mean error rate of the consensus sequences was 0.03%, with no detectable chimeras due to a rigorous UMI-barcode filtering strategy. The simplicity and accessibility of this method paves way for widespread use of high-accuracy amplicon sequencing in a variety of genomic applications.
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razoralign: Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers and Nanopore sequencing https://t.co/bF8dtF8ELk
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Sequence correction provided by ONT Research

Repository: medaka
User: nanoporetech
Language: Python
Stargazers: 43
Subscribers: 33
Forks: 8
Open Issues: 7
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Authors: 4
Total Words: 9770
Unqiue Words: 2705

2.021 Mikeys
#2. Transferrin plays a central role to maintain coagulation balance by interacting with clotting factors
Xiaopeng Tang, Zhiye Zhang, Mingqian Fang, Yajun Han, Sheng Wang, Min Xue, Yaxiong Li, Li Zhang, Jian Wu, Biqing Yang, Qiumin Lu, Xiaoping Du, Ren Lai
Coagulation balance is maintained through fine-tuning interactions among clotting factors. Physiological concentrations of clotting factors are huge difference. Especially, coagulation proteases concentration (pM to nM) is much lower than their natural inactivator antithrombin III (AT-III, ~3 μM). Here we show that transferrin (normal plasma concentration ~40 μM) interacts with fibrinogen, thrombin, FXIIa and AT-III with different affinity to maintain coagulation balance. Normally, transferrin is sequestered by binding with fibrinogen (normal plasma concentration ~10 μM) with a molar ratio of 4:1. In atherosclerosis, abnormally up-regulated transferrin interacts with and potentiates thrombin/FXIIa and blocks AT-IIIs inactivation on coagulation proteases by binding to AT-III, and thus induces hypercoagulability. In mouse models, transferrin-overexpression aggravated atherosclerosis while transferrin-knockdown, anti-transferrin antibody or designed peptides interfering transferrin-thrombin/FXIIa interactions alleviated it....
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biorxivpreprint: Transferrin plays a central role to maintain coagulation balance by interacting with clotting factors https://t.co/kYGfAHOTrR #bioRxiv
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Authors: 13
Total Words: 0
Unqiue Words: 0

2.019 Mikeys
#3. Analysis of the expression of PIWI-interacting RNAs during cardiac differentiation of human pluripotent stem cells
Alejandro La Greca, María Agustina Scarafía, María Clara Hernández Cañás, Nelba Pérez, Sheila Castañeda, Carolina Colli, Alan Miqueas Möbbs, Natalia Lucía Santín Velazque, Gabriel Neiman, Ximena Garate, Cyntia Aban, Ariel Waisman, Lucía Natalia Moro, Gustavo Sevlever, Carlos Luzzani, Santiago Miriuka
PIWI-interacting RNAs (piRNAs) are a class of non-coding RNAs initially thought to be restricted almost exclusively to germ line cells. In recent years, accumulating evidence has demonstrated that piRNAs are actually expressed in somatic cells like pluripotent, neural, cardiac and even cancer cells. However, controversy still remains around the existence and function of somatic piRNAs. Using small RNA-seq samples from H9 pluripotent stem cells differentiated to mesoderm progenitors and cardiomyocytes we identified the expression of 447 piRNAs, of which 241 were detected in pluripotency, 218 in mesoderm and 171 in cardiac cells. The majority of them originated from the sense strand of protein coding and lncRNAs genes in all stages of differentiation, though no evidences for secondary piRNAs (ping-pong loop) were found. Genes hosting piRNAs in cardiac samples were related to critical biological processes in the heart, like contraction and cardiac muscle development. Our results indicate that somatic piRNAs might have a role in...
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biorxivpreprint: Analysis of the expression of PIWI-interacting RNAs during cardiac differentiation of human pluripotent stem cells https://t.co/kBwl8kHcWI #bioRxiv
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Authors: 16
Total Words: 8035
Unqiue Words: 2576

2.007 Mikeys
#4. β-Actin and Nuclear Myosin I are responsible for nucleolar reorganization during DNA Repair.
Elena Cerutti, Lauriane Daniel, Lise-Marie Donnio, Damien Neuillet, Charlene Magnani, Pierre-Olivier Mari, Giuseppina Giglia-Mari
During DNA Repair, ribosomal DNA and RNA polymerase I (rDNA/RNAP1) are reorganized within the nucleolus. Until now, the proteins and the molecular mechanism governing this reorganisation remained unknown. Here we show that Nuclear Myosin I (NMI) and Nuclear Beta Actin (ACTβ) are essential for the proper reorganisation of the nucleolus, after completion of the DNA Repair reaction. In NMI and ACTβ depleted cells, the rDNA/RNAP1 complex can be displaced at the periphery of the nucleolus after DNA damage but cannot re-enter within the nucleolus after completion of the DNA Repair. Both proteins act concertedly in this process. NMI binds the damaged rDNA at the periphery of the nucleolus, while ACTβ brings the rDNA back within the nucleolus after DNA repair completion. Our results reveal a previously unidentified function for NMI and ACTβ and disclose how these two proteins work in coordination to re-establish the proper rDNA position after DNA repair.
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biorxivpreprint: β-Actin and Nuclear Myosin I are responsible for nucleolar reorganization during DNA Repair. https://t.co/alxSFMZ5oo #bioRxiv
NeuroSarah: RT @biorxivpreprint: β-Actin and Nuclear Myosin I are responsible for nucleolar reorganization during DNA Repair. https://t.co/alxSFMZ5oo…
sbotlite: RT @biorxivpreprint: β-Actin and Nuclear Myosin I are responsible for nucleolar reorganization during DNA Repair. https://t.co/alxSFMZ5oo…
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Authors: 7
Total Words: 0
Unqiue Words: 0

2.004 Mikeys
#5. The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): insight into the deep-sea adaptive evolution of vesicomyids
Mei Yang, Lin Gong, Jixing Sui, Xinzheng Li
The deep sea is one of the most extreme environments on earth, with low oxygen, high hydrostatic pressure and high levels of toxins. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, “G(A)nT” motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the...
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biorxivpreprint: The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): insight into the deep-sea adaptive evolution of vesicomyids https://t.co/6MhSjCYkBm #bioRxiv
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Authors: 4
Total Words: 11605
Unqiue Words: 4361

2.003 Mikeys
#6. Cis-regulatory basis of sister cell type divergence in the vertebrate retina
Daniel P Murphy, Andrew E. O. Hughes, Karen A Lawrence, Connie A Myers, Joseph C Corbo
Multicellular organisms evolved via repeated functional divergence of transcriptionally related sister cell types, but the mechanisms underlying sister cell type divergence are not well understood. Here, we study a canonical pair of sister cell types, retinal photoreceptors and bipolar cells, to identify the key cis -regulatory features that distinguish them. By comparing open chromatin maps and transcriptomic profiles, we found that while photoreceptor and bipolar cells have divergent transcriptomes, they share remarkably similar cis -regulatory grammars, marked by enrichment of K50 homeodomain binding sites. However, cell class-specific enhancers are distinguished by enrichment of E-box motifs in bipolar cells, and Q50 homeodomain motifs in photoreceptors. We show that converting K50 motifs to Q50 motifs represses reporter expression in bipolar cells, while photoreceptor expression is maintained. These findings suggest that partitioning of Q50 motifs within cell type-specific cis -regulatory elements was a critical step in the...
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Astro_Erik: RT @biorxivpreprint: Cis-regulatory basis of sister cell type divergence in the vertebrate retina https://t.co/u9JWl1uzt5 #bioRxiv
Brian_S_Clark: RT @biorxivpreprint: Cis-regulatory basis of sister cell type divergence in the vertebrate retina https://t.co/u9JWl1uzt5 #bioRxiv
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Authors: 5
Total Words: 0
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2.003 Mikeys
#7. Whole genome sequencing of dog specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host associated genes
Frans Kooyman, Jaap Wagenaar, Aldert Zomer
Giardia duodenalis (Syn. G. intestinalis or G. lamblia) infects over 280 million people each year and numerous animals. G. duodenalis can be subdivided into 8 assemblages with different host specificity. Unculturable assemblages have so far resisted genome sequencing efforts. In this study we isolated single and pooled cysts of assemblage C and D from dog faeces by FACS and sequenced them using multiple displacement amplification and Illumina paired end sequencing. The genomes of assemblages C and D were compared with genomes of assemblages A and B from humans and assemblage E from ruminants and pigs. The genomes obtained from the pooled cysts and from the single cysts were considered complete (>99% marker genes observed) and the allelic sequence heterozygosity (ASH) of assemblage C and D was 0.89% and 0.74%, respectively. Higher than for assemblage B (> 0.43%) and much higher than for assemblages A and E (<0.01%). The flavohemoglobin and 4Fe-4S binding domain family gene involved in O2 and NO detoxification were only present in...
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biorxivpreprint: Whole genome sequencing of dog specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host associated genes https://t.co/qa90zbAVyt #bioRxiv
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Authors: 3
Total Words: 9908
Unqiue Words: 2764

2.0 Mikeys
#8. PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD
Mahmoud M Elguindy, Florian Kopp, Mohammad Goodarzi, Frederick Rehfeld, Anu Thomas, Tsung-Cheng Chang, Joshua T Mendell
NORAD is a highly-conserved and abundant long noncoding RNA (lncRNA) that is required for maintenance of genomic stability in mammals. Although initial characterization of NORAD established it as a negative regulator of PUMILIO (PUM) proteins in the cytoplasm, a nuclear role for NORAD in genome maintenance through an interaction with the RNA binding protein RBMX has also been reported. Here we addressed the relative contributions of NORAD :PUM and NORAD :RBMX interactions to the regulation of genomic stability by this lncRNA. Extensive RNA FISH and fractionation experiments established that NORAD localizes predominantly to the cytoplasm with or without DNA damage. Moreover, genetic rescue experiments demonstrated that PUM binding is required for maintenance of genomic stability by NORAD whereas binding of RBMX is dispensable for this function. These data therefore establish an essential role for the NORAD :PUM interaction in genome maintenance and provide a foundation for further mechanistic dissection of this pathway.
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biorxivpreprint: PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD https://t.co/cCmLiDKwRF #bioRxiv
razoralign: PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD https://t.co/dFu3TtVUvb
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Authors: 7
Total Words: 8769
Unqiue Words: 2633

1.998 Mikeys
#9. Efficient differentiation and polarization of primary cultured neurons on poly(lactic acid) scaffolds with microgrooved structures
Asako Otomo, Mahoko T. Ueda, Toshinori Fujie, Arihiro Hasebe, Yosuke Okamura, Shinji Takeoka, Shinji Hadano, So Nakagawa
Synthetic biodegradable polymers including poly(lactic acid) (PLA) are attractive cell culture substrates because their surfaces can be micropatterned to support cell adhesion. The cell adhesion properties of a scaffold mainly depend on its surface chemical and structural features; however, it remains unclear how these characteristics affect the growth and differentiation of cultured cells or their gene expression. In this study, we fabricated two differently structured PLA nanosheets: flat and microgrooved. We assessed the growth and differentiation of mouse primary cultured cortical neurons on these two types of nanosheets after pre-coating with poly-D-lysine and vitronectin. Interestingly, prominent neurite bundles were formed along the grooves on the microgrooved nanosheets, whereas thin and randomly extended neurites were only observed on the flat nanosheets. Comparative RNA sequencing analyses revealed that the expression of genes related to postsynaptic density, dendritic shafts, and asymmetric synapses was significantly...
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biorxivpreprint: Efficient differentiation and polarization of primary cultured neurons on poly(lactic acid) scaffolds with microgrooved structures https://t.co/ngVINEgEsq #bioRxiv
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Authors: 8
Total Words: 7134
Unqiue Words: 2165

1.997 Mikeys
#10. Nup93 modulates spatiotemporal dynamics and function of the HOXA gene cluster during differentiation
Ajay S Labade, Adwait Salvi, Krishanpal Karmodiya, Kundan Sengupta
The nuclear pore complex (NPC) regulates nuclear transport of RNA and proteins. Also, nucleoporins regulate chromatin organization and gene expression. However, the role of nucleoporins in the temporal regulation of gene expression during differentiation is unclear. Here we investigated the role of nucleoporin Nup93, in regulating HOXA gene expression during differentiation. ChIP-Seq analysis revealed that Nup93 associates with genes involved in development and differentiation such as HOXA. Furthermore, Nup93 occupancy overlaps with the chromatin organizer - CTCF, suggesting a co-regulatory role of Nup93 and CTCF in HOXA gene regulation. Interestingly, Nup93 and CTCF showed antagonistic roles in regulating expression levels of genes at the 3′ and 5 ′ end of the HOXA gene cluster in undifferentiated cells. Furthermore, HOXA gene locus untethered from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. In addition, occupancy of Nup93 and CTCF on HOXA gene locus progressively declined during...
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biorxivpreprint: Nup93 modulates spatiotemporal dynamics and function of the HOXA gene cluster during differentiation https://t.co/mONDYkzEq0 #bioRxiv
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Authors: 4
Total Words: 11285
Unqiue Words: 3004

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