Expanding the landscape of antibody discovery by Johnson, Shelbe, DeKosky, Brandon J

“…In this issue of Cell Reports Methods, Wagner et al. introduce a method that combines antibody-ribosome-mRNA complexes, antigen cell surface display, and single-cell RNA sequencing to successfully screen diverse antibody gene libraries against a library of viral receptor proteins.…”
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Multi-omics analysis and modelling of T cell immunity and interferon signalling pathways for engineered T cell therapy by Pavillet, CE

“…Cell type annotation methods are evaluated for their ability to identify closely-related T cell populations in single-cell RNA sequencing (scRNA-seq) data. In the following chapter, single-cell and spatial transcriptomics methods, mainly scRNA-seq, single-cell immune profiling, Slide-seq, in situ sequencing and Molecular Cartography enable the comprehensive analysis of immune infiltrates in tissue biopsies from patients with TNBC. …”

Molecular mechanisms relevant to the maintenance of locomotor control by Guo, F

“…We have then validated hits from the RNA-seq data by optimising comprehensive validation approaches. …”

Pathway and network analysis of more than 2500 whole cancer genomes by Reyna, MA, Haan, D, Paczkowska, M, Verbeke, LPC, Vazquez, M, Kahraman, A, Pulido-Tamayo, S, Barenboim, J, Wadi, L, Dhingra, P, Shrestha, R, Getz, G, Lawrence, MS, Pedersen, JS, Rubin, MA, Wheeler, DA, Brunak, S, Izarzugaza, JMG, Khurana, E, Marchal, K, von Mering, C, Sahinalp, SC, Valencia, A, PCAWG Drivers and Functional Interpretation Working Group, Reimand, J, Stuart, JM, Raphael, BJ, PCAWG Consortium

“…RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. …”

Comprehensive insights into Sitobion avenae preferences and performance on Pakistan’s wheat cultivars leading to identification of potential RNAi targets by Mukhtar, Ruhma, Afzal, Eijab, Noureen, Rabia, Zeeshan, Nadia, Afroz, Amber

“…Therefore, these proteins have the potential to serve as RNA interference targets, against which double-stranded RNA could be designed and expressed in wheat cultivars to make them resistant to local S. avenae infestation and avert yield loss.…”
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Cardiac conduction system regeneration prevents arrhythmias after myocardial infarction by Sayers, JR, Martinez-Navarro, H, Sun, X, de Villiers, C, Sigal, S, Weinberger, M, Rodriguez, CC, Riebel, LL, Berg, LA, Camps, J, Herring, N, Rodriguez, B, Sauka-Spengler, T, Riley, PR

“…Tissue-cleared whole-organ imaging identified disorganized bundling of conduction fibers after MI and global His–Purkinje disruption. Single-cell RNA sequencing (scRNA-seq) revealed specific molecular changes to regenerate the conduction network versus aberrant electrical alterations during fibrotic repair. …”

Dysregulation of the Pdx1/Ovol2/Zeb2 axis in dedifferentiated β-cells triggers the induction of genes associated with epithelial-mesenchymal transition in diabetes by de Jesus, Daniel S., Mak, Tracy C. S., Wang, Yi-Fang, von Ohlen, Yorrick, Bai, Ying, Kane, Eva, Chabosseau, Pauline, Chahrour, Catherine M., Distaso, Walter, Salem, Victoria, Tomas, Alejandra, Stoffel, Markus, Rutter, Guy A., Latreille, Mathieu

“…Single-cell RNA-seq (scRNA-seq) indicatedthat this EMT signature is enriched specifically inb-cells. …”
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Effects of nnav1.5 expression modulation on mhc I antigen processing machinery and invasion potential of breast cancer cells by Din, Ahmad Hafiz Murtadha Noor

“…However, in MDA-MB-231 spheroid, both TTX and siRNA failed to induce expressional changes. On the invasion ability, siRNA pre-treated spheroid failed to form. …”
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Selectivity of stop codon recognition in translation termination is modulated by multiple conformations of GTS loop in eRF1 by Li, Yan, Pillay, Shubhadra, Frolova, Ludmila, Pervushin, Konstantin, Wong, Leo E.

“…To explore such feasibility, we positioned N-domain in a pre-termination ribosomal complex using the binding interface between N-domain and model RNA oligonucleotides mimicking Helix 44 of 18S rRNA. …”
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Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development by Subroto, Toto, Firdaus, Ade Rizqi Ridwan, Kusumawardani, Shinta, Tohari, Taufik Ramdani, Nababan, Theresia Adventina, Pertiwi, Wulan, Fadhlillah, Muhammad, Kusuma, Sri Agung Fitri, Rukayadi, Yaya

“…This study aims to isolate the RNA-dependent RNA polymerase (RdRp) gene of the dengue virus (DENV) isolates from Indonesia, determine the serotype of the local DENV strain through homology modeling, and express the recombinant RdRp protein in Escherichia coli BL21 (DE3), as the target for anti-dengue drug development. …”
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Draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes) by Thiel, Vera, Hamilton, Trinity L., Tomsho, Lynn P., Burhans, Richard, Gay, Scott E., Ramaley, Robert F., Schuster, Stephan Christoph, Steinke, Laurey, Bryant, Donald A.

“…The draft genome is predicted to encode 2,457 protein coding genes and 37 tRNA encoding genes and two rRNA operons.…”
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Optimizing Cas9-mediated HDR in HEK293 by Lee, Cheryl

“…With its programmable guide RNA sequence for specific gene targeting, it allows for precise genome editing including substitutions, knock-outs, and knock-ins. …”
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Stability of peptide nucleic acid influenced by peptoid-like sidechains : MD simulation study. by Yeo, Sven Hwea Jie.

“…Modifications are based on a recent work of Prof Liu’s lab, involving γ-N modification of PNA aeg backbone with amino-peptoid sidechain (APS) experimentally shown to retain its hybridisation affinity with DNA/RNA. Focusing on RNA, we analysed structural features as well as solute-solvent interactions to better understand the mechanisms governing hybridisation characteristics. …”
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Transcriptomic profiling of polymicrobial biofilm dynamics on catheters in Vitro by Lai, Valerie Jia Hui

“…Our study was also extended to mixed microbial communities given that molecular interactions within constituents of polymicrobial communities on the surface of urinary catheters are poorly defined. RNA sequencing was employed to map mRNA reads to gene expression in single and mixed species biofilm. …”
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Tropism of subgroup J avian leukosis virus as detected by in situ hybridization by Arshad, S. S., Smith, L. M., Howes, K., Russell, P. H., Venugopal, K., Payne, L. N.

“…Virus-specific RNA was detected mainly in the heart, kidney, proventriculus and adrenal in locations similar to those of the Gag protein. …”
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Computational analysis for infectious diseases surveillance and host-pathogen interactions (in the context of Influenza A viruses) by Beyene, Biruhalem Taye

“…Recently, high throughput technologies such as mRNA microarray-based gene expression, genome-wide siRNA screening, and proteomic analysis are providing in-depth insights into host-pathogen interactions of IAVs. …”
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Laser capture microdissection of single neurons with morphological visualization using fluorescent proteins fused to transmembrane proteins by Chang, Ching Ching, Chong, Hai Tarng, Tashiro, Ayumu

“…Using this method in mice, we laser-captured neuronal somata and successfully isolated RNA. We determined that ∼100 cells are sufficient to obtain a sample required for downstream applications such as quantitative PCR. …”
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Heme-Regulated eIF2α Kinase Modulates Hepatic FGF21 and is Activated by PPARβ/δ Deficiency by Zarei, Mohammad, Barroso, Emma, Leiva, Rosana, Barniol-Xicota, Marta, Pujol, Eugènia, Escolano, Carmen, Vázquez, Santiago, Palomer, Xavier, Pardo, Virginia, González-Rodríguez, Águeda, Valverde, Ángela M., Quesada-López, Tania, Villarroya, Francesc, Wahli, Walter, Vázquez-Carrera, Manuel

“…Increased Fgf21 expression was observed in liver of PPARβ/δ-null mice and in mouse primary hepatocytes when this receptor was knocked down by small interfering RNA (siRNA). Increased Fgf21 was associated with enhanced protein levels in the heme-regulated eukaryotic translation initiation factor 2α (eIF2α) kinase (HRI). …”
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Overexpression of 4EBP1, p70S6K, Akt1 or Akt2 differentially promotes Coxsackievirus B3-induced apoptosis in HeLa cells by Xing, X., Huang, L., Li, X., Li, Z., Zhou, W., Tian, L., Chen, J., Chen, C., Ma, Xing, Yang, Z.

“…Compared with controls, the expression of CVB3 mRNA was increased at 3, 6, 12 and 24 h postinfection (p. i.) in all groups. …”
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Solution X-ray scattering studies on the dengue virus non-structural protein 5 and -3 as well as the capsid protein by Saw, Wuan Geok

“…Dengue virus (DENV), which is the causative agent of dengue, is a single positive-stranded RNA virus. The structural information of two DENV non-structural proteins, NS5 and NS3, which play a central role in the genome replication, were gathered using small-angle X-ray scattering (SAXS). …”
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