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Journal articles on the topic 'Analyse RNAseq'

Author: Grafiati

Published: 2 November 2024

Last updated: 31 July 2025

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1

Cribbs, Adam P., Sebastian Luna-Valero, Charlotte George, et al. "CGAT-core: a python framework for building scalable, reproducible computational biology workflows." F1000Research 8 (April 4, 2019): 377. http://dx.doi.org/10.12688/f1000research.18674.1.

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In the genomics era computational biologists regularly need to process, analyse and integrate large and complex biomedical datasets. Analysis inevitably involves multiple dependent steps, resulting in complex pipelines or workflows, often with several branches. Large data volumes mean that processing needs to be quick and efficient and scientific rigour requires that analysis be consistent and fully reproducible. We have developed CGAT-core, a python package for the rapid construction of complex computational workflows. CGAT-core seamlessly handles parallelisation across high performance compu

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Cribbs, Adam P., Sebastian Luna-Valero, Charlotte George, et al. "CGAT-core: a python framework for building scalable, reproducible computational biology workflows." F1000Research 8 (July 16, 2019): 377. http://dx.doi.org/10.12688/f1000research.18674.2.

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In the genomics era computational biologists regularly need to process, analyse and integrate large and complex biomedical datasets. Analysis inevitably involves multiple dependent steps, resulting in complex pipelines or workflows, often with several branches. Large data volumes mean that processing needs to be quick and efficient and scientific rigour requires that analysis be consistent and fully reproducible. We have developed CGAT-core, a python package for the rapid construction of complex computational workflows. CGAT-core seamlessly handles parallelisation across high performance compu

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Portet, Anaïs, Eve Toulza, Ana Lokmer, et al. "Experimental Infection of the Biomphalaria glabrata Vector Snail by Schistosoma mansoni Parasites Drives Snail Microbiota Dysbiosis." Microorganisms 9, no. 5 (2021): 1084. http://dx.doi.org/10.3390/microorganisms9051084.

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Host-parasite interaction can result in a strong alteration of the host-associated microbiota. This dysbiosis can affect the fitness of the host; can modify pathogen interaction and the outcome of diseases. Biomphalaria glabrata is the snail intermediate host of the trematode Schistosoma mansoni, the agent of human schistosomiasis, causing hundreds of thousands of deaths every year. Here, we present the first study of the snail bacterial microbiota in response to Schistosoma infection. We examined the interplay between B. glabrata, S. mansoni and host microbiota. Snails were infected and the m

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Allen, S. J. W., S. H. Krawczyk, L. R. McGee, N. Bischofberger, A. S. Mulato, and J. M. Cherrington. "Inhibition of HIV-1 RNase H Activity by Nucleotide Dimers and Monomers." Antiviral Chemistry and Chemotherapy 7, no. 1 (1996): 37–45. http://dx.doi.org/10.1177/095632029600700107.

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Nucleotide dimers and monomers were shown to inhibit human immunodeficiency virus type 1 (HIV) RNase H activity. Several effective inhibitors were identified and placed into three general groups based on biochemical characterization of their inhibition, The first group (group A) inhibited HIV RNase H and the closely related feline immunodeficiency virus (FIV) RNase H, but did not inhibit less related retroviral or cellular RNases H or HIV reverse transcriptase (RT). The second group (group B) inhibited the RNase H activity of several retroviruses as well as the reverse transcriptase function o

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Orlandi, Elisa, Elisa De Tomi, Rachele Campagnari, et al. "Human Melanoma Cells Differentially Express RNASEL/RNase-L and miR-146a-5p under Sex Hormonal Stimulation." Current Issues in Molecular Biology 44, no. 10 (2022): 4790–802. http://dx.doi.org/10.3390/cimb44100326.

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Polymorphisms in the ribonuclease L (RNASEL) coding gene and hsa-miR-146a-5p (miR-146a) have been associated with melanoma in a sex-specific manner. We hypothesized that RNASEL and miR-146a expression could be influenced by sex hormones playing a role in the female advantages observed in melanoma incidence and survival. Thus, we explored the effects of testosterone and 17β-estradiol on RNASEL and miR-146a expression in LM-20 and A375 melanoma cell lines. Direct targeting of miR-146a to the 3’ untranslated region (3′UTR) of RNASEL was examined using a luciferase reporter system. Our results ind

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Ahrenfeldt, Johanne, Ditte S. Christensen, Andreas B. Østergaard, Judit Kisistók, Mateo Sokač, and Nicolai J. Birkbak. "The ratio of adaptive to innate immune cells differs between genders and associates with improved prognosis and response to immunotherapy." PLOS ONE 18, no. 2 (2023): e0281375. http://dx.doi.org/10.1371/journal.pone.0281375.

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Immunotherapy has revolutionised cancer treatment. However, not all cancer patients benefit, and current stratification strategies based primarily on PD1 status and mutation burden are far from perfect. We hypothesised that high activation of an innate response relative to the adaptive response may prevent proper tumour neoantigen identification and decrease the specific anticancer response, both in the presence and absence of immunotherapy. To investigate this, we obtained transcriptomic data from three large publicly available cancer datasets, the Cancer Genome Atlas (TCGA), the Hartwig Medi

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Oczkowicz, Maria, Małgorzata Świątkiewicz, Katarzyna Ropka-Molik, Artur Gurgul, and Kacper Żukowski. "Effects of Different Sources of Fat in the Diet of Pigs on the Liver Transcriptome Estimated by RNA-Seq." Annals of Animal Science 16, no. 4 (2016): 1073–90. http://dx.doi.org/10.1515/aoas-2016-0033.

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Abstract In this study, we have attempted to analyse the impact of dietary fats on the liver transcriptome in pigs. Four nutritional groups were created. The animals’ diets differed among groups in terms of the presence of corn dried distillers’ grains with solubles (DDGS) (group I - no DDGS, groups II, III, IV - 20% DDGS) as well as the type of fat (rapeseed oil - groups I and II, beef tallow - group III, coconut oil - group IV) used. Using the RNA-Seq method we identified 39 differentially expressed genes (DEGs) as a result of Cuffdiff analysis of the differences among all groups. Analysis o

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Penttinen, Jenni, Dwi Ari Pujianto, Petra Sipilä, Ilpo Huhtaniemi, and Matti Poutanen. "Discovery in Silico and Characterization in Vitro of Novel Genes Exclusively Expressed in the Mouse Epididymis." Molecular Endocrinology 17, no. 11 (2003): 2138–51. http://dx.doi.org/10.1210/me.2003-0008.

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Abstract Epididymal proteins interact with sperm during their passage through the epididymis and thus contribute to the maturation and fertilizing capacity of the spermatozoa. In the present study we have discovered five novel epididymis-specific genes through in silico analysis of expressed sequence tags (ESTs) at the UniGene library collection. The strategy used is a powerful way to discover novel epididymis-specific genes. The full-length cDNA sequences were determined, and computational tools were used to characterize the genomic structures and to predict putative functions for the encoded

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Malvisi, Michela, Nico Curti, Daniel Remondini, et al. "Combinatorial Discriminant Analysis Applied to RNAseq Data Reveals a Set of 10 Transcripts as Signatures of Exposure of Cattle to Mycobacterium avium subsp. paratuberculosis." Animals 10, no. 2 (2020): 253. http://dx.doi.org/10.3390/ani10020253.

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Paratuberculosis or Johne’s disease in cattle is a chronic granulomatous gastroenteritis caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP). Paratuberculosis is not treatable; therefore, the early identification and isolation of infected animals is a key point to reduce its incidence. In this paper, we analyse RNAseq experimental data of 5 ELISA-negative cattle exposed to MAP in a positive herd, compared to 5 negative-unexposed controls. The purpose was to find a small set of differentially expressed genes able to discriminate between exposed animals in a preclinica

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Ramanauskas, Karolis, and Boris Igić. "The evolutionary history of plant T2/S-type ribonucleases." PeerJ 5 (September 11, 2017): e3790. http://dx.doi.org/10.7717/peerj.3790.

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A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-r

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Good-Avila, S. V., D. Majumder, H. Amos, and A. G. Stephenson. "Characterization of self-incompatibility in Campanula rapunculoides (Campanulaceae) through genetic analyses and microscopy." Botany 86, no. 1 (2008): 1–13. http://dx.doi.org/10.1139/b07-100.

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In this paper, we seek to identify the genetic basis of self-incompatibility (SI) in Campanula rapunculoides L. through diallel analysis of full siblings; to characterize the growth of pollen tubes in vivo after incompatible and compatible pollination; and to determine whether the SI system is based on pistil S-RNases. Pollinations were performed among individuals from five diallel crosses and scored for both fruit set and pollen-tube growth to determine the genetic basis of SI. On a subset of these individuals with known cross-(in)compatibility relationships, additional crosses were performed

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Oden, Élise. "La génomique équine : tour d’horizon des outils disponibles pour les applications actuelles et à venir." Le Nouveau Praticien Vétérinaire équine 17, no. 59 (2023): 48–53. http://dx.doi.org/10.1051/npvequi/2024005.

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Depuis quelques décennies, de nombreux outils technologiques initialement destinés à l’étude de la génomique humaine ont été rapidement déployés chez les animaux d’élevage, dont les chevaux. Tout d’abord, le génotypage permet l’analyse des variations génétiques dans l’ADN génomique d’un organisme : par exemple, les marqueurs microsatellites, séquences répétées présentes partout dans les génomes eucaryotes ou bien les SNP (Single Nucleotide Polymorphism) qui correspondent à des variations d’une seule base nucléotidique. En laboratoire, le génotypage est actuellement utilisé pour la réalisation

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Yang, Qin, Yan Fu, Yalan Liu, Tingting Zhang, Shu Peng, and Jie Deng. "Microscopic and Transcriptome Analysis Reveals that the Self-incompatibility in Rabbiteye Blueberry Belongs to the S-RNase-based Gametophytic Type." J. Amer. Soc. Hort. Sci. 149, no. 4 (2024): 179–94. http://dx.doi.org/10.21273/jashs05364-23.

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Berry fruits produced by Vaccinium (Ericaceae) plants are small but have a signature flavor and have become increasingly popular in the 21st century. However, self-incompatibility (SI) results in a relatively low fruit-set ratio and reduced fruit quality in Vaccinium. In this study, using Vaccinium ashei (V. ashei) styles after cross-pollination (CP) and self-pollination (SP) as material, transcriptomics and gene expression analyses were performed using high-throughput RNA sequencing and quantitative real-time polymerase chain reaction (qRT-PCR). Subsequently, evolutionary analysis and conserv

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Shlyakhovenko, V. О., І. І. Ganusevich, О. А. Samoylenko, Yu M. Samchenko, А. V. Verbinenko, and O. A. Solovyova. "HUMAN PERIPHERAL BLOOD RIBONUCLEASES REACTIVATION AFTER SORPTION ON NANOPLATELETS OF LAPONITE®." Oncology 25, no. 4 (2023): 302–5. http://dx.doi.org/10.15407/oncology.2023.04.302.

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Summary. Aim: to investigate the possibility of enzymatic reactivation of RNase activity of peripheral blood cells of patients with colorectal cancer (CRC) after sorption on nanoplates Laponite® RD (Lap). Objects and methods: the study was performed with the cell suspension of peripheral blood of CRC patients. Samples of cell lysates were combined with a 1% suspension of Lap nanoplates. Then RNase was extracted with 0,25 N H2SO4 or 2% solution of sodium dodecyl sulfate (DDS). The zymogram technique was used to analyze RNase activity. Results: it was found that RNases bind with nanoplates Lap a

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Yasuda, T., D. Nadano, H. Takeshita, and K. Kishi. "Two distinct secretory ribonucleases from human cerebrum: purification, characterization and relationships to other ribonucleases." Biochemical Journal 296, no. 3 (1993): 617–25. http://dx.doi.org/10.1042/bj2960617.

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Two RNAases from human cerebrum were purified to an electrophoretically homogeneous state and their molecular masses were 22.0 kDa (tentatively called RNAase HB-1) and 19.0 kDa (RNAase HB-2). Analyses of the amino acid compositions, N-terminal amino acid sequences and catalytic properties of these enzymes provided strong evidence that they were strictly related to the secretory (sec) RNAases, such as the pancreatic enzyme, very similar immunologically to urinary sec RNAase, but clearly distinguishable from urinary non-secretory (nonsec) RNAase. There were several differences between HB-1 and H

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Szymańska, Hanna, Krystyna Życzko, and Tadeusz Zabolewicz. "Relationship between RNASE1, ANG and RNASE6 gene polymorphism and the values of blood indices in suckling piglets." Acta Veterinaria Hungarica 67, no. 3 (2019): 385–400. http://dx.doi.org/10.1556/004.2019.039.

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The relationship between PcR-restriction fragment length polymorphism in RNASE1 (296 A/G), ANG (149 G/T) and RNASE6 (389 C/T) genes and the values of haematological and biochemical blood indices was analysed in crossbred suckling piglets (n = 473), aged 21 ± 3 days (younger, n = 274) and 35 ± 3 days (older, n = 199), descending from Polish Large White × Polish Landrace sows and Duroc × Pietrain boars. The observed distribution of all genotypes was consistent with the Hardy-Weinberg equilibrium. Anaemia was more common in younger piglets with RNASE1 GA genotype but in the blood of older GA pigl

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Kanaya, S., and T. Uchida. "Comparison of the primary structures of ribonuclease U2 isoforms." Biochemical Journal 240, no. 1 (1986): 163–70. http://dx.doi.org/10.1042/bj2400163.

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The primary structures of the two isoforms of ribonuclease U2, RNAases U2-A and U2-B, were analysed and compared with each other. Among the chymotryptic peptides obtained from the reduced and S-carboxymethylated enzymes, only peptides C-3 were different from each other in terms of chromatographic behaviour on reverse-phase h.p.l.c. On the basis of chemical analyses of these peptides, it was shown that RNAase U2-B had an isopeptide bond in which Asp-32 was linked to Gly-33 through the beta-carboxy group in its side chain instead of the alpha-carboxy group. Deamidation of Asn-32 in RNAase U2-A l

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Watari, Akiko, Toshio Hanada, Hisayo Yamane, et al. "A Low Transcriptional Level of Se-RNase in the Se -haplotype Confers Self-compatibility in Japanese Plum." Journal of the American Society for Horticultural Science 132, no. 3 (2007): 396–406. http://dx.doi.org/10.21273/jashs.132.3.396.

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Most commercial cultivars of japanese plum (Prunus salicina Lindl.) exhibit S-RNase-based gametophytic self-incompatibility (GSI), although some self-compatible (SC) cultivars exist. In this study, we characterized S-RNase and SFB, the pistil and pollen S determinants of the specificity of the GSI reaction, respectively, from four S-haplotypes, including a SC (Se ) and three SI (Sa , Sb , and Sc ) S-haplotypes of japanese plum. The genomic organization and structure of the SC Se-haplotype appear intact, because the relative transcriptional orientation of its S-RNase and SFB and their intergene

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Filatov, Dmitry A. "Heterochiasmy and Sex Chromosome Evolution in Silene." Genes 14, no. 3 (2023): 543. http://dx.doi.org/10.3390/genes14030543.

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The evolution of a non-recombining sex-specific region is a key step in sex chromosome evolution. Suppression of recombination between the (proto-) X- and Y-chromosomes in male meiosis creates a non-recombining Y-linked region (NRY), while the X-chromosome continues to recombine in females. Lack of recombination in the NRY defines its main properties—genetic degeneration and accumulation of repetitive DNA, making X and Y chromosomes very different from each other. How and why recombination suppression on sex chromosomes evolves remains controversial. A strong difference in recombination rates

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Hegedüs, Attila, Zoltán Szabó, József Nyéki, Júlia Halász, and Andrzej Pedryc. "Molecular Analysis of S-haplotypes in Peach, a Self-compatible Prunus Species." Journal of the American Society for Horticultural Science 131, no. 6 (2006): 738–43. http://dx.doi.org/10.21273/jashs.131.6.738.

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The most commercially grown peach [Prunus persica (L.) Batsch.] cultivars do not require cross-pollination for reasonable fruit set; however, self-incompatibility is a well-known feature within the Prunoideae subfamily. Isoelectric focusing and native polyacrylamide gel electrophoresis of S-ribonucleases; PCR analyses of S-RNase and S-haplotype-specific F-box genes as well as DNA sequencing were carried out to survey the self-(in)compatibility allele pool and to uncover the nature of self-compatibility in peach. From 25 cultivars and hybrids with considerable diversity in phenotype and origin,

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Fagagnini, Andrea, Andrea Pica, Sabrina Fasoli, et al. "Onconase dimerization through 3D domain swapping: structural investigations and increase in the apoptotic effect in cancer cells*." Biochemical Journal 474, no. 22 (2017): 3767–81. http://dx.doi.org/10.1042/bcj20170541.

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Onconase® (ONC), a protein extracted from the oocytes of the Rana pipiens frog, is a monomeric member of the secretory ‘pancreatic-type’ RNase superfamily. Interestingly, ONC is the only monomeric ribonuclease endowed with a high cytotoxic activity. In contrast with other monomeric RNases, ONC displays a high cytotoxic activity. In this work, we found that ONC spontaneously forms dimeric traces and that the dimer amount increases about four times after lyophilization from acetic acid solutions. Differently from RNase A (bovine pancreatic ribonuclease) and the bovine seminal ribonuclease, which

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Bastard, Clara, Charline Caumont, Laura Samaison, et al. "Fluorescent In Situ Hybridization Testing Allows the Diagnosis of NRG1 Gene Fusions in Lung and Pancreas Cancers with No Other Identified Oncogenic Driver." Cancers 17, no. 14 (2025): 2347. https://doi.org/10.3390/cancers17142347.

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Some pancreatic ductal-type (PDADK) and lung adenocarcinomas (LADK) lacking other molecular drivers are reported to harbor NRG1 fusions as potential novel therapeutic targets. We investigated the feasibility of a fluorescent in situ hybridization (FISH)-based diagnosis of NRG1 fusions in a case series of PDADK and LADK lacking other identified oncogenic drivers. First, among a case series of PDADK, KRAS analyses (PCR followed in PCR-negative cases by RNA sequencing—RNAseq) found 27/162 (16.7%) KRAS wild-type cases, among which 1/162 (0.6%) NRG1 fusion was diagnosed using FISH. Secondly, among

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Lamping, Mario, Damian Tobias Rieke, Frederick Klauschen, et al. "Clinical impact of comprehensive versus targeted genomic analysis for precision oncology." Journal of Clinical Oncology 37, no. 15_suppl (2019): e13033-e13033. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e13033.

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e13033 Background: Panel sequencing (PS) has become a standard-of-care in cancer diagnostics. More comprehensive analyses such as whole-exome (WES) or RNA sequencing (RNAseq) allow for the detection of rare and unknown genetic aberrations that are not covered by predefined assays. The clinical impact of targeted versus comprehensive genomic assays were analyzed in patients presented at the Charité Molecular Tumor Board (MTB). Methods: Patients (pts) with advanced and/or metastatic cancer for whom no standard therapy was available were discussed in the MTB to allocate diagnostic profiling and g

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Potari-gul, L., D. Modos, D. Turei, et al. "P020 Mapping the changing intercellular communication and its downstream effect in Ulcerative Colitis." Journal of Crohn's and Colitis 15, Supplement_1 (2021): S138—S139. http://dx.doi.org/10.1093/ecco-jcc/jjab076.149.

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Abstract Background Intercellular communication is essential for growing and differentiating in multicellular organisms by transducing the signal from cell to cell. Despite its importance, the molecular background is less discovered due to the lack of data. This gap has started to be addressed with the appearance of single-cell omics approaches providing an insight among others into the gene expression of individual cells. Methods We have developed a method to predict and compare cell-cell signalling interactions using single-cell RNAseq data from colon biopsies. Transcriptomic data alone is n

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Jones, Eleri, Supatra Marsh, Ryan O'Shaughnessy, et al. "O14 Junctional epidermolysis bullosa: repairing the epidermal lipid barrier." British Journal of Dermatology 189, no. 1 (2023): e10-e10. http://dx.doi.org/10.1093/bjd/ljad174.014.

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Abstract Junctional epidermolysis bullosa (JEB) caused by loss of function mutations in basement membrane genes, including that encoding laminin-332, is among the most severe forms of epidermolysis bullosa. Affected individuals suffer from blistering from birth, leading to scarring, granulation tissue and susceptibility to infection. In generalized severe JEB, there is a 50% mortality rate in the first 2 years of life, often due to failure to thrive or overwhelming infection. Using cells with knockdown of laminin-α3 we generated a RNAseq data set and have identified a new pathway altered in JE

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Miller, Jason R., Kari A. Dilley, Derek M. Harkins, Timothy B. Stockwell, Reed S. Shabman, and Granger G. Sutton. "A host subtraction database for virus discovery in human cell line sequencing data." F1000Research 7 (January 23, 2018): 98. http://dx.doi.org/10.12688/f1000research.13580.1.

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The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number non-viral reads in the dataset to allow for efficient secondary analyses.

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Miller, Jason R., Kari A. Dilley, Derek M. Harkins, Timothy B. Stockwell, Reed S. Shabman, and Granger G. Sutton. "A host subtraction database for virus discovery in human cell line sequencing data." F1000Research 7 (July 12, 2018): 98. http://dx.doi.org/10.12688/f1000research.13580.2.

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The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number non-viral reads in the dataset to allow for efficient secondary analyses.

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Miller, Jason R., Kari A. Dilley, Derek M. Harkins, Timothy B. Stockwell, Reed S. Shabman, and Granger G. Sutton. "A host subtraction database for virus discovery in human cell line sequencing data." F1000Research 7 (May 21, 2019): 98. http://dx.doi.org/10.12688/f1000research.13580.3.

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The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number non-viral reads in the dataset to allow for efficient secondary analyses.

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Mumal, Iqra, Liming Xu, Fupan Yao, et al. "ETMR-19. SINGLE CELL ANALYSES OF ETMRs REVEAL THAT C19MC+ POPULATION DRIVES CELL CYCLE PROGRESSION AND STEM CELL MAINTENANCE." Neuro-Oncology 22, Supplement_3 (2020): iii326—iii327. http://dx.doi.org/10.1093/neuonc/noaa222.222.

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Abstract Embryonal tumors with multilayered rosettes (ETMRs) are highly fatal diseases characterized by recurrent amplification of C19MC, an oncogenic miRNA cluster. While C19MC was discovered as a major driver of ETMRs, its direct role in ETMRs remains unknown. As ETMRs exhibit significant heterogeneity in C19MC expression, we employed single cell transcriptomics to investigate features of C19MC+ population. We conducted single-nuclei RNAseq of 23,269 cells from 6 primary and 2 matched recurrent ETMRs. We also conducted single-cell RNAseq of human neural stem cells (hNSC-5miR) and ETMR cell l

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Eiteneuer, Constantin, David Velasco, Joseph Atemia, et al. "GXP: Analyze and Plot Plant Omics Data in Web Browsers." Plants 11, no. 6 (2022): 745. http://dx.doi.org/10.3390/plants11060745.

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Next-generation sequencing and metabolomics have become very cost and work efficient and are integrated into an ever-growing number of life science research projects. Typically, established software pipelines analyze raw data and produce quantitative data informing about gene expression or concentrations of metabolites. These results need to be visualized and further analyzed in order to support scientific hypothesis building and identification of underlying biological patterns. Some of these tools already exist, but require installation or manual programming. We developed “Gene Expression Plo

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Belcaid, Zineb, Archana Balan, Christopher Cherry, et al. "Immunogenomic features of pathologic response to neoadjuvant immune checkpoint blockade in esophageal cancer." Journal of Clinical Oncology 39, no. 15_suppl (2021): 4042. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.4042.

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4042 Background: Improving immunotherapy efficacy remains an unmet need in esophagogastric cancer and a deeper understanding of tumor and immune system dynamics during therapy may tailor immuno-oncology approaches. Methods: We performed whole exome sequencing (WES) and bulk RNA sequencing (RNAseq) of 70 serial tumor samples from 23 patients with stage II/III esophageal/gastroesophageal junction (E/GEJ) cancer treated on a phase 1B clinical trial with neoadjuvant nivolumab with or without relatlimab (anti-LAG-3) and chemoradiation followed by surgery (NCT03044613; CA209-906). Pathologic respons

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Tollervey, David. "Genetic and biochemical analyses of yeast RNase MRP." Molecular Biology Reports 22, no. 2-3 (1996): 75–79. http://dx.doi.org/10.1007/bf00988709.

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Cafournet, Cérane, Sofia Zanin, Anne Guimier, et al. "Novel ELAC2 Mutations in Individuals Presenting with Variably Severe Neurological Disease in the Presence or Absence of Cardiomyopathy." Life 13, no. 2 (2023): 445. http://dx.doi.org/10.3390/life13020445.

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Transcription of mitochondrial DNA generates long polycistronic precursors whose nucleolytic cleavage yields the individual mtDNA-encoded transcripts. In most cases, this cleavage occurs at the 5′- and 3′-ends of tRNA sequences by the concerted action of RNAseP and RNaseZ/ELAC2 endonucleases, respectively. Variants in the ELAC2 gene have been predominantly linked to severe to mild cardiomyopathy that, in its milder forms, is accompanied by variably severe neurological presentations. Here, we report five patients from three unrelated families. Four of the patients presented mild to moderate car

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Ushijima, Koichiro, Hidenori Sassa, Mihoko Tamura, et al. "Characterization of the S-Locus Region of Almond (Prunus dulcis): Analysis of a Somaclonal Mutant and a Cosmid Contig for an S Haplotype." Genetics 158, no. 1 (2001): 379–86. http://dx.doi.org/10.1093/genetics/158.1.379.

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Abstract Almond has a self-incompatibility system that is controlled by an S locus consisting of the S-RNase gene and an unidentified “pollen S gene.” An almond cultivar “Jeffries,” a somaclonal mutant of “Nonpareil” (ScSd), has a dysfunctional Sc haplotype both in pistil and pollen. Immunoblot and genomic Southern blot analyses detected no Sc haplotype-specific signal in Jeffries. Southern blot showed that Jeffries has an extra copy of the Sd haplotype. These results indicate that at least two mutations had occurred to generate Jeffries: (1) deletion of the Sc haplotype and (2) duplication of

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Kaulen, Leon D., Evgeniya Denisova, Felix Hinz, et al. "PATH-35. INTEGRATED GENOMIC ANALYSES OF IMMUNODEFICIENCY-ASSOCIATED EPSTEIN-BARR VIRUS- (EBV) POSITIVE PRIMARY CNS LYMPHOMAS." Neuro-Oncology 26, Supplement_8 (2024): viii186. http://dx.doi.org/10.1093/neuonc/noae165.0734.

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Abstract Immunodeficiency-associated primary CNS lymphoma (PCNSL) represents a distinct clinicopathological entity, which is typically Epstein-Barr virus positive (EBV+) and carries an inferior prognosis. Genetic alterations that characterize EBV related CNS lymphomagenesis remain unclear precluding molecular classification and targeted therapies. In this study, a comprehensive genetic analysis of 22 EBV+ PCNSL, integrated clinical and pathological information with exome and RNA sequencing (RNASeq) data. Deconvolution of bulk RNA sequencing data was performed using CIBERSORTx to characterize t

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Kaulen, L. D., E. Denisova, F. Hinz, et al. "P20.12.B INTEGRATED GENETIC ANALYSES OF IMMUNODEFICIENCY-ASSOCIATED EPSTEIN-BARR VIRUS- (EBV) POSITIVE PRIMARY CNS LYMPHOMAS." Neuro-Oncology 26, Supplement_5 (2024): v118. http://dx.doi.org/10.1093/neuonc/noae144.399.

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Abstract BACKGROUND Immunodeficiency-associated primary CNS lymphoma (PCNSL) represents a distinct clinicopathological entity, which is typically Epstein-Barr virus-positive (EBV+) and carries an inferior prognosis. Genetic alterations that characterize EBV-related CNS lymphomagenesis remain unclear precluding molecular classification and targeted therapies. MATERIAL AND METHODS In this study, a comprehensive genetic analysis of 22 EBV+ PCNSL, integrated clinical and pathological information with exome and RNA sequencing (RNASeq) data. Deconvolution of bulk RNA sequencing data was performed us

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Lee, Seul, Jae-Hwan Kim, Kwangmin Na, et al. "Abstract 6780: Characterization of immunological heterogeneity in the tumor microenvironment by integrated analyses using single cell RNAseq, spatial RNAseq and multiplex IHC." Cancer Research 83, no. 7_Supplement (2023): 6780. http://dx.doi.org/10.1158/1538-7445.am2023-6780.

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Abstract Heterogeneity in resistant to immunotherapies of tumor microenvironment (TME) has been implicated in immunotherapies to cause immune evasion or drug resistance. This study was conducted to explore the heterogeneity of TME through multiplex IHC, spatial and RNA sequencing analysis. We selected a sample from a lung adenocarcinoma patient without EGFR-activating mutation and expressing 30% of PD-L1. For quantitative analysis by multiplex IHC, various markers including CD4, CD8, FoxP3, granzyme B, CD20 and pan-cytokeratin were stained with 7 different fluorescence dyes, which was imaged w

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Cer, Regina Z., J. Enrique Herrera-Galeano, Kenneth G. Frey, et al. "Differential MicroRNA Analyses of Burkholderia pseudomallei- and Francisella tularensis-Exposed hPBMCs Reveal Potential Biomarkers." International Journal of Genomics 2017 (2017): 1–13. http://dx.doi.org/10.1155/2017/6489383.

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Increasing evidence that microRNAs (miRNAs) play important roles in the immune response against infectious agents suggests that miRNA might be exploitable as signatures of exposure to specific infectious agents. In order to identify potential early miRNA biomarkers of bacterial infections, human peripheral blood mononuclear cells (hPBMCs) were exposed to two select agents, Burkholderia pseudomallei K96243 and Francisella tularensis SHU S4, as well as to the nonpathogenic control Escherichia coli DH5α. RNA samples were harvested at three early time points, 30, 60, and 120 minutes postexposure,

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Coulibaly, Daouda, Feng Gao, Yang Bai, et al. "Molecular Research Progress on Gametophytic Self-Incompatibility in Rosaceae Species." Horticulturae 10, no. 10 (2024): 1101. http://dx.doi.org/10.3390/horticulturae10101101.

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Self-incompatibility (SI) is a complex mechanism that prevents plants from self-fertilizing to preserve and promote genetic variability. The angiosperm species have developed two different SI systems, the sporophytic (SSI) and the gametophytic (GSI) systems. SI is a significant impediment to steady fruit production in fruit tree species of the Rosaceae. In Rosaceae, GSI is genetically regulated via a single locus, named the ‘S-locus’, which includes a minimum of two polymorphic and relatively intercorrelated S genes: a pistil-expressed S-RNase gene and several pollen-expressed SFBB (S-locus F-

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Lobon-Iglesias, María-Jesús, Arnault Tauziede-Espariat, Mamy Andrianteranagna, Zhiyan Han, Julien Masliah-Planchon, and Franck Bourdeaut. "ATRT-27. COST-EFFECTIVE ASSAYS TO SUBGROUP ATRT IN THE DAILY ROUTINE." Neuro-Oncology 22, Supplement_3 (2020): iii281. http://dx.doi.org/10.1093/neuonc/noaa222.026.

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Abstract Three atypical teratoid rhabdoid tumors (ATRT) molecular subgroups with different bio-clinical characteristics have been reported (TYR, SHH and MYC). Molecular subgrouping relies on either methylation profiling (reference methods), or expression profiling. However, the cost-effectiveness of such pangenomic screening is questionable. This work aims to study the reliability of alternative techniques for subgroup classification in the daily routine. Illumina EPIC-arrays were performed on 46 samples. Among those cases, expression profiling were analysed by RNAseq (n=30). We designed a 26-

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Muhowski, Elizabeth M., and Laura M. Rogers. "Dual TCR-Expressing T Cells in Cancer: How Single-Cell Technologies Enable New Investigation." ImmunoHorizons 7, no. 5 (2023): 299–306. http://dx.doi.org/10.4049/immunohorizons.2200062.

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Abstract TCR diversity measures are often used to understand the immune response in cancer. Traditional measures of diversity rely on bulk RNA sequencing (RNAseq) of the β-chain variable regions. However, the full αβ TCR repertoire is a combination of both the α- and β-chains, which are encoded by separate genes. In contrast with bulk RNAseq, single-cell RNAseq (scRNAseq) allows paired chain analyses, yielding a more accurate measure of the repertoire. Interestingly, ∼30% of mature peripheral T cells express multiple TCR alleles (e.g., two α-chains) and may exhibit dual Ag specificity. scRNAse

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WILHELM, Marcelle, Mansour BOUTABOUT, and François-Xavier WILHELM. "Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase–RNase H domain exhibits polymerase and RNase H activities." Biochemical Journal 348, no. 2 (2000): 337–42. http://dx.doi.org/10.1042/bj3480337.

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Replication of the Saccharomyces cerevisiae Ty1 retrotransposon requires a reverse transcriptase capable of synthesizing Ty1 DNA. The first description of an active form of a recombinant Ty1 enzyme with polymerase and RNase H activities is reported here. The Ty1 enzyme was expressed as a hexahistidine-tagged fusion protein in Escherichia coli to facilitate purification of the recombinant protein by metal-chelate chromatography. Catalytic activity of the recombinant protein was detected only when amino acid residues encoded by the integrase gene were added to the N-terminus of the reverse trans

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Tadokoro, Takashi, Dong-Ju You, Yumi Abe, et al. "Structural, Thermodynamic, and Mutational Analyses of a Psychrotrophic RNase HI†,‡." Biochemistry 46, no. 25 (2007): 7460–68. http://dx.doi.org/10.1021/bi7001423.

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Velichko, Sharlene, Johnathon Anderson, Stephanie Ryan, and Reen Wu. "Global gene expression analysis of Act1’s effects in airway epithelial cells (161.17)." Journal of Immunology 186, no. 1_Supplement (2011): 161.17. http://dx.doi.org/10.4049/jimmunol.186.supp.161.17.

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Abstract Act1/CIKS is an intracellular protein that has been shown to play an important role in mediating IL-17A and IL-25 signaling effects. Recently, defects in Act1 function and/or expression has been implicated in inflammatory disease, such as psoriatic arthritis and atopic dermatitis. We have found that the modulation of Act1 expression levels in human airway epithelial cells changes the expression levels of some genes, in the absence of cytokine stimulation. RNAseq is a powerful new technique to quantitatively measure changes at the transcriptome level. Here we describe the use of RNAseq

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Zoroddu, Stefano, Luca Sanna, Valentina Bordoni, et al. "RNAseq Analysis of Novel 1,3,4-Oxadiazole Chalcogen Analogues Reveals Anti-Tubulin Properties on Cancer Cell Lines." International Journal of Molecular Sciences 24, no. 14 (2023): 11263. http://dx.doi.org/10.3390/ijms241411263.

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1,3,4-Oxadiazole derivatives are among the most studied anticancer drugs. Previous studies have analyzed the action of different 1,3,4-oxadiazole derivatives and their effects on cancer cells. This study investigated the characterization of two new compounds named 6 and 14 on HeLa and PC-3 cancer cell lines. Based on the previously obtained IC50, cell cycle effects were monitored by flow cytometry. RNA sequencing (RNAseq) was performed to identify differentially expressed genes, followed by functional annotation using gene ontology (GO), KEGG signaling pathway enrichment, and protein–protein i

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Mora-Márquez, Fernando, José Luis Vázquez-Poletti, and Unai López de Heredia. "NGScloud2: optimized bioinformatic analysis using Amazon Web Services." PeerJ 9 (April 16, 2021): e11237. http://dx.doi.org/10.7717/peerj.11237.

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Background NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made the software obsolete. NGScloud2 is an enhanced and expanded version of NGScloud that permits the access to ad hoc cloud computing infrastructure, scaled according to the complexity of each experiment. Methods NGSc

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Skoczek, Halina, and Michał Borys. "Rybonukleaza w korzeniach i węzłach krzewienia dwóch odmian jęczmienia [Ribonuclease in roots and nodes of two barley cultivars]." Acta Agrobotanica 32, no. 2 (2015): 173–83. http://dx.doi.org/10.5586/aa.1979.016.

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Cultivar Union which, compared with cultivar Lubuski has a larger root system, was found to show a significantly higher RNase activity. The nodes of cv. Union show a lower RNase activity per gram of tissue fresh weight and a higher specific activity, in comparison with cv. Lubuski. The number of RNase isoenzymes in the roots of both examined cultivars is the same. No difference in the number of RNase isoenzymes between the nodes of the examined cultivars was found either. On the other hand, certain differences between the examined cultivars in some RNase isoenzymes activities were observed in

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Norero, Natalia, María Rey Burusco, Sebastián D’Ippólito, et al. "Genome-Wide Analyses of Aspartic Proteases on Potato Genome (Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress." Plants 11, no. 4 (2022): 544. http://dx.doi.org/10.3390/plants11040544.

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Aspartic proteases are proteolytic enzymes widely distributed in living organisms and viruses. Although they have been extensively studied in many plant species, they are poorly described in potatoes. The present study aimed to identify and characterize S. tuberosum aspartic proteases. Gene structure, chromosome and protein domain organization, phylogeny, and subcellular predicted localization were analyzed and integrated with RNAseq data from different tissues, organs, and conditions focused on abiotic stress. Sixty-two aspartic protease genes were retrieved from the potato genome, distribute

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Pruefer, Franz, K. Vazquez-Santillan, L. Muñoz-Galindo, J. L. Cruz-Colin, V. Maldonado та Jorge Melendez-Zajgla. "TIMP4 Modulates ER-α Signalling in MCF7 Breast Cancer Cells". Folia Biologica 62, № 2 (2016): 75–81. http://dx.doi.org/10.14712/fb2016062020075.

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Tissue inhibitor of metalloprotease 4 (TIMP4) contributes to poor prognosis in breast and other tumours. However, the mechanisms of how TIMP4 influences breast cancer cell behaviour are unknown. Our aim was to explore the signalling pathways modulated by TIMP4 in breast cancer cells. Human recombinant TIMP4 was added to MCF7 breast cancer cells and RNASeq was performed. TIMP4 RNASeq results were validated by RT-PCR. Network analyses of TIMP4-exposed cells showed that ER-α, HIF1A and TGF-β signalling were activated, whereas FOXO3 signalling was downregulated. ER-α protein levels were increased

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Erster, S. H., L. A. Finn, D. A. Frendewey, and D. M. Helfman. "Use of RNase H and primer extension to analyze RNA splicing." Nucleic Acids Research 16, no. 13 (1988): 5999–6014. http://dx.doi.org/10.1093/nar/16.13.5999.

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