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1. The emergence and promise of single-cell temporal-omics approaches

Author:
Lederer, Alex R; La Manno, Gioele
Source:
Current opinion in biotechnology 2020 v.63 pp. 70-78
ISSN:
0958-1669
Subject:
transcriptomics,   etc   ; disease progression; embryogenesis; gene expression; methodology; multivariate analysis; transcriptome;     Show all 7 Subjects
Abstract:
... Single-cell transcriptomics enables the measurement of gene expression in complex biological systems at the resolution of individual cells. Multivariate analysis of single-cell data helps describe the variation in expression accompanying cellular processes during embryonic development, disease progression and in response to stimuli. Likewise, new methods have extended the possibilities of single-c ...
DOI:
10.1016/j.copbio.2019.12.005

2. An Omnivore’s Dilemma: Toxoplasma gondii’s Flexible Metabolic Networks

Author:
Kim, Kami
Source:
Trends in parasitology 2020 v.36 no.5 pp. 408-410
ISSN:
1471-4922
Subject:
transcriptomics,   etc   ; Toxoplasma gondii; biochemical pathways; metabolomics; models; nutrients; omnivores; pathogens;     Show all 8 Subjects
Abstract:
... Host cells provide protection from the environment for intracellular pathogens, but acquisition of nutrients and sensing of changes in the host cell bring new challenges. Krishnan et al. have recently developed a comprehensive genome-scale metabolic model (GEM) of the Toxoplasma gondii metabolic network that incorporates genetic, transcriptomic, and metabolomic data. ...
DOI:
10.1016/j.pt.2020.02.002

3. Real-Time Volatilomics: A Novel Approach for Analyzing Biological Samples

Author:
Majchrzak, Tomasz; Wojnowski, Wojciech; Rutkowska, Małgorzata; Wasik, Andrzej
Source:
Trends in plant science 2020 v.25 no.3 pp. 302-312
ISSN:
1360-1385
Subject:
transcriptomics,   etc   ; ecosystems; genomics; mass spectrometry; metabolomics; plant analysis; proteomics;     Show all 7 Subjects
Abstract:
... The use of the ‘omics techniques in environmental research has become common-place. The most widely implemented of these include metabolomics, proteomics, genomics, and transcriptomics. In recent years, a similar approach has also been taken with the analysis of volatiles from biological samples, giving rise to the so-called ‘volatilomics’ in plant analysis. Developments in direct infusion mass sp ...
DOI:
10.1016/j.tplants.2019.12.005

4. Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics

Author:
Rich-Griffin, Charlotte; Stechemesser, Annika; Finch, Jessica; Lucas, Emma; Ott, Sascha; Schäfer, Patrick
Source:
Trends in plant science 2020 v.25 no.2 pp. 186-197
ISSN:
1360-1385
Subject:
transcriptomics,   etc   ; data collection; genomics; sequence analysis; tissues; transcription (genetics);     Show all 6 Subjects
Abstract:
... Plant function is the result of the concerted action of single cells in different tissues. Advances in RNA-seq technologies and tissue processing allow us now to capture transcriptional changes at single-cell resolution. The incredible potential of single-cell RNA-seq lies in the novel ability to study and exploit regulatory processes in complex tissues based on the behaviour of single cells. Impo ...
DOI:
10.1016/j.tplants.2019.10.008

5. MazF activation causes ACA sequence-independent and selective alterations in RNA levels in Escherichia coli

Author:
Akiyama, Kentaro; Fujisawa, Kazuki; Kondo, Hiro; Netsu, Yuya; Nishikawa, Koji; Takata, Yoshio; Nakamura, Yuya; Kino, Yuta; Ayukawa, Shotaro; Yamamura, Masayuki; Hayashi, Nobuhiro; Tagawa, Yoh-ichi; Nakashima, Nobutaka
Source:
Archives of microbiology 2020 v.202 no.1 pp. 105-114
ISSN:
0302-8933
Subject:
transcriptomics,   etc   ; Escherichia coli K12; RNA; chromosomes; gene expression regulation; genes;     Show all 6 Subjects
Abstract:
... Escherichia coli MazF is a toxin protein that cleaves RNA at ACA sequences. Its activation has been thought to cause growth inhibition, primarily through indiscriminate cleavage of RNA. To investigate responses following MazF activation, transcriptomic profiles of mazF-overexpressing and non-overexpressing E. coli K12 cells were compared. Analyses of differentially expressed genes demonstrated tha ...
DOI:
10.1007/s00203-019-01726-9

6. Method for RNA extraction and transcriptomic analysis of single fungal spores

Author:
Geoghegan, Ivey A.; Emes, Richard D.; Archer, David B.; Avery, Simon V.
Source:
MethodsX 2020 v.7 pp. 100760
ISSN:
2215-0161
Subject:
transcriptomics,   etc   ; Aspergillus niger; DNA; conidia; fungi; mammals; messenger RNA; phenotype;     Show all 8 Subjects
Abstract:
... Transcriptomic analysis of single cells has been increasingly in demand in recent years, thanks to technological and methodological advances as well as growing recognition of the importance of individuals in biological systems. However, the majority of these studies have been performed in mammalian cells, due to their ease of lysis and high RNA content. No single cell transcriptomic analysis has y ...
DOI:
10.1016/j.mex.2019.12.002
PubMed:
31908984
PubMed Central:
PMC6938798

7. LncRNA MIR4435‐2HG‐mediated upregulation of TGF‐β1 promotes migration and proliferation of nonsmall cell lung cancer cells

Author:
Yang, Mei; He, Xiaohua; Huang, Xiaoxian; Wang, Jiyang; He, Yuxin; Wei, Li
Source:
Environmental toxicology 2020 v.35 no.5 pp. 582-590
ISSN:
1520-4081
Subject:
transcriptomics,   etc   ; lung neoplasms; microRNA; neoplasm cells; neoplasm progression; non-coding RNA; transforming growth factor beta 1;     Show all 7 Subjects
Abstract:
... The roles of long noncoding RNAs (lncRNAs) have been shown to play critical roles in tumor progression. Here, it was identified that lncRNA MIR4435‐2HG was highly expressed in lung cancer tissues, especially in nonsmall cell lung cancer (NSCLC). A consistent result was obtained in lung cancer cells. Functional experiments showed that knockdown of MIR4435‐2HG reduced the proliferation and migration ...
DOI:
10.1002/tox.22893

8. Transcriptome analysis of antennal cytochrome P450s and their transcriptional responses to plant and locust volatiles in Locusta migratoria

Author:
Wu, Haihua; Liu, Yongmei; Shi, Xuekai; Zhang, Xueyao; Ye, Changlü; Zhu, Kun Yan; Zhu, Fang; Zhang, Jianzhen; Ma, Enbo
Source:
International journal of biological macromolecules 2020 v.149 pp. 741-753
ISSN:
0141-8130
Subject:
transcriptomics,   etc   ; Locusta migratoria; antennae; biosynthesis; cytochrome P-450; enzymes; mitochondria; odor compounds; phylogeny; transcription (genetics);     Show all 10 Subjects
Abstract:
... Cytochrome P450 monooxygenases (P450s) constitute a large superfamily of heme-thiolate proteins that are involved in the biosynthesis or degradation of endogenous compounds and detoxification of exogenous chemicals. It has been reported that P450s could serve as odorant-degrading enzymes (ODEs) to inactivate odorants to avoid saturating the antennae. However, there is little information about P450 ...
DOI:
10.1016/j.ijbiomac.2020.01.309

9. Gene Expression and Diet Breadth in Plant-Feeding Insects: Summarizing Trends

Author:
Birnbaum, Stephanie S.L.; Abbot, Patrick
Source:
Trends in ecology & evolution 2020 v.35 no.3 pp. 259-277
ISSN:
0169-5347
Subject:
transcriptomics,   etc   ; environmental factors; evolution; foraging; gene expression; genes; host plants; phenotypic plasticity; phytophagous insects; transcription (genetics);     Show all 10 Subjects
Abstract:
... Transcriptomic studies lend insights into the role of transcriptional plasticity in adaptation and specialization. Recently, there has been growing interest in understanding the relationship between variation in herbivorous insect gene expression and the evolution of diet breadth. We review the studies that have emerged on insect gene expression and host plant use, and outline the questions and ap ...
DOI:
10.1016/j.tree.2019.10.014

10. Genome‐wide Transcriptional Analysis of Tetrahymena thermophila Response to Exogenous Cholesterol

Author:
Najle, Sebastián R.; Hernández, Josefina; Ocaña‐Pallarès, Eduard; García Siburu, Nicolás; Nusblat, Alejandro D.; Nudel, Clara B.; Slamovits, Claudio H.; Uttaro, Antonio D.
Source:
Thejournal of eukaryotic microbiology 2020 v.67 no.2 pp. 209-222
ISSN:
1066-5234
Subject:
transcriptomics,   etc   ; RNA interference; Tetrahymena thermophila; cholesterol; genes; metabolism; phytosterols; squalene; transcription (genetics); triterpenoids;     Show all 10 Subjects
Abstract:
... The ciliate Tetrahymena thermophila does not require sterols for growth and synthesizes pentacyclic triterpenoid alcohols, mainly tetrahymanol, as sterol surrogates. However, when sterols are present in the environment, T. thermophila efficiently incorporates and modifies them. These modifications consist of desaturation reactions at positions C5(6), C7(8), and C22(23), and de‐ethylation at C24 of ...
DOI:
10.1111/jeu.12774

11. SRSF1-3, a splicing and somatic hypermutation regulator, controls transcription of IgV genes via chromatin regulators SATB2, UBN1 and histone variant H3.3

Author:
Singh, Amit Kumar; Tamrakar, Anubhav; Jaiswal, Ankit; Kanayama, Naoki; Kodgire, Prashant
Source:
Molecular immunology 2020 v.119 pp. 69-82
ISSN:
0161-5890
Subject:
transcriptomics,   etc   ; RNA; chromatin; gene expression regulation; gene overexpression; genes; histones; promoter regions; transcription (genetics); transcription factors;     Show all 10 Subjects
Abstract:
... SRSF1, a member of the SR protein family, is an important splicing factor and regulator of splicing. Multiple splicing isoforms have been reported for this gene. SRSF1–3, a splicing isoform of SRSF1, is necessary for AID-dependent SHM of IgV genes. However, its precise role in SHM remains enigmatic. Transcriptomic analysis of SRSF1–3 reconstituted cells shows upregulation of transcription factor S ...
DOI:
10.1016/j.molimm.2020.01.005

12. STATR: A simple analysis pipeline of Ribo-Seq in bacteria

Author:
Choe, Donghui; Palsson, Bernhard; Cho, Byung-Kwan
Source:
The journal of microbiology 2020 v.58 no.3 pp. 217-226
ISSN:
1225-8873
Subject:
transcriptomics,   etc   ; bacteria; gene expression; genes; high-throughput nucleotide sequencing; messenger RNA; protein content; protein synthesis; ribosomes;     Show all 9 Subjects
Abstract:
... Gene expression changes in response to diverse environmental stimuli to regulate numerous cellular functions. Genes are expressed into their functional products with the help of messenger RNA (mRNA). Thus, measuring levels of mRNA in cells is important to understand cellular functions. With advances in next-generation sequencing (NGS), the abundance of cellular mRNA has been elucidated via transcr ...
DOI:
10.1007/s12275-020-9536-2
PubMed:
31989542
PubMed Central:
PMC7209825

13. The neuropeptidome of Carabus (Coleoptera, Adephaga: Carabidae)

Author:
Ragionieri, Lapo; Predel, Reinhard
Source:
Insect biochemistry and molecular biology 2020 v.118 pp. 103309
ISSN:
0965-1748
Subject:
transcriptomics,   etc   ; Carabidae; ancestry; beneficial insects; biopesticides; genes; hormones; immunohistochemistry; insect larvae; mass spectrometry; neuropeptides; pests; predators;     Show all 13 Subjects
Abstract:
... Neuropeptides are signaling molecules involved in the regulation of virtually all physiological functions of Metazoa. In insects, more than 50 neuropeptide genes can be present in a single species, and thus neuropeptidergic systems are attractive targets for the development of environmentally friendly pesticides. Such approaches require not only knowledge of the neuropeptidomes of pests, but also ...
DOI:
10.1016/j.ibmb.2019.103309

14. The remarkable morphological diversity of leaf shape in sweet potato (Ipomoea batatas): the influence of genetics, environment, and G×E

Author:
Gupta, Sonal; Rosenthal, David M.; Stinchcombe, John R.; Baucom, Regina S.
Source:
Thenew phytologist 2020 v.225 no.5 pp. 2183-2195
ISSN:
0028-646X
Subject:
transcriptomics,   etc   ; Ipomoea batatas; agronomic traits; gene expression; genes; genetic factors; leaves; morphometry; surveys; sweet potatoes;     Show all 10 Subjects
Abstract:
... Leaf shape, a spectacularly diverse plant trait, varies across taxonomic levels, geography and in response to environmental differences. However, comprehensive intraspecific analyses of leaf shape variation across variable environments is surprisingly absent. Here, we performed a multilevel analysis of leaf shape using diverse accessions of sweet potato (Ipomoea batatas), and uncovered the role of ...
DOI:
10.1111/nph.16286

15. Transcriptome analyses provide insights into development of the Zingiber zerumbet flower, revealing potential genes related to floral organ formation and patterning

Author:
Zhao, Tong; Specht, Chelsea D.; Dong, Zhicheng; Ye, Yushi; Liu, Huanfang; Liao, Jingping
Source:
Plant growth regulation 2020 v.90 no.2 pp. 331-345
ISSN:
0167-6903
Subject:
transcriptomics,   etc   ; Zingiber zerumbet; androecium; evolution; flowering; flowers; genes; gynoecium; transcription factors; transcriptome;     Show all 10 Subjects
Abstract:
... The flower of Zingiber zerumbet is characterized by a distinctive labellum, a highly modified floral organ believed to be formed by the fusion of several infertile members of the androecial whorl (staminodes). Across the Zingiberaceae, the number of staminodes involved in labellum formation varies from two to four, and these are reflected in the number of lobes that comprise the mature labellum. R ...
DOI:
10.1007/s10725-020-00575-7

16. Square one: zygote polarity and early embryogenesis in flowering plants

Author:
Wang, Kai; Chen, Houming; Miao, Yingjing; Bayer, Martin
Source:
Current opinion in plant biology 2020 v.53 pp. 128-133
ISSN:
1369-5266
Subject:
transcriptomics,   etc   ; Angiospermae; auxins; embryo (plant); embryogenesis; fluorescence; grasses; image analysis; zygote;     Show all 9 Subjects
Abstract:
... In the last two decades, work on auxin signaling has helped to understand many aspects of the fundamental process underlying the specification of tissue types in the plant embryo. However, the immediate steps after fertilization including the polarization of the zygote and the initial body axis formation remained poorly understood. Valuable insight into these enigmatic processes has been gained by ...
DOI:
10.1016/j.pbi.2019.10.002

17. Optimization and Multiomic Basis of Phenyllactic Acid Overproduction by Lactobacillus plantarum

Author:
Wu, Wenyu; Deng, Gang; Liu, Chenjian; Gong, Xiaowei; Ma, Guanghui; Yuan, Qingqing; Yang, En; Li, Xiaoran; Luo, Yiyong
Source:
Journal of agricultural and food chemistry 2020 v.68 no.6 pp. 1741-1749
ISSN:
1520-5118
Subject:
transcriptomics,   etc   ; Lactobacillus plantarum; amino acids; biochemical pathways; biosynthesis; carbon metabolism; energy; fermentation; genomics; metabolomics; phenyllactic acid;     Show all 11 Subjects
Abstract:
... The goal of this study was to explore the regulatory mechanisms of phenyllactic acid (PLA) overaccumulation in Lactobacillus plantarum. The dynamics of PLA production revealed that 24 h was a suitable fermentation time, at which one of the largest differences in PLA content between strains S1 and YM-4-3 was 22.42 mg/L. Additionally, an optimization experiment showed that PLA production under the o ...
DOI:
10.1021/acs.jafc.9b07136

18. Microfluidic Platform for Next-Generation Sequencing Library Preparation with Low-Input Samples

Author:
Murphy, Travis W.; Hsieh, Yuan-Pang; Zhu, Bohan; Naler, Lynette B.; Lu, Chang
Source:
Analytical chemistry 2020 v.92 no.3 pp. 2519-2526
ISSN:
1520-6882
Subject:
transcriptomics,   etc   ; DNA; DNA libraries; biocompatible materials; biomarkers; epigenetics; genomics; high-throughput nucleotide sequencing; patients; prognosis;     Show all 10 Subjects
Abstract:
... Advances in next-generation sequencing (NGS) have made available a wealth of information that had previously been inaccessible to researchers and clinicians. NGS has been applied to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant tool capable of accelerating diagnosis, prognosis, and biomarker discovery. However, these NGS assays have yet to be pract ...
DOI:
10.1021/acs.analchem.9b04086
PubMed:
31894965
PubMed Central:
PMC7002211

19. Comparative transcriptome analysis of different stages of Plasmodium falciparum to explore vaccine and drug candidates

Author:
Guleria, Vandana; Jaiswal, Varun
Source:
Genomics 2020 v.112 no.1 pp. 796-804
ISSN:
0888-7543
Subject:
transcriptomics,   etc   ; Plasmodium falciparum; infectious diseases; malaria; pathogens; protein synthesis; proteins; transcriptome; vaccines;     Show all 9 Subjects
Abstract:
... Malaria is a life-threatening disease causes huge burden on human health. Every year >200 million cases of malaria are reported globally. Researchers have carried out research on transcriptome of different stages of Plasmodium species to understand complex pathology of pathogens and to discover therapeutics. Researchers are targeting different stages of Plasmodium falciparum separately. Hence, to ...
DOI:
10.1016/j.ygeno.2019.05.018

20. Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using transcriptomes: examining controversial relationships via degeneracy coding and interrogation of gene conflict

Author:
Skinner, Rachel K.; Dietrich, Christopher H.; Walden, Kimberly K. O.; Gordon, Eric; Sweet, Andrew D.; Podsiadlowski, Lars; Petersen, Malte; Simon, Chris; Takiya, Daniela M.; Johnson, Kevin P.
Source:
Systematic entomology 2020 v.45 no.1 pp. 85-113
ISSN:
0307-6970
Subject:
transcriptomics,   etc   ; Cercopoidea; Cicadoidea; Membracoidea; amino acids; data collection; genes; phylogeny; phytophagous insects; statistical analysis; transcriptome;     Show all 11 Subjects
Abstract:
... The hemipteran suborder Auchenorrhyncha is a highly diverse, ecologically and agriculturally important group of primarily phytophagous insects which has been a source of phylogenetic contention for many years. Here, we have used transcriptome sequencing to assemble 2139 orthologues from 84 auchenorrhynchan species representing 27 families; this is the largest and most taxonomically comprehensive p ...
DOI:
10.1111/syen.12381