transcript levels
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2022 ◽  
Vol 295 ◽  
pp. 110815
Jianhua Luo ◽  
Yue Zhou ◽  
Qinwei Pan ◽  
Qin Mu ◽  
Tingting Gu

2022 ◽  
Vol 23 (1) ◽  
Yanyu Liang ◽  
Milton Pividori ◽  
Ani Manichaikul ◽  
Abraham A. Palmer ◽  
Nancy J. Cox ◽  

Abstract Background Polygenic risk scores (PRS) are valuable to translate the results of genome-wide association studies (GWAS) into clinical practice. To date, most GWAS have been based on individuals of European-ancestry leading to poor performance in populations of non-European ancestry. Results We introduce the polygenic transcriptome risk score (PTRS), which is based on predicted transcript levels (rather than SNPs), and explore the portability of PTRS across populations using UK Biobank data. Conclusions We show that PTRS has a significantly higher portability (Wilcoxon p=0.013) in the African-descent samples where the loss of performance is most acute with better performance than PRS when used in combination.

Olabisi Ojo ◽  
Diana L. Williams ◽  
Linda B. Adams ◽  
Ramanuj Lahiri

Mycobacterium leprae, the causative agent of leprosy, is an obligate intracellular pathogen primarily residing within host macrophages and Schwann cells. Whole genome sequencing predicts a highly degraded genome with approximately one third of the coding capacity resulting in the loss of many catabolic pathways. Therefore, it can be assumed that M. leprae obtains many of the necessary metabolites for intracellular survival and growth from the host cells. In this study, global transcriptomic analyses were done on freshly harvested M. leprae growing in athymic mouse footpads for five months (MFP5) and compared to those held in axenic medium for 48 (ML48) and 96 (ML96) hours. Results show that all of the genes and pseudogenes were transcribed under both in vivo and in vitro conditions. 24% and 33% of gene transcript levels were significantly altered in ML48 and ML96 respectively, compared to MFP5. Approximately 45% (39/86) of lipid metabolism genes were significantly downregulated in ML96 compared to MFP5, majority of which are in the β-oxidation pathway. Cholesterol oxidase, acyl-CoA dehydrogenase, and coenzyme F420-dependent oxidoreductase, were significantly upregulated in both ML48 and ML96 compared to MFP5. 30% of cell wall and cell processes functional category genes had altered gene transcription at 96hr compared to MFP5. 40% of 57 genes associated with mycobacterial virulence showed significantly altered transcript levels with 52% significantly downregulated in ML96, including most of the Pro-Glu/Pro-Pro-Glu genes. All 111 hypothetical protein genes with unknown function were expressed. Adenosine triphosphate (ATP) synthesis in M. leprae appears to be significantly downregulated under ex vivo conditions. This is the first study comparing M. leprae global gene expression during in vivo growth and ex vivo stationery phase in axenic medium confirming that during the growth phase in the footpads of experimentally infected mice, M. leprae is metabolically active and its primary source of energy production is probably lipids.

2022 ◽  
Ethan Ashby ◽  
Lucinda Paddock ◽  
Hannah L Betts ◽  
Geneva Miller ◽  
Anya Porter ◽  

Trypanosoma brucei , the causative agent of Human and Animal African trypanosomiasis, cycles between a mammalian host and a tsetse fly vector. The parasite undergoes huge changes in morphology and metabolism as it adapts to each host environment. These changes are reflected in the differing transcriptomes of parasites living in each host. While changes in the transcriptome have been well catalogued for parasites differentiating from the mammalian bloodstream to the insect stage, it remains unclear whether chromatin interacting proteins mediate transcriptomic changes during life cycle adaptation. We and others have shown that chromatin interacting bromodomain proteins localize to transcription start sites in bloodstream parasites, but whether the localization of bromodomain proteins changes as parasites differentiate from bloodstream to insect stage parasites remains unknown. To address this question, we performed Cleavage Under Target and Release Using Nuclease (CUT&RUN) timecourse experiments using a tagged version of Bromodomain Protein 3 (Bdf3) in parasites differentiating from bloodstream to insect stage forms. We found that Bdf3 occupancy at most loci increased at 3 hours following onset of differentiation and decreased thereafter. A number of sites with increased bromodomain protein occupancy lie proximal to genes known to have altered transcript levels during differentiation, such as procyclins, procyclin associated genes, and invariant surface glycoproteins. While most Bdf3 occupied sites are observed throughout differentiation, a very small number appear de novo as differentiation progresses. Notably, one such site lies proximal to the procyclin gene locus, which contains genes essential for remodeling surface proteins following transition to the insect stage. Overall, these studies indicate that occupancy of chromatin interacting proteins is dynamic during life cycle stage transitions, and provides the groundwork for future studies aimed at uncovering whether changes in bromodomain protein occupancy affect transcript levels of neighboring genes. Additionally, the optimization of CUT&RUN for use in Trypanosoma brucei may prove helpful for other researchers as an alternative to Chromatin Immunoprecipitation (ChIP).

Antioxidants ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 144
Alexandros Mavrommatis ◽  
Maria-Eleftheria Zografaki ◽  
Sofia Marka ◽  
Eleni D. Myrtsi ◽  
Elisavet Giamouri ◽  

Although carotenoids generally possess antimicrobial and antioxidant properties, the in vivo synergistic action of carotenoid blends derived from plant-based by-products has not been thoroughly studied. Therefore, the carotenoid characterization and antimicrobial potential of Citrus reticulata extract as well as the impact of this carotenoid-rich extract (CCE) dietary supplementation on the performance, meat quality, and immune-oxidative status of broiler chickens were determined. One hundred and twenty one-day-old hatched chicks (Ross 308) were allocated to two dietary groups, with four replicate pens of 15 birds each. Birds were fed either a basal diet (CON) or the basal diet supplemented with 0.1% CCE (25 mg carotenoid extract included in 1 g of soluble starch) for 42 d. β-Cryptoxanthin, β -Carotene, Zeaxanthin, and Lutein were the prevailing carotenoid compounds in the Citrus reticulata extract. The CCE feed additive exerted inhibitory properties against both Gram-positive (Staphylococcus aureus) and negative (Klebsiella oxytoca, Escherichia coli, and Salmonella typhimurium) bacteria. Both the broiler performance and meat quality did not substantially differ, while the breast muscle malondialdehyde (MDA) concentration tended to decrease (p = 0.070) in the CCE-fed broilers. The inclusion of CCE decreased the alanine aminotransferase and MDA concentration, and the activity of glutathione peroxidase, while the activity of superoxide dismutase was increased in the blood. Catalase and NADPH oxidase 2 relative transcript levels were significantly downregulated in the livers of the CCE-fed broilers. Additionally, Interleukin 1β and tumor necrosis factor (TNF) relative transcript levels were downregulated in the livers of the CCE- fed broilers, while TNF and interferon γ (IFNG) tended to decrease in the spleens and bursa of Fabricius, respectively. The present study provided new insights regarding the beneficial properties of carotenoids contained in Citrus reticulata in broilers’ immune-oxidative status. These promising outcomes could be the basis for further research under field conditions.

Yanna Reis Praça ◽  
Paula Beatriz Santiago ◽  
Sébastien Charneau ◽  
Samuel Coelho Mandacaru ◽  
Izabela Marques Dourado Bastos ◽  

Triatomines have evolved salivary glands that produce versatile molecules with various biological functions, including those leading their interactions with vertebrate hosts’ hemostatic and immunological systems. Here, using high-throughput transcriptomics and proteomics, we report the first sialome study on the synanthropic triatomine Triatoma sordida. As a result, 57,645,372 reads were assembled into 26,670 coding sequences (CDS). From these, a total of 16,683 were successfully annotated. The sialotranscriptomic profile shows Lipocalin as the most abundant protein family within putative secreted transcripts. Trialysins and Kazal-type protease inhibitors have high transcript levels followed by ubiquitous protein families and enzyme classes. Interestingly, abundant trialysin and Kazal-type members are highlighted in this triatomine sialotranscriptome. Furthermore, we identified 132 proteins in T. sordida salivary gland soluble extract through LC-MS/MS spectrometry. Lipocalins, Hemiptera specific families, CRISP/Antigen-5 and Kazal-type protein inhibitors proteins were identified. Our study provides a comprehensive description of the transcript and protein compositions of the salivary glands of T. sordida. It significantly enhances the information in the Triatominae sialome databanks reported so far, improving the understanding of the vector’s biology, the hematophagous behaviour, and the Triatominae subfamily’s evolution.

Antioxidants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 70
Katarzyna Ciacka ◽  
Marcin Tyminski ◽  
Agnieszka Gniazdowska ◽  
Urszula Krasuska

Seed ageing is associated with a high concentration of reactive oxygen species (ROS). Apple (Malus domestica Borkh.) seeds belong to the orthodox type. Due to a deep dormancy, they may be stored in dry condition at 5 °C for a long time, without viability loss. In the laboratory, artificial ageing of apple seeds is performed by imbibition in wet sand at warm temperature (33 °C). The aim of the work was to study nitric oxide (NO) as a seed vigour preservation agent. Embryos isolated from apple seeds subjected to accelerated ageing for 7, 14, 21 or 40 days were fumigated with NO. Embryo quality was estimated by TTC and MDA tests. ROS level was confirmed by NBT staining. We analysed the alteration in transcript levels of CAT, SOD and POX. NO fumigation of embryos of seeds aged for 21 days stimulated germination and increased ROS level which correlated to the elevated expression of RBOH. The increased total antioxidant capacity after NO fumigation was accompanied by the increased transcript levels of genes encoding enzymatic antioxidants, that could protect against ROS overaccumulation. Moreover, post-aged NO application diminished the nitro-oxidative modification of RNA, proving NO action as a remedy in oxidative remodelling after seeds ageing.

Agronomy ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 40
Maria Gerakari ◽  
Nikolina Cheimona ◽  
Eleni Tani ◽  
Ilias Travlos ◽  
Demosthenis Chachalis ◽  

Lolium spp. are troublesome weeds mainly found in winter cereal crops worldwide, including Europe. In recent years resistant mechanisms have been evolved to several important herbicides. In this study we investigated the mechanisms responsible for conferring glyphosate resistance in some Lolium spp. populations. A holistic approach was used, based on dose-response experiments, determination of shikimic acid concentration in plant leaf tissue, as well as molecular analyses. More specifically, in three Lolium spp. populations the existence of a mutation in the Pro-106 codon of the 5-enolpyruvylshikimate-3 phosphate synthase (EPSPS) gene was investigated as well as the relative transcript levels of four ABC-transporter genes were monitored at three time points after glyphosate application. The results demonstrated that glyphosate resistance is a multifactor phenomenon. Relative transcript levels of the ABC-transporter genes were abundant at very early time points after glyphosate treatments. Dose-response experiments and shikimate analyses were in accordance with the findings of the quantitative PCR (qPCR) analyses. We suggest that relative expression ratio of ABC-transporter genes can be a useful tool to rapidly identify Lolium spp. populations resistant to glyphosate.

2021 ◽  
Mitsutoshi Okamoto ◽  
Tomoko Niki ◽  
Mirai Azuma ◽  
Kenichi Shibuya ◽  
Kazuo Ichimura

Abstract Delphinium flowers are highly sensitive to ethylene and its sepals abscise during senescence, which is associated with increases in 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC oxidase (ACO) activities and ethylene production in gynoecium and receptacle. Three ACS genes (DgACS1, DgACS2, and DgACS3) and three ACO genes (DgACO1, DgACO2, and DgACO3) were cloned from Delphinium grandiflorum cv. Super Grand Blue. To investigate the contribution of these genes to ethylene production, their expression was analyzed in these genes in the gynoecium and receptacle during natural senescence and following ethylene exposure and pollination. Ethylene production in the gynoecium and receptacle increased during natural flower senescence. The transcript levels of the ACS and ACO genes in these organs, excluding DgACS2 in the receptacle, increased during senescence. Exposure to ethylene accelerated sepal abscission and more strongly increased ethylene production in the receptacle than in the gynoecium. DgACS1 transcript levels in the gynoecium and DgACS2 and DgACO3 transcript levels in the receptacle were increased by ethylene exposure. Pollination accelerated sepal abscission and increased ethylene production in the gynoecium and receptacle. Pollination slightly affected ACS and ACO transcript levels in the gynoecium, whereas DgACO3 transcript level in the receptacle were markedly increased. These results reveal that ACS and ACO gene expression is differently regulated in the gynoecium and receptacle, and some of these genes are more strongly upregulated by ethylene exposure and pollination in the receptacle than in the gynoecium, suggesting the significance of the receptacle to sepal abscission.

2021 ◽  
Vol 12 ◽  
Wataru Yamazaki ◽  
Dunarel Badescu ◽  
Seang Lin Tan ◽  
Jiannis Ragoussis ◽  
Teruko Taketo

The sex chromosome complement, XX or XY, determines sexual differentiation of the gonadal primordium into a testis or an ovary, which in turn directs differentiation of the germ cells into sperm and oocytes, respectively, in eutherian mammals. When the X monosomy or XY sex reversal occurs, XO and XY females exhibit subfertility and infertility in the mouse on the C57BL/6J genetic background, suggesting that functional germ cell differentiation requires the proper sex chromosome complement. Using these mouse models, we asked how the sex chromosome complement affects gene transcription in the oocytes during follicular growth. An oocyte accumulates cytoplasmic components such as mRNAs and proteins during follicular growth to support subsequent meiotic progression, fertilization, and early embryonic development without de novo transcription. However, how gene transcription is regulated during oocyte growth is not well understood. Our results revealed that XY oocytes became abnormal in chromatin configuration, mitochondria distribution, and de novo transcription compared to XX or XO oocytes near the end of growth phase. Therefore, we compared transcriptomes by RNA-sequencing among the XX, XO, and XY oocytes of 50–60 µm in diameter, which were still morphologically comparable. The results showed that the X chromosome dosage limited the X-linked and autosomal gene transcript levels in XO oocytes whereas many genes were transcribed from the Y chromosome and made the transcriptome in XY oocytes closer to that in XX oocytes. We then compared the transcript levels of 3 X-linked, 3 Y-linked and 2 autosomal genes in the XX, XO, and XY oocytes during the entire growth phase as well as at the end of growth phase using quantitative RT-PCR. The results indicated that the transcript levels of most genes increased with oocyte growth while largely maintaining the X chromosome dosage dependence. Near the end of growth phase, however, transcript levels of some X-linked genes did not increase in XY oocytes as much as XX or XO oocytes, rendering their levels much lower than those in XX oocytes. Thus, XY oocytes established a distinct transcriptome at the end of growth phase, which may be associated with abnormal chromatin configuration and mitochondria distribution.

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