Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica)

Quantitative phosphoproteome and transcriptome analysisof ligand-stimulated MCF-7 human breast cancer cells wasperformed to understand the mechanisms of tamoxifen resistanceat a system level. Phosphoproteome data revealed thatWT cells were more enriched with phospho-proteins thantamoxifen-resistant cells after stimulation with ligands.Surprisingly, decreased phosphorylation after ligand perturbationwas more common than increased phosphorylation.In particular, 17?-estradiol induced down-regulation inWT cells at a very high rate. 17?-Estradiol and the ErbBligand heregulin induced almost equal numbers of up-regulatedphospho-proteins in WT cells. Pathway and motifactivity analyses using transcriptome data additionallysuggested that deregulated activation of GSK3? (glycogensynthasekinase 3?) and MAPK1/3 signaling might be associatedwith altered activation of cAMP-responsive elementbindingprotein and AP-1 transcription factors intamoxifen-resistant cells, and this hypothesis was validatedby reporter assays. An examination of clinical samples revealedthat inhibitory phosphorylation of GSK3? at serine 9was significantly lower in tamoxifen-treated breast cancerpatients that eventually had relapses, implying that activationof GSK3? may be associated with the tamoxifen-resistantphenotype. Thus, the combined phosphoproteomeand transcriptome data set analyses revealed distinct signal

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Faculty Opinions recommendation of Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718022014.793479111 ◽

2013 ◽

Author(s):

Julin Maloof

Keyword(s):

Population Genomics ◽

Transcriptome Data ◽

Next Generation

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Faculty Opinions recommendation of The dynamics of strigolactone perception in Striga hermonthica : a working hypothesis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.732740367.793543152 ◽

2018 ◽

Author(s):

Peter McCourt

Keyword(s):

Striga Hermonthica ◽

Working Hypothesis

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Evaluation of Sorghum Genotypes for Tolerance to Striga hermonthica (Del.) Benth. (Lamiales: Orobanchaceae) and Yield in the Rain Fed Areas of Damazin, Sudan

International Journal of Life-Sciences Scientific Research ◽

10.21276/ijlssr.2017.3.3.7 ◽

2017 ◽

Vol 3 (3) ◽

Author(s):

Evans Jimmy Kenyi ◽

Abdel Gabbar El Tayib Babikri ◽

Siraj Mohammed Omer ◽

Philip Wani Marchelo-D’Ragga

Keyword(s):

Striga Hermonthica ◽

Sorghum Genotypes

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Comparative transcriptomic and metabolomic analyses of carotenoid biosynthesis reveal the basis of white petal color in Brassica napus

Planta ◽

10.1007/s00425-020-03536-6 ◽

2021 ◽

Vol 253 (1) ◽

Author(s):

Ledong Jia ◽

Junsheng Wang ◽

Rui Wang ◽

Mouzheng Duan ◽

Cailin Qiao ◽

...

Keyword(s):

Brassica Napus ◽

Molecular Mechanisms ◽

Flower Color ◽

Carotenoid Biosynthesis ◽

Differentially Expressed ◽

Transcriptome Data ◽

Oilseed Crops ◽

Qrt Pcr ◽

Carotenoid Metabolism ◽

Rapeseed Cultivar

Abstract Main conclusion The molecular mechanism underlying white petal color in Brassica napus was revealed by transcriptomic and metabolomic analyses. Abstract Rapeseed (Brassica napus L.) is one of the most important oilseed crops worldwide, but the mechanisms underlying flower color in this crop are known less. Here, we performed metabolomic and transcriptomic analyses of the yellow-flowered rapeseed cultivar ‘Zhongshuang 11’ (ZS11) and the white-flowered inbred line ‘White Petal’ (WP). The total carotenoid contents were 1.778-fold and 1.969-fold higher in ZS11 vs. WP petals at stages S2 and S4, respectively. Our findings suggest that white petal color in WP flowers is primarily due to decreased lutein and zeaxanthin contents. Transcriptome analysis revealed 10,116 differentially expressed genes with a fourfold or greater change in expression (P-value less than 0.001) in WP vs. ZS11 petals, including 1,209 genes that were differentially expressed at four different stages and 20 genes in the carotenoid metabolism pathway. BnNCED4b, encoding a protein involved in carotenoid degradation, was expressed at abnormally high levels in WP petals, suggesting it might play a key role in white petal formation. The results of qRT-PCR were consistent with the transcriptome data. The results of this study provide important insights into the molecular mechanisms of the carotenoid metabolic pathway in rapeseed petals, and the candidate genes identified in this study provide a resource for the creation of new B. napus germplasms with different petal colors.

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Blood transcriptome analysis of patients with uncomplicated bacterial infection and sepsis

BMC Research Notes ◽

10.1186/s13104-021-05488-w ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Velma Herwanto ◽

Benjamin Tang ◽

Ya Wang ◽

Maryam Shojaei ◽

Marek Nalos ◽

...

Keyword(s):

Bacterial Infection ◽

Healthy Controls ◽

Beta Globin ◽

Transcriptome Data ◽

Valuable Resource ◽

Globin Mrna ◽

Blood Samples ◽

Data Description ◽

Pathway Activation ◽

Blood Transcriptome

Abstract Objectives Hospitalized patients who presented within the last 24 h with a bacterial infection were recruited. Participants were assigned into sepsis and uncomplicated infection groups. In addition, healthy volunteers were recruited as controls. RNA was prepared from whole blood, depleted from beta-globin mRNA and sequenced. This dataset represents a highly valuable resource to better understand the biology of sepsis and to identify biomarkers for severe sepsis in humans. Data description The data presented here consists of raw and processed transcriptome data obtained by next generation RNA sequencing from 105 peripheral blood samples from patients with uncomplicated infections, patients who developed sepsis, septic shock patients, and healthy controls. It is provided as raw sequenced reads and as normalized log2 transformed relative expression levels. This data will allow performing detailed analyses of gene expression changes between uncomplicated infections and sepsis patients, such as identification of differentially expressed genes, co-regulated modules as well as pathway activation studies.

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Constraints to Pearl Millet (Pennisetum glaucum) Production and Farmers’ Approaches to Striga hermonthica Management in Burkina Faso

Sustainability ◽

10.3390/su13158460 ◽

2021 ◽

Vol 13 (15) ◽

pp. 8460

Author(s):

Armel Rouamba ◽

Hussein Shimelis ◽

Inoussa Drabo ◽

Mark Laing ◽

Prakash Gangashetty ◽

...

Keyword(s):

Burkina Faso ◽

Pearl Millet ◽

Management Practices ◽

Pennisetum Glaucum ◽

Control Measures ◽

Striga Hermonthica ◽

Soil Conditions ◽

Management Options ◽

Central Plateau ◽

South Central

Pearl millet (Pennisetum glaucum) is a staple food crop in Burkina Faso that is widely grown in the Sahelian and Sudano-Sahelian zones, characterised by poor soil conditions and erratic rainfall, and high temperatures. The objective of this study was to document farmers’ perceptions of the prevailing constraints affecting pearl millet production and related approaches to manage the parasitic weeds S. hermonthica. The study was conducted in the Sahel, Sudano-Sahelian zones in the North, North Central, West Central, Central Plateau, and South Central of Burkina Faso. Data were collected through a structured questionnaire and focus group discussions involving 492 participant farmers. Recurrent drought, S. hermonthica infestation, shortage of labour, lack of fertilisers, lack of cash, and the use of low-yielding varieties were the main challenges hindering pearl millet production in the study areas. The majority of the respondents (40%) ranked S. hermonthica infestation as the primary constraint affecting pearl millet production. Respondent farmers reported yield losses of up to 80% due to S. hermonthica infestation. 61.4% of the respondents in the study areas had achieved a mean pearl millet yields of <1 t/ha. Poor access and the high cost of introduced seed, and a lack of farmers preferred traits in the existing introduced pearl millet varieties were the main reasons for their low adoption, as reported by 32% of respondents. S. hermonthica management options in pearl millet production fields included moisture conservation using terraces, manual hoeing, hand weeding, use of microplots locally referred to as ‘zaï’, crop rotation and mulching. These management techniques were ineffective because they do not suppress the below ground S. hermonthica seed, and they are difficult to implement. Integrated management practices employing breeding for S. hermonthica resistant varieties with the aforementioned control measures could offer a sustainable solution for S. hermonthica management and improved pearl millet productivity in Burkina Faso.

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Noni fruit’s water spot appearance on the second day of harvest: a trade-off between resistance and energy

Chemical and Biological Technologies in Agriculture ◽

10.1186/s40538-020-00207-2 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Tian Wu ◽

Danyan Hu ◽

Qingfen Wang

Keyword(s):

Statistical Analysis ◽

Molecular Level ◽

Morinda Citrifolia ◽

Transcriptome Data ◽

Trade Off ◽

Kegg Pathways ◽

Available Energy ◽

Climacteric Fruit ◽

The Relationship ◽

Insight Into

Abstract Background Noni (Morinda citrifolia Linn.) is a tropical tree that bears climacteric fruit. Previous observations and research have shown that the second day (2 d) after harvest is the most important demarcation point when the fruit has the same appearance as the freshly picked fruit (0 d); however, they are beginning to become water spot appearance. We performed a conjoint analysis of metabolome and transcriptome data for noni fruit of 0 d and 2 d to reveal what happened to the fruit at the molecular level. Genes and metabolites were annotated to KEGG pathways and the co-annotated KEGG pathways were used as a statistical analysis. Results We found 25 pathways that were significantly altered at both metabolic and transcriptional levels, including a total of 285 differentially expressed genes (DEGs) and 11 differential metabolites through an integrative analysis of transcriptomics and metabolomics. The energy metabolism and pathways originating from phenylalanine were disturbed the most. The upregulated resistance metabolites and genes implied the increase of resistance and energy consumption in the postharvest noni fruit. Most genes involved in glycolysis were downregulated, further limiting the available energy. This lack of energy led noni fruit to water spot appearance, a prelude to softening. The metabolites and genes related to the resistance and energy interacted and restricted each other to keep noni fruit seemingly hard within two days after harvest, but actually the softening was already unstoppable. Conclusions This study provides a new insight into the relationship between the metabolites and genes of noni fruit, as well as a foundation for further clarification of the post-ripening mechanism in noni fruit.

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