Uncovering the transcriptional response of popcorn (Zea mays L. var. everta) under long-term aluminum toxicity

AbstractTo date, the investigation of genes involved in Al resistance has focused mainly on microarrays and short periods of Al exposure. We investigated genes involved in the global response under Al stress by tracking the expression profile of two inbred popcorn lines with different Al sensitivity during 72 h of Al stress. A total of 1003 differentially expressed genes were identified in the Al-sensitive line, and 1751 were identified in the Al-resistant line, of which 273 were shared in both lines. Genes in the category of “response to abiotic stress” were present in both lines, but there was a higher number in the Al-resistant line. Transcription factors, genes involved in fatty acid biosynthesis, and genes involved in cell wall modifications were also detected. In the Al-resistant line, GST6 was identified as one of the key hub genes by co-expression network analysis, and ABC6 may play a role in the downstream regulation of CASP-like 5. In addition, we suggest a class of SWEET transporters that might be involved in the regulation of vacuolar sugar storage and may serve as mechanisms for Al resistance. The results and conclusions expand our understanding of the complex mechanisms involved in Al toxicity and provide a platform for future functional analyses and genomic studies of Al stress in popcorn.

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High-throughput transcriptomic analysis reveals new players in popcorn (Zea mays) aluminum resistance

10.21203/rs.2.15209/v1 ◽

2019 ◽

Author(s):

Vitor Batista Pinto ◽

Priscila Gonçalves Ferreira ◽

Pedro Marcus Pereira Vidigal ◽

Tiago Antônio de Oliveira Mendes ◽

Maximiller Dal-Bianco ◽

...

Keyword(s):

Cell Wall ◽

High Throughput ◽

Defense Response ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Metabolic Process ◽

Differentially Expressed ◽

Resistant Line ◽

Al Stress ◽

Sensitive Line

Abstract BackgroundAt the date, the investigation of genes involved in Al resistance has focused mainly in gene expression profiles based on microarray and in short periods of exposure to Al. Under a long term of Al exposure, such as 72 h, resistance maintenance mechanisms might be created in which several metabolic processes are working simultaneously. To investigate new players involved in defense response under Al stress, we tracked the expression profile of two Al-contrasting popcorn inbreed lines during 72 h under Al-stress using Illumina high-throughput mRNA sequencing technology.ResultsA total of 1,121 differentially expressed genes (DEGs) were identified in the Al-sensitive line and 2,872 DEGs in the Al-resistant line, of which 384 were shared in both lines. Genes categorized in lipid metabolic process and oxidation-reduction were present in both lines, but lipid metabolic process was up-regulated in the Al-resistant line but down-regulated in the Al-sensitive line. The biological process category revealed that the down-regulated genes on the Al-resistant line were involved in signaling. The most significant GO modules were clustered in response to a stimulus. Differentially expressed transporters were also found in both lines, including ABC transporters, Nramp, aquaporins, SWEET transporters, Al-activated malate transporter (ALMT), and multidrug and toxic compound extrusion (MATE). Several transcription factors and genes involved in cell wall modifications were also detected.ConclusionsThe Al-resistant line presented genes that play a role in an efficient oxidative system against ROS, involved in cell wall stiffening and dynamic changes of the cell wall to prevent the Al ion transport via the symplast. Also, we detected transporters belonging to families already known to perform a role in Al-detoxification and organic acid exclusion, and we proposed a class of SWEET transporters that might be involved in regulation of vacuolar sugar storage under Al-stress. Although the exact functions of these genes remain to be investigated, these results provide a platform for functional analysis of the defense response against Al-stress in maize.

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Registered Report: Transcriptional Analysis of Savings Memory Suggests Forgetting Is Due to Retrieval Failure

10.31234/osf.io/h59jv ◽

2020 ◽

Author(s):

Robert Calin-Jageman ◽

Irina Calin-Jageman ◽

Tania Rosiles ◽

Melissa Nguyen ◽

Annette Garcia ◽

...

Keyword(s):

Memory Trace ◽

Aplysia Californica ◽

Transcriptional Response ◽

Transcriptional Analysis ◽

Retrieval Failure ◽

Initial Learning ◽

Rigorous Test ◽

Stage 1 ◽

Induced Changes

[[This is a Stage 2 Registered Report manuscript now accepted for publication at eNeuro. The accepted Stage 1 manuscript is posted here: https://psyarxiv.com/s7dft, and the pre-registration for the project is available here (https://osf.io/fqh8j, 9/11/2019). A link to the final Stage 2 manuscript will be posted after peer review and publication.]] There is fundamental debate about the nature of forgetting: some have argued that it represents the decay of the memory trace, others that the memory trace persists but becomes inaccessible due to retrieval failure. These different accounts of forgetting lead to different predictions about savings memory, the rapid re-learning of seemingly forgotten information. If forgetting is due to decay, then savings requires re-encoding and should thus involve the same mechanisms as initial learning. If forgetting is due to retrieval failure, then savings should be mechanistically distinct from encoding. In this registered report we conducted a pre-registered and rigorous test between these accounts of forgetting. Specifically, we used microarray to characterize the transcriptional correlates of a new memory (1 day after training), a forgotten memory (8 days after training), and a savings memory (8 days after training but with a reminder on day 7 to evoke a long-term savings memory) for sensitization in Aplysia californica (n = 8 samples/group). We found that the re-activation of sensitization during savings does not involve a substantial transcriptional response. Thus, savings is transcriptionally distinct relative to a newer (1-day old) memory, with no co-regulated transcripts, negligible similarity in regulation-ranked ordering of transcripts, and a negligible correlation in training-induced changes in gene expression (r = .04 95% CI [-.12, .20]). Overall, our results suggest that forgetting of sensitization memory represents retrieval failure.

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The long-term bio-behavioural effects of juvenile sildenafil treatment in Sprague-Dawley versus Flinders Sensitive Line rats

Acta Neuropsychiatrica ◽

10.1017/neu.2021.4 ◽

2021 ◽

pp. 1-20

Author(s):

Juandré Lambertus Bernardus Saayman ◽

Stephanus Frederik Steyn ◽

Christiaan Beyers Brink

Keyword(s):

Sprague Dawley ◽

Long Term Effects ◽

Bdnf Level ◽

Treatment Groups ◽

Sd Rats ◽

Behavioural Effects ◽

Sensitive Line ◽

Level Analysis ◽

Flinders Sensitive Line

Abstract Objective: To investigate the long-term effects of juvenile sub-chronic sildenafil (SIL) treatment on the depressive-like behaviour and hippocampal brain-derived neurotrophic factor (BDNF) levels of adult Sprague-Dawley (SD) versus Flinders Sensitive Line (FSL) rats. Methods: SD and FSL rats were divided into pre-pubertal and pubertal groups, whereafter 14-day saline or SIL treatment was initiated. Pre-pubertal and pubertal rats were treated from postnatal day 21 (PND21) and PND35, respectively. The open field and forced swim tests (FST) were performed on PND60, followed by hippocampal BDNF level analysis one day later. Results: FSL rats displayed greater immobility in the FST compared to SD rats (p < 0.0001), which was reduced by SIL (p < 0.0001), regardless of treatment period. Hippocampal BDNF levels were unaltered by SIL in all treatment groups (p > 0.05). Conclusion: Juvenile sub-chronic SIL treatment reduces the risk of depressive-like behaviour manifesting during young adulthood in genetically susceptible rats.

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Root iTRAQ protein profile analysis of two Citrus species differing in aluminum-tolerance in response to long-term aluminum-toxicity

BMC Genomics ◽

10.1186/s12864-015-2133-9 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 30

Author(s):

Huan-Xin Jiang ◽

Lin-Tong Yang ◽

Yi-Ping Qi ◽

Yi-Bin Lu ◽

Zeng-Rong Huang ◽

...

Keyword(s):

Aluminum Toxicity ◽

Profile Analysis ◽

Protein Profile ◽

Aluminum Tolerance ◽

Citrus Species

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The GATA3 X308_Splice breast cancer mutation is a hormone context-dependent oncogenic driver

Oncogene ◽

10.1038/s41388-020-1376-3 ◽

2020 ◽

Vol 39 (32) ◽

pp. 5455-5467

Author(s):

Natascha Hruschka ◽

Mark Kalisz ◽

Maria Subijana ◽

Osvaldo Graña-Castro ◽

Francisco Del Cano-Ochoa ◽

...

Keyword(s):

Breast Cancer ◽

Progesterone Receptors ◽

Transcriptional Response ◽

Molecular Data ◽

Fine Tuning ◽

Driver Mutations ◽

Breast Cancer Patients ◽

Oncogenic Driver ◽

Functional Analyses

Abstract As the catalog of oncogenic driver mutations is expanding, it becomes clear that alterations in a given gene might have different functions and should not be lumped into one class. The transcription factor GATA3 is a paradigm of this. We investigated the functions of the most common GATA3 mutation (X308_Splice) and five additional mutations, which converge into a neoprotein that we called “neoGATA3,” associated with excellent prognosis in patients. Analysis of available molecular data from >3000 breast cancer patients revealed a dysregulation of the ER-dependent transcriptional response in tumors carrying neoGATA3-generating mutations. Mechanistic studies in vitro showed that neoGATA3 interferes with the transcriptional programs controlled by estrogen and progesterone receptors, without fully abrogating them. ChIP-Seq analysis indicated that ER binding is reduced in neoGATA3-expressing cells, especially at distal regions, suggesting that neoGATA3 interferes with the fine tuning of ER-dependent gene expression. This has opposite outputs in distinct hormonal context, having pro- or anti-proliferative effects, depending on the estrogen/progesterone ratio. Our data call for functional analyses of putative cancer drivers to guide clinical application.

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Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance

Frontiers in Microbiology ◽

10.3389/fmicb.2019.01605 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 4

Author(s):

Marcin Jan Szafran ◽

Martyna Gongerowska ◽

Tomasz Małecki ◽

Marie Elliot ◽

Dagmara Jakimowicz

Keyword(s):

Streptomyces Coelicolor ◽

Transcriptional Response

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Afghanistan-US Relations

Oxford Research Encyclopedia of American History ◽

10.1093/acrefore/9780199329175.013.637 ◽

2019 ◽

Author(s):

Paul D. Miller

Keyword(s):

Strategic Partnership ◽

Terrorist Attacks ◽

Short Term ◽

Global Response ◽

The Past ◽

Thrust Front ◽

Past Half Century ◽

Partnership Agreement ◽

Past Half

Afghanistan has twice been thrust front and center of US national security concerns in the past half-century: first, during the Soviet-Afghan War, when Afghanistan served as a proxy for American efforts to combat Soviet influence; and second, as the frontline state and host for America’s global response to al-Qaida’s terrorist attacks of 2001. In both instances, American involvement swung from intensive investment and engagement to withdrawal and neglect. In both cases, American involvement reflected US concerns more than Afghan realities. And both episodes resulted in short-term successes for American security with long-term consequences for Afghanistan and its people. The signing of a strategic partnership agreement between the two countries in 2012 and a bilateral security agreement in 2013 created the possibility of a steadier and more forward-looking relationship—albeit one that the American and Afghan people may be less inclined to pursue as America’s longest war continues to grind on.

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Signet ring gastric and esophageal adenocarcinomas: characteristics and prognostic implications

Diseases of the Esophagus ◽

10.1093/dote/doaa016 ◽

2020 ◽

Vol 33 (11) ◽

Author(s):

Niall Khan ◽

Claire L Donohoe ◽

Alexander W Phillips ◽

S Michael Griffin ◽

John V Reynolds

Keyword(s):

Oncological Outcome ◽

High Volume ◽

Tumor Location ◽

Curative Intent ◽

Signet Ring ◽

Genomic Studies ◽

Prognostic Implications ◽

Long Term Prognosis ◽

Esophagogastric Adenocarcinoma

Summary Controversy exists as to the relevance of the signet ring carcinoma (SRC) histological subtype of esophagogastric adenocarcinoma to long-term prognosis, with some studies reporting a worsened oncological outcome and others no clinically relevant impact. A retrospective analysis of outcomes of patients who underwent surgery with curative intent in two high-volume centers (2000–2015) was undertaken. Tumors were analyzed according to location (esophageal, junctional or gastric). Propensity score matching (PSM) analysis was used to match patients with signet ring histology to those without (195 SRC vs. 573 non-SRC), based on age, tumor location, use of neoadjuvant and adjuvant chemotherapy and pathological stage. A total of 2,500 patients with esophagogastric adenocarcinomas were treated, of whom 198 (7.9%) had signet ring histology. Signet ring tumors were more likely to have positive lymph nodes at pathological analysis (59% vs. 50%, P = 0.009). The 5-year survival rate for patients with early signet ring tumors (Stage 0/I/IIa) was 65% versus 85% for other early cancers (P < 0.003). Patients with esophageal signet ring tumors had a particularly poor prognosis with 23% 2-year survival and none alive at 5 years. With PSM, overall survival (OS) was significantly poorer in the signet ring group (44.3 ± 8.6 vs. 59.8 ± 8.5 months, 5-year OS 41% vs. 50%, P = 0.027). Signet ring cells within esophagogastric adenocarcinoma are associated with a poorer prognosis. Genomic studies to identify the composition of such tumors as well as identify strategies to improve treatment for this subtype are warranted.

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