scholarly journals Unraveling the role of male reproductive tract and haemolymph in cantharidin-exuding Lydus trimaculatus and Mylabris variabilis (Coleoptera: Meloidae): a comparative transcriptomics approach

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Emiliano Fratini ◽  
Marco Salvemini ◽  
Fabrizio Lombardo ◽  
Maurizio Muzzi ◽  
Marco Molfini ◽  
...  
Keyword(s):  
Reproductive Tract ◽  
De Novo ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Fluid Loss ◽  
Male Reproductive Tract ◽  
Reflex Bleeding ◽  
Accessory Glands ◽  
Conserved Genes ◽  
Blister Beetle

Abstract Background Meloidae (blister beetles) are known to synthetize cantharidin (CA), a toxic and defensive terpene mainly stored in male accessory glands (MAG) and emitted outward through reflex-bleeding. Recent progresses in understanding CA biosynthesis and production organ(s) in Meloidae have been made, but the way in which self-protection is achieved from the hazardous accumulation and release of CA in blister beetles has been experimentally neglected. To provide hints on this pending question, a comparative de novo assembly transcriptomic approach was performed by targeting two tissues where CA is largely accumulated and regularly circulates in Meloidae: the male reproductive tract (MRT) and the haemolymph. Differential gene expression profiles in these tissues were examined in two blister beetle species, Lydus trimaculatus (Fabricius, 1775) (tribe Lyttini) and Mylabris variabilis (Pallas, 1781) (tribe Mylabrini). Upregulated transcripts were compared between the two species to identify conserved genes possibly involved in CA detoxification and transport. Results Based on our results, we hypothesize that, to avoid auto-intoxication, ABC, MFS or other solute transporters might sequester purported glycosylated CA precursors into MAG, and lipocalins could bind CA and mitigate its reactivity when released into the haemolymph during the autohaemorrhaging response. We also found an over-representation in haemolymph of protein-domains related to coagulation and integument repairing mechanisms that likely reflects the need to limit fluid loss during reflex-bleeding. Conclusions The de novo assembled transcriptomes of L. trimaculatus and M. variabilis here provided represent valuable genetic resources to further explore the mechanisms employed to cope with toxicity of CA in blister beetle tissues. These, if revealed, might help conceiving safe and effective drug-delivery approaches to enhance the use of CA in medicine.

scholarly journals De Novo Transcriptome Study Identifies Candidate Genes Involved in Resistance to Austropuccinia psidii (Myrtle Rust) in Syzygium luehmannii (Riberry)

2018 ◽  
Vol 108 (5) ◽  
pp. 627-640 ◽  
Author(s):  
Peri A. Tobias ◽  
David I. Guest ◽  
Carsten Külheim ◽  
Robert F. Park
Keyword(s):  
De Novo ◽  
Expression Profiles ◽  
Interleukin 1 ◽  
Gene Expression Profiles ◽  
Early Gene ◽  
De Novo Transcriptome ◽  
Myrtle Rust ◽  
Wide Range ◽  
The Family ◽  
Austropuccinia Psidii

Austropuccinia psidii, causal agent of myrtle rust, was discovered in Australia in 2010 and has since become established on a wide range of species within the family Myrtaceae. Syzygium luehmannii, endemic to Australia, is an increasingly valuable berry crop. Plants were screened for responses to A. psidii inoculation, and specific resistance, in the form of localized necrosis, was determined in 29% of individuals. To understand the molecular basis underlying this response, mRNA was sequenced from leaf samples taken preinoculation, and at 24 and 48 h postinoculation, from four resistant and four susceptible plants. Analyses, based on de novo transcriptome assemblies for all plants, identified significant expression changes in resistant plants (438 transcripts) 48 h after pathogen exposure compared with susceptible plants (three transcripts). Most significantly up-regulated in resistant plants were gene homologs for transcription factors, receptor-like kinases, and enzymes involved in secondary metabolite pathways. A putative G-type lectin receptor-like kinase was exclusively expressed in resistant individuals and two transcripts incorporating toll/interleukin-1, nucleotide binding site, and leucine-rich repeat domains were up-regulated in resistant plants. The results of this study provide the first early gene expression profiles for a plant of the family Myrtaceae in response to the myrtle rust pathogen.

Gene Expression Profiles in Acute Myeloid Leukemia (AML): From Diagnosis to Prognosis.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2996-2996
Author(s):  
Sanggyu Lee ◽  
Jianjun Chen ◽  
Goulin Zhou ◽  
Run Shi ◽  
Masha Kocherginsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Major Change ◽  
Molecular Signature ◽  
Human Leukemia ◽  
Prognostic Information ◽  
Myeloid Progenitor Cells ◽  
Novel Transcripts

Abstract Chromosome translocations are among the most common genetic abnormalities in human leukemia. The abnormally expressed genes from each translocation can be used to identify specific markers for clinical diagnosis of each translocation. Microarrays have identified genes differentially expressed in different translocations but the results between laboratories are not always compatible. We used SAGE to quantitate gene expression in bone marrow(BM) samples from 22 patients with four types of AML, [de novo AML M2 with t(8;21), AML M3 or M3V with t(15;17), AML M4Eo with inv(16), AML M5 with t(9;11) or secondary t(9;11)].We made SAGE libraries from CD15+ leukemic myeloid progenitor cells, collecting over 106 SAGE tags, of which 209,486 were unique tags; 136,010 were known genes and ESTs, and 73,476 were novel transcripts. SAGE tags for further analysis were selected based on a 5-fold difference between patient’s samples and normal CD15+ BM; they were also statistically significantly different at the 5% level. Using these strict criteria, we identified 2,381 unique tags, of which 2,053 were known genes and ESTs, and 328 were novel transcripts that were either specific for each translocation or were common(55) SAGE tags for all 4 translocations. The major change in all translocations was a decrease in expression in leukemia cells compared with normal cells; the decrease was least in the t(8;21) cells. Changes in expression of these known genes, which fall into different gene ontology functional categories, varied by translocation. Those associated with macromolecular biosynthesis, transport and transcription were most altered in the t(8;21); those related to defense response and apoptosis were altered in the t(15;17); cell proliferation genes were most affected by the t(9;11). From this analysis, we identified the functional molecular signature of each translocation. We designed a custom microarray to validate our SAGE data analysis. Our initial microarray contained 349 probes including 212 known genes, 61 ESTs, 28 novel sequences based on our data and 48 genes reported by others. We have now included 65 additional probes that appeared to be correlated with survival. Using 63 samples with the four translocations [16 inv(16), 4 t(9;11), 20 t(15;17), 4 t(8;21) and 19 other translocations], we are validating which genes provide a robust, reproducible “fingerprint” for each translocation, for all translocations, and which ones provide reliable information related to prognosis and survival. Our results will provide new insights into genes that collaborate with each translocation to lead to a fully leukemic phenotype as well as which genes appear to provide valid prognostic information.

scholarly journals Gammaherpesvirus Lytic Gene Expression as Characterized by DNA Array

2002 ◽  
Vol 76 (12) ◽  
pp. 6244-6256 ◽  
Author(s):  
Joo Wook Ahn ◽  
Kenneth L. Powell ◽  
Paul Kellam ◽  
Dagmar G. Alber
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Expression Profiles ◽  
Cdna Array ◽  
Gene Expression Profiles ◽  
Hierarchical Cluster ◽  
Murine Gammaherpesvirus ◽  
Transcription Profiles ◽  
A Genome

ABSTRACT Gammaherpesviruses are associated with a number of diseases including lymphomas and other malignancies. Murine gammaherpesvirus 68 (MHV-68) constitutes the most amenable animal model for this family of pathogens. However experimental characterization of gammaherpesvirus gene expression, at either the protein or RNA level, lags behind that of other, better-studied alpha- and beta-herpesviruses. We have developed a cDNA array to globally characterize MHV-68 gene expression profiles, thus providing an experimental supplement to a genome that is chiefly annotated by homology. Viral genes started to be transcribed as early as 3 h postinfection (p.i.), and this was followed by a rapid escalation of gene expression that could be seen at 5 h p.i. Individual genes showed their own transcription profiles, and most genes were still being expressed at 18 h p.i. Open reading frames (ORFs) M3 (chemokine-binding protein), 52, and M9 (capsid protein) were particularly noticeable due to their very high levels of expression. Hierarchical cluster analysis of transcription profiles revealed four main groups of genes and allowed functional predictions to be made by comparing expression profiles of uncharacterized genes to those of genes of known function. Each gene was also categorized according to kinetic class by blocking de novo protein synthesis and viral DNA replication in vitro. One gene, ORF 73, was found to be expressed with α-kinetics, 30 genes were found to be expressed with β-kinetics, and 42 genes were found to be expressed with γ-kinetics. This fundamental characterization furthers the development of this model and provides an experimental basis for continued investigation of gammaherpesvirus pathology.

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

scholarly journals Comprehensive Clinical and Molecular Characterization of KRASG12C-Mutant Colorectal Cancer

2021 ◽  
pp. 613-621
Author(s):  
Jason T. Henry ◽  
Oluwadara Coker ◽  
Saikat Chowdhury ◽  
John Paul Shen ◽  
Van K. Morris ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Trials ◽  
De Novo ◽  
Expression Profiles ◽  
Single Gene ◽  
Gene Expression Profiles ◽  
Progression Free Survival ◽  
Cancer Center ◽  
Data Set ◽  
External Data

PURPOSE KRAS p.G12C mutations occur in approximately 3% of metastatic colorectal cancers (mCRC). Recently, two allosteric inhibitors of KRAS p.G12C have demonstrated activity in early phase clinical trials. There are no robust studies examining the behavior of this newly targetable population. METHODS We queried the MD Anderson Cancer Center data set for patients with colorectal cancer who harbored KRAS p.G12C mutations between January 2003 and September 2019. Patients were analyzed for clinical characteristics, overall survival (OS), and progression-free survival (PFS) and compared against KRAS nonG12C. Next, we analyzed several internal and external data sets to assess immune signatures, gene expression profiles, hypermethylation, co-occurring mutations, and proteomics. RESULTS Among the 4,632 patients with comprehensive molecular profiling, 134 (2.9%) were found to have KRAS p.G12C mutations. An additional 53 patients with single gene sequencing were included in clinical data but excluded from prevalence analysis allowing for 187 total patients. Sixty-five patients had de novo metastatic disease and received a median of two lines of chemotherapy without surgical intervention. For the first three lines of chemotherapy, the median PFS was 6.4 months (n = 65; 95% CI, 5.0 to 7.4 months), 3.9 months (n = 47; 95% CI, 2.9 to 5.9 months), and 3.0 months (n = 21; 95% CI, 2.0 to 3.4 months), respectively. KRAS p.G12C demonstrated higher rates of basal EGFR activation compared with KRAS nonG12C. When compared with an internal cohort of KRAS nonG12C, KRAS p.G12C patients had worse OS. CONCLUSION PFS is poor for patients with KRAS p.G12C metastatic colorectal cancer. OS was worse in KRAS p.G12C compared with KRAS nonG12C patients. Our data highlight the innate resistance to chemotherapy for KRAS p.G12C patients and serve as a historical comparator for future clinical trials.

Co-Expression of BAALC with ERG, TCF4, and CD133 Indicates a Shared Pathway in Acute Myeloid and Lymphoblastic Leukemia.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2755-2755 ◽  
Author(s):  
Claudia D. Baldus ◽  
Michael Radmacher ◽  
Guido Marcucci ◽  
Dieter Hoelzer ◽  
Eckhard Thiel ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Expression Profiles ◽  
Lymphoblastic Leukemia ◽  
Gene Expression Profiles ◽  
Newly Diagnosed ◽  
Time Points ◽  
Normal Cytogenetics ◽  
Acute Myeloid

Abstract The human gene BAALC (Brain And Acute Leukemia, Cytoplasmic) is a molecular marker of hematopoietic progenitor cells and is aberrantly expressed in subsets of acute myeloid (AML) and lymphoblastic (ALL) leukemias. High mRNA expression levels of BAALC have been shown to adversely impact outcome in newly diagnosed AML patients (pts) with normal cytogenetics. To gain insight into the functional role of BAALC and its significance to normal hematopoiesis and leukemogenesis we compared gene expression profiles of normal CD34+ progenitors with those of AML and ALL blasts (using oligonucleotide microarrays; HG-U133 plus 2.0, Affymetrix, Santa Clara, CA). First we explored the regulation of BAALC expression during lineage specific maturation of in vitro differentiated human CD34+ bone marrow cells selected from healthy individuals. Microarray analyses were carried out using CD34+ cells stimulated in vitro with EPO, TPO, or G/GM-CSF to induce lineage-specific differentiation. At day 0 of culture and at three different time points during differentiation (days 4, 7, 11) cells were harvested, and if necessary purified by immunomagnetic beads and used for microarray studies. Experiments of all lineages and time points were done in triplicates. A total of 276 genes were identified showing similar changes in expression (with downregulation during differentiation) as BAALC at the three time points in all lineages with a correlation coefficient of R>0.95. This set of 276 BAALC co-expressed genes was investigated in an AML expression dataset generated from 51 adult pts with newly diagnosed de novo AML and normal cytogenetics (Cancer and Leukemia Group B). After exclusion of probesets expressed in fewer than 20% of pt samples, 21 probesets representing 14 named genes 6 of which are known to be involved in AML (BAALC, CD34, CD133, SOX4, ERG, SEPT6) and 4 implicated in lymphoid development (TCF4, SH2D1A, ITM2A, ITM2C) were found to be overexpressed (a significance level of P=0.01 was used) in pts of the highest third compared to pts of the lowest third of BAALC expression values as measured by real-time RT-PCR. We next applied these same 21 BAALC co-expressed probesets to an ALL expression dataset generated from 66 adult pts with newly diagnosed standard risk B-lineage precursor ALL (from the German ALL GMALL study group). A BAALC specific cluster uncovered 7 probesets representing 4 different co-expressed genes: BAALC, CD133, and the transcription factors ERG and TCF4. Thus, applying a BAALC specific expression signature to AML and ALL gene expression profiles revealed 3 genes (CD133, ERG, TCF4), which are highly associated with BAALC in myeloid and lymphoid blasts. Interestingly in non-malignant lymphoid and myeloid cells the oncogeneic ETS transcription factor ERG has shown specificity to immature cells, while its mechanistical role in leukemogenesis remains unknown. ERG and TCF4 may directly regulate BAALC and indicate a specific pathway implicated in leukemogenesis, while co-expression of CD133 and BAALC suggests shared stem cell characteristics. Functional studies are in progress to further explore these findings.

Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks

2004 ◽  
Vol 16 (2) ◽  
pp. 247-255 ◽  
Author(s):  
Matthew S. Wong ◽  
R. Michael Raab ◽  
Isidore Rigoutsos ◽  
Gregory N. Stephanopoulos ◽  
Joanne K. Kelleher
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Dna Microarrays ◽  
Cell Function ◽  
De Novo ◽  
Expression Profiles ◽  
Mammalian Cell Culture ◽  
Gene Expression Profiles ◽  
Tca Cycle ◽  
Glycolytic Flux

An important objective in postgenomic biology is to link gene expression to function by developing physiological networks that include data from the genomic and functional levels. Here, we develop a model for the analysis of time-dependent changes in metabolites, fluxes, and gene expression in a hepatic model system. The experimental framework chosen was modulation of extracellular glutamine in confluent cultures of mouse Hepa1-6 cells. The importance of glutamine has been demonstrated previously in mammalian cell culture by precipitating metabolic shifts with glutamine depletion and repletion. Our protocol removed glutamine from the medium for 24 h and returned it for a second 24 h. Flux assays of glycolysis, the tricarboxylic acid (TCA) cycle, and lipogenesis were used at specified intervals. All of these fluxes declined in the absence of glutamine and were restored when glutamine was repleted. Isotopomer spectral analysis identified glucose and glutamine as equal sources of lipogenic carbon. Metabolite measurements of organic acids and amino acids indicated that most metabolites changed in parallel with the fluxes. Experiments with actinomycin D indicated that de novo mRNA synthesis was required for observed flux changes during the depletion/repletion of glutamine. Analysis of gene expression data from DNA microarrays revealed that many more genes were anticorrelated with the glycolytic flux and glutamine level than were correlated with these indicators. In conclusion, this model may be useful as a prototype physiological regulatory network where gene expression profiles are analyzed in concert with changes in cell function.

Morphometry of the testis follicles in Triatoma rubrofasciata (De Geer, 1773) (Hemiptera, Triatominae)

2007 ◽  
Vol 57 (4) ◽  
pp. 393-400 ◽  
Author(s):  
Teresa Cristina Monte Gonçalves ◽  
Simone Patrícia Carneiro Freitas ◽  
Jacenir Reis Dos Santos-Mallet ◽  
José Eduardo Serrão ◽  
Elias Seixas Lorosa
Keyword(s):  
Phylogenetic Analysis ◽  
Reproductive Tract ◽  
Common Ancestor ◽  
Ejaculatory Duct ◽  
Seminal Vesicles ◽  
Male Reproductive Tract ◽  
Accessory Glands ◽  
Morphometrical Analysis ◽  
Left And Right ◽  
Triatoma Rubrofasciata

AbstractThe male reproductive tract in Triatominae has a pair of testes, two vasa deferentia, a pair of seminal vesicles, four pairs of accessory glands, and an ejaculatory duct, which opens in the aedeagus. In species of the genus Triatoma each testis is formed by seven testicular follicles. Because Triatoma rubrofasciata has a common ancestor with species of Triatoma occurring in North America and because the length of testis follicles varies among different species of Triatoma a morphometrical analysis of the follicles was conducted. Triatoma rubrofasciata has seven testis follicles of variable length that are similar between left and right testes. The statistics allowed the classification in a long follicle, two medium follicles, two that are short, and two that are very short. This finding is compared with data available for other Triatominae and it is emphasized that the length of follicles testis should be included in future phylogenetic analysis of Triatominae.

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