scholarly journals Sex-Biased Gene Expression of Mesobuthus martensii Collected from Gansu Province, China, Reveals Their Different Therapeutic Potentials

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Songyu Gao ◽  
Feng Wu ◽  
Xintong Chen ◽  
Ying Yang ◽  
Yina Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Proteinase Inhibitors ◽  
Cysteine Proteinase ◽  
Gansu Province ◽  
Differentially Expressed ◽  
Sexually Dimorphic ◽  
Significant Differential Expression ◽  
Therapeutic Drugs ◽  
The Difference

The scorpions, named Mesobuthus martensii, commonly called Quanxie (全蝎) in Chinese, have been widely used as one of the animal medicines for more than 1,000 years because of the strong toxicity of their venoms. Meanwhile, scorpions are sexually dimorphic in appearance, and many exhibit traits associated with sex-biased gene expression, including maternal care, mating competition, female mating choices, ecology, and even venom composition and lethality. This study aims to explore the differences in composition of the venom of scorpions of different sex using the method of transcriptomics. Whole de novo transcriptomes were performed on the samples of M. martensii captured from Gansu Province to identify their sex-biased gene expression. The conserved CO-1 sequences of the captured samples matched that of M. martensii. A total of 8,444 (35.15%), 7,636 (31.78%), 8,510 (35.42%), 7,840 (32.63%), 9,980 (41.54%), and 11,829 (49.23%) unigenes were annotated with GO, KEGG, Pfam, Swissprot, eggNOG, and NR databases. Moreover, a total of 43 metalloproteases, 40 potassium channel toxins, 24 phospholipases, 12 defensins, 10 peroxiredoxins, 9 cysteine proteinase inhibitors, 7 serine protease inhibitors, 6 sodium channel toxins, 2 NDBPs, 1 calcium channel toxin, 1 waprin-like peptide, 1 antibacterial peptide, 1 antimicrobial peptide, and 1 anticoagulant peptide were screened out. With the fold change of 2 and 0.5, p value < 0.01, and q value < 0.05 as thresholds, a total of 41 out of 157 (26.11%) toxin-related unigenes had significant differential expression, and this ratio was much higher than the ratio of differentially expressed unigenes out of all annotated ones (8.84%). Of these differentially expressed toxins, 28 were upregulated and occupied the majority, up to 68.30%. The female scorpions showed more upregulated unigenes that annotated with toxins and had the potential to be used as more effective therapeutic drugs. In addition, this method of omics can be further used as a useful way to identify the difference between female and male toxic animals.

scholarly journals Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2273
Author(s):  
Menelaos Kavouras ◽  
Emmanouil E. Malandrakis ◽  
Ewout Blom ◽  
Kyriaki Tsilika ◽  
Theodoros Danis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
De Novo ◽  
Close Association ◽  
Ionic Channels ◽  
Long Term Potentiation ◽  
General Term ◽  
The Difference ◽  
Common Sole

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.

scholarly journals De NovoTranscriptome Assembly and Differential Gene Expression Profiling of ThreeCapra hircusSkin Types during Anagen of the Hair Growth Cycle

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Teng Xu ◽  
Xudong Guo ◽  
Hui Wang ◽  
Xiaoyuan Du ◽  
Xiaoyu Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
De Novo ◽  
Growth Cycle ◽  
Hair Shaft ◽  
Hair Follicles ◽  
Differentially Expressed ◽  
Kegg Pathway Database ◽  
Anagen Phase

Despite that goat is one of the best nonmodel systems for villus growth studies and hair biology, limited gene resources associated with skin or hair follicles are available. In the present study, using Illumina/Solexa sequencing technology, wede novoassembled 130 million mRNA-Seq reads into a total of 49,115 contigs. Searching public databases revealed that about 45% of the total contigs can be annotated as known proteins, indicating that some of the assembled contigs may have previously uncharacterized functions. Functional classification by KOG and GO showed that activities associated with metabolism are predominant in goat skin during anagen phase. Many signaling pathways was also created based on the mapping of assembled contigs to the KEGG pathway database, some of which have been previously demonstrated to have diverse roles in hair follicle and hair shaft formation. Furthermore, gene expression profiling of three skin types identified ~6,300 transcript-derived contigs that are differentially expressed. These genes mainly enriched in the functional cluster associated with cell cycle and cell division. The large contig catalogue as well as the genes which were differentially expressed in different skin types provide valuable candidates for further characterization of gene functions.

scholarly journals HIV-1–infected dendritic cells show 2 phases of gene expression changes, with lysosomal enzyme activity decreased during the second phase

Blood ◽  
2009 ◽  
Vol 114 (1) ◽  
pp. 85-94 ◽  
Author(s):  
Andrew N. Harman ◽  
Marianne Kraus ◽  
Chris R. Bye ◽  
Karen Byth ◽  
Stuart G. Turville ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dendritic Cells ◽  
Antigen Processing ◽  
De Novo ◽  
Cathepsin L ◽  
Transcriptional Response ◽  
Differentially Expressed ◽  
Second Phase ◽  
Genes Encoding ◽  
Hiv 1

AbstractDendritic cells (DCs) play a key role in the pathogenesis of HIV infection. HIV interacts with these cells through 2 pathways in 2 temporal phases, initially via endocytosis and then via de novo replication. Here the transcriptional response of human DCs to HIV-1 was studied in these phases and at different stages of the virus replication cycle using purified HIV-1 envelope proteins, and inactivated and viable HIV-1. No differential gene expression was detected in response to envelope. However, more than 100 genes were differentially expressed in response to entry of viable and inactivated HIV-1 in the first phase. A completely different set of genes was differentially expressed in the second phase, predominantly in response to viable HIV-1, including up-regulation of immune regulation genes, whereas genes encoding lysosomal enzymes were down-regulated. Cathepsins B, C, S, and Z RNA and protein decreased, whereas cathepsin L was increased, probably reflecting a concomitant decrease in cystatin C. The net effect was markedly diminished cathepsin activity likely to result in enhanced HIV-1 survival and transfer to contacting T lymphocytes but decreased HIV-1 antigen processing and presentation to these T cells.

scholarly journals hnRNP U is differentially expressed in whole blood from patients with sepsis.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Whole Blood ◽  
Differentially Expressed ◽  
Significant Differential Expression ◽  
Hnrnp U ◽  
Significant Gene ◽  
Nuclear Ribonucleoprotein ◽  
Microarray Datasets

We probed published and public microarray datasets (1, 2) to discover the most significant gene expression changes in the blood of patients with sepsis. We identified significant differential expression of the heterogenous nuclear ribonucleoprotein hnRNP U in whole blood from patients with sepsis.

scholarly journals Leishmania infection induces a limited differential gene expression in the sand fly midgut

2020 ◽  
Author(s):  
Iliano V. Coutinho-Abreu ◽  
Tiago D. Serafim ◽  
Claudio Meneses ◽  
Shaden Kamhawi ◽  
Fabiano Oliveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Early Time ◽  
Differentially Expressed ◽  
Sand Fly ◽  
Leishmania Infection ◽  
Lutzomyia Longipalpis ◽  
Late Time ◽  
Time Points

Abstract Background: Phlebotomine sand flies are the vectors of Leishmania worldwide. To develop in the sand fly midgut, Leishmania multiplies and undergoes multiple stage differentiations leading to the infective form, the metacyclic promastigotes. To gain a better understanding of the influence of Leishmania infection on midgut gene expression, we performed RNA-Seq comparing uninfected and Leishmania infantum -infected Lutzomyia longipalpis midguts at seven time points which cover the various Leishmania developmental stages including early time points when blood digestion is taking place, and late time points when the parasites are undergoing metacyclogenesis. Results: Out of over 13,841 transcripts assembled de novo , only 113 sand fly transcripts, about 1%, were differentially expressed. Further, we observed a low overlap of differentially expressed sand fly transcripts across different time points suggesting that each Leishmania stage influences midgut gene expression in a specific manner. Two main patterns of sand fly gene expression modulation were noted. At early time points (days 1-4), more transcripts were down-regulated by Leishmania infection at large fold changes (> -32 fold). Among the down-regulated genes, the transcription factor Forkhead/HNF-3 and hormone degradation enzymes were differentially regulated on day 4 and appear to be the upstream regulators of nutrient transport, digestive enzymes, and peritrophic matrix proteins. Conversely, at later time points (days 6 onwards), most of the differentially expressed transcripts were up-regulated by small fold changes (< 32 fold). The molecular function of these genes has been associated with the metabolism of lipids and detoxification of xenobiotics. Conclusion: Overall, it appears that Leishmania modulates sand fly gene expression early on in order to overcome the barriers imposed by the midgut, yet it behaves like a commensal at later time points, where a massive number of parasites in the anterior midgut results only in modest changes in midgut gene expression.

scholarly journals Leishmania infection induces a limited differential gene expression in the sand fly midgut

2019 ◽  
Author(s):  
Iliano V. Coutinho-Abreu ◽  
Tiago D. Serafim ◽  
Claudio Meneses ◽  
Shaden Kamhawi ◽  
Fabiano Oliveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Early Time ◽  
Differentially Expressed ◽  
Sand Fly ◽  
Leishmania Infection ◽  
Lutzomyia Longipalpis ◽  
Late Time ◽  
Blood Digestion ◽  
Time Points

Abstract Background: Phlebotomine sand flies are the vectors of Leishmania worldwide. To develop in the sand fly midgut, Leishmania multiplies and undergoes multiple stage differentiations leading to the infective form, the metacyclic promastigotes. To gain a better understanding of the influence of Leishmania infection in midgut gene expression, we performed RNA-Seq comparing uninfected Lutzomyia longipalpis midguts and Leishmania infantum-infected Lutzomyia longipalpis midguts at seven time points which cover the various developmental Leishmania stages including early time points when blood digestion is taking place and late time points when the parasites are undergoing metacyclogenesis. Results: Out of over 13,841 transcripts assembled de novo, only 113 sand fly transcripts, about 1%, were differentially expressed. Further, we observed a low overlap of differentially expressed sand fly transcripts across different time points suggesting a specific influence of each Leishmania stage on midgut gene expression. Two main patterns of sand fly gene expression modulation were noticed. At early time points (days 1-4), more transcripts were down-regulated by Leishmania infection at large fold changes (> -32 fold). Among the down-regulated genes, the transcription factor Forkhead/HNF-3 and hormone degradation enzymes were differentially regulated on day 4 and appear to be the upstream regulators of nutrient transport, digestive enzymes, and peritrophic matrix proteins. Conversely, at later time points (days 6 onwards), most of the differentially expressed transcripts were up-regulated by small fold changes (< 32 fold), and the molecular function of such genes are associated with the metabolism of lipids and detoxification of xenobiotics (P450). Conclusion: Overall, it appears that Leishmania modulates sand fly gene expression early on in order to overcome the barriers imposed by the midgut, yet it behaves like a commensal at later time points, when modest midgut gene expression changes correlate with a massive amount of parasites in the anterior midgut.

scholarly journals Leishmania infection induces a limited differential gene expression in the sand fly midgut

2020 ◽  
Author(s):  
Iliano V. Coutinho-Abreu ◽  
Tiago D. Serafim ◽  
Claudio Meneses ◽  
Shaden Kamhawi ◽  
Fabiano Oliveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Early Time ◽  
Differentially Expressed ◽  
Sand Fly ◽  
Leishmania Infection ◽  
Developmental Cycle ◽  
Lutzomyia Longipalpis ◽  
Sand Flies ◽  
Time Points

Abstract Background: Sand flies are the vectors of Leishmania parasites. To develop in the sand fly midgut, Leishmania multiplies and undergoes various stage differentiations giving rise to the infective form, the metacyclic promastigotes. To determine the changes in sand fly midgut gene expression caused by the presence of Leishmania, we performed RNA-Seq of uninfected and Leishmania infantum-infected Lutzomyia longipalpis midguts from seven different libraries corresponding to time points which cover the various Leishmania developmental stages. Results: The combined transcriptomes resulted in the de novo assembly of 13,841 sand fly midgut transcripts. Importantly, only 113 sand fly transcripts, about 1%, were differentially expressed in the presence of Leishmania parasites. Further, we observed distinct differentially expressed sand fly midgut transcripts corresponding to the presence of each of the various Leishmania stages suggesting that each parasite stage influences midgut gene expression in a specific manner. Two main patterns of sand fly gene expression modulation were noted. At early time points (days 1-4), more transcripts were down-regulated by Leishmania infection at large fold changes (> 32 fold). Among the down-regulated genes, the transcription factor Forkhead/HNF-3 and hormone degradation enzymes were differentially regulated on day 2 and appear to be the upstream regulators of nutrient transport, digestive enzymes, and peritrophic matrix proteins. Conversely, at later time points (days 6 onwards), most of the differentially expressed transcripts were up-regulated by Leishmania infection with small fold changes (< 32 fold). The molecular functions of these genes have been associated with the metabolism of lipids and detoxification of xenobiotics. Conclusion: Overall, our data suggest that the presence of Leishmania produces a limited change in the midgut transcript expression profile in sand flies. Further, Leishmania modulates sand fly gene expression early on in the developmental cycle in order to overcome the barriers imposed by the midgut, yet it behaves like a commensal at later time points where a massive number of parasites in the anterior midgut results only in modest changes in midgut gene expression.

scholarly journals Transcriptomics of Type 2 Diabetic and Healthy Human Neutrophils

2019 ◽  
Author(s):  
Sarah E. Kleinstein ◽  
Jamison McCorrison ◽  
Alaa Ahmed ◽  
Hatice Hasturk ◽  
Thomas E. Van Dyke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Inflammatory Diseases ◽  
Differentially Expressed ◽  
Human Neutrophils ◽  
Rna Seq ◽  
Bioinformatics Pipeline ◽  
Healthy Human ◽  
Significant Differential Expression ◽  
The Impact

ABSTRACTObjectivesChronic inflammatory diseases, including diabetes and cardiovascular disease, are heterogeneous and often co-morbid, with increasing global prevalence. Uncontrolled type 2 diabetes (T2D) can result in severe inflammatory complications. As neutrophils are essential to inflammation, we conducted RNA-seq transcriptomic analyses to investigate the association between neutrophil gene expression and T2D phenotype. Further, as specialized pro-resolving lipid mediators, including resolvin E1 (RvE1), can actively resolve inflammation, we further surveyed the impact of RvE1 on isolated neutrophils.MethodsCell isolation and RNA-seq analysis of neutrophils from N=11 T2D and N=7 healthy individuals with available clinical data was conducted. Additionally, cultured neutrophils (N=3 T2D, N=3 healthy) were perturbed with increasing RvE1 doses (0nM, 1nM, 10nM, or 100nM) prior to RNA-seq. Data was evaluated through a bioinformatics pipeline including pathway analysis and post hoc false-discovery rate (FDR)-correction.ResultsWe observed significant differential expression of 50 genes between T2D and healthy neutrophils (p<0.05), including decreased T2D gene expression in inflammatory- and lipid-related genes SLC9A4, NECTIN2 and PLPP3 (p<0.003). RvE1 treatment induced dose-dependent differential gene expression (uncorrected p<0.05) across groups, including 59 healthy and 216 T2D neutrophil genes. Comparing T2D to healthy neutrophils, 1097 genes were differentially expressed across RvE1 doses, including two significant genes, LILRB5 and AKR1C1, involved in inflammation (p<0.05).ConclusionsInflammatory- and lipid-related genes were differentially expressed between T2D and healthy neutrophils, and RvE1 dose-dependently modified gene expression in both groups. Unraveling the mechanisms regulating abnormalities in diabetic neutrophil responses could lead to better diagnostics and therapeutics targeting inflammation and inflammation resolution.

scholarly journals Performance of gene expression analyses using de novo assembled transcripts in polyploid species

2018 ◽  
Author(s):  
Ling-Yun Chen ◽  
Diego F. Morales-Briones ◽  
Courtney N. Passow ◽  
Ya Yang
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Reference Genes ◽  
De Novo ◽  
Differentially Expressed ◽  
Supplementary Information ◽  
Network Analyses ◽  
Gene Expression Analyses ◽  
Polyploidy Event ◽  
Differential Gene

AbstractMotivationQuality of gene expression analyses using de novo assembled transcripts in species experienced recent polyploidization is yet unexplored.ResultsFive plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or better than Corset and Grouper in precision, but lower in sensitivity. In species that lack polyploidy event in the past few million years, DGE analyses using de novo assembled transcriptome identified 50–76% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species with more recent polyploidy event, the percentage decreased to 7–30%. In addition, 7–89% of differentially expressed genes from de novo assembly are contaminations. Gene co-expression network analyses using de novo assemblies vs. mapping to the reference genes recovered the same module that significantly correlated with treatment in one of the five species tested.Availability and ImplementationCommands and scripts used in this study are available at https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/; Analysis files are available at Dryad doi: [email protected] informationSupplementary data are available at Bioinformatics online

Sign in / Sign up

Export Citation Format

Share Document