Although advances have been made in understanding the role of hypoxia in the stem cell niche, almost nothing is known about a potentially similar role of hypoxia in maintaining the tumor stem cell ...(TSC) niche. Here we show that a highly tumorigenic fraction of side population (SP) cells is localized in the hypoxic zones of solid tumors in vivo. We first identified a highly migratory, invasive, and tumorigenic fraction of post-hypoxic side population cells (SPm(hox) fraction) in a diverse group of solid tumor cell lines, including neuroblastoma, rhabdomyosarcoma, and small-cell lung carcinoma. To identify the SPm((hox)) fraction, we used an "injured conditioned medium" derived from bone marrow stromal cells treated with hypoxia and oxidative stress. We found that a highly tumorigenic SP fraction migrates to the injured conditioned medium in a Boyden chamber. We show that as few as 100 SPm((hox)) cells form rapidly growing tumors in vivo. In vitro exposure to hypoxia increases the SPm((hox)) fraction significantly. Quantitative real-time polymerase chain reaction and immunofluorescence studies showed that SPm((hox)) cells expressed Oct-4, a "stemness" gene having a potential role in TSC maintenance. In nude mice xenografts, SPm((hox)) cells were localized to the hypoxic zones, as demonstrated after quantum dot labeling. These results suggest that a highly tumorigenic SP fraction migrates to the area of hypoxia; this migration is similar to the migration of normal bone marrow SP fraction to the area of injury/hypoxia. Furthermore, the hypoxic microenvironment may serve as a niche for the highly tumorigenic fraction of SP cells.
Fruit softening during ripening is mainly a consequence of solubilization and depolymerization of cell wall components mediated by the action of a complex set of enzymes and proteins. In the present ...work, we performed a comparative study of the changes in physiological properties, cell wall-associated polysaccharide contents and expression of cell wall-related genes during different fruit developmental stages of four strawberry (Fragaria x ananassa Duch.) cultivars (Camarosa, Cristal, Monterey, and Portola). The four cultivars showed different fruit firmness values being Camarosa and Cristal the firmest, Monterey the softest, and Portola with an intermediate value between them. Additionally, in order to obtain a correlation between mRNA transcriptional levels and fruit firmness with physiological properties, we have analyzed the abundance of five mRNAs (FaEXPA2, FaEXPA4, FaXTH1, FaXTH2 and FaPG1). We have found a correlation between fruit firmness and mRNA abundance levels for FaEXPA2, FaEXPA4, FaXTH1 and FaPG1. For these four mRNAs we have observed higher transcript levels in the softest cultivar (Monterey) than in the other two firmer cultivars (Cristal and Camarosa) at the 50% ripe or ripe stage. Finally, the results showed that exist a correlation between cell wall-modifying enzymes, physiological properties and firmness, which would explain the fruit softening process that reduces post-harvest life.
Revealing the metabolic profiles of carbohydrates with their regulatory genes and metabolites is conducive to understanding their mechanism of utilization in
Streptococcus thermophilus
MN-ZLW-002 ...during pH-controlled batch fermentation. Transcriptomics and metabolomics were used to study carbohydrate metabolism. More than 200 unigenes were involved in carbohydrate transport. Of these unigenes, 55 were involved in the phosphotransferase system (PTS), which had higher expression levels than those involved in ABC protein-dependent systems, permeases, and symporters. The expression levels of the genes involved in the carbohydrate transport systems and phosphate transport system were high at the end-lag and end-exponential growth phases, respectively. In addition, 166 differentially expressed genes (DEGs) associated with carbohydrate metabolism were identified. Most genes had their highest expression levels at the end-lag phase. The
pfk
,
ldh
,
zwf
, and
E3.2.1.21
genes involved in the glycolytic pathway had higher expression levels at the end-exponential growth phase than the mid-exponential growth phase. The results showed high expression levels of
lacZ
and
galKTM genes
and reabsorption of extracellular galactose.
S. thermophilus
MN-ZLW-002 can metabolize and utilize galactose. Overall, this comprehensive network of carbohydrate metabolism is useful for further studies of the control of glycolytic pathway during the high-density culture of
S
.
thermophilus
.
Tea plant (Camellia sinensis (L.) O. Kuntze) is a perennial evergreen woody plant, and its leaves contain various beneficial ingredients and have healthy efficacy. HD-Zip (homeodomain-leucine zipper) ...transcription factors (TFs) are widely distributed in plants and play an important role in plant growth and environmental response. To date, knowledge on HD-Zip gene family in tea plant is still limited. In this study, 33 HD-Zip TFs were selected based on the genomic and transcriptomic databases of tea plant. The conserved domains and common motifs of these TFs were predicted and analyzed. These 33 Cshdz TFs were divided into four groups (HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV). The interaction network of the HD-Zip proteins of tea plant was established based on the data of Arabidopsis. In addition, the expression levels of these Cshdz genes in tea plant cv. ‘Longjing43’ were detected and analyzed under five abiotic stress treatments. Results showed that the different expression profiles of Cshdz genes were associated with different abiotic stress treatments. Our findings suggested a potential relationship between the resistance of tea plant and its Cshdz genes.
•A total of 33 HD-Zip transcription factors were isolated from tea plant.•The phylogenetic tree, conserved motifs, and characteristics were performed.•The expression profiles of Cshdz genes response to abiotic stress treatments in tea plant.
Sperm enriched X-linked transcripts vary between Holstein-Friesian cattle and Murrah buffalo. The transcripts expression levels of the biologically relevant genes suggest that the transcripts RPL10 ...and RPS4X had a significant correlation with field fertility in cattle and buffalo, respectively. The fertility predictive ability of these expressed transcripts can be used for selecting the high-fertile bulls.
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•Transcript pools of cattle and buffalo spermatozoa corresponding to the X-linked genes are enriched with two mRNA categories regulating embryonic organ development and reproduction processes.•mRNA expression levels of X-linked genes in sperm vary between Holstein-Friesian cattle and Murrah buffalo.•X-linked genes RPL10, ZCCHC13 in cattle and AKAP4, TSPAN6, RPL10 and RPS4X in buffalo influence sperm kinematics.•X-linked genes RPL10 and RPS4X may regulate the field fertility rate of cattle and buffalo, respectively.
The role of sperm expressed X-linked genes on bull fertility has not been studied in detail. The objective of the present study was to assess the influence of X-linked genes on the sperm functional parameters and field fertility rate in the Holstein Friesian cattle (n = 12) and Murrah buffalo (n = 7) bulls. The enrichment analysis (cattle = 8; buffalo = 8) of the X-linked genes was carried out using retrospective RNA-seq data and mRNA expression levels of functionally relevant genes were validated using the RT-qPCR. The mRNA expression levels of these genes were functionally associated with sperm attributes and field fertility rate. The sperm transcriptome studies revealed that the total number of expressed genes and the transcript content of the X-linked genes in the mature sperm were very low in both species, and only 23.31% of these genes were commonly expressed between them. The transcript pool corresponding to the X-linked genes represents embryonic organ development (p = 0.03) and reproduction (p = 0.02) processes in cattle and buffalo sperm, respectively. The mRNA expression levels of X-linked genes, RPL10 and ZCCHC13 in cattle; AKAP4, TSPAN6, RPL10 and RPS4X in buffalo were significantly (p < 0.05) correlated with sperm kinematics. Importantly, the mRNA expression levels of the genes RPL10 (r = −0.68) and RPS4X (r = 0.81) had a significant correlation with the field fertility rate in cattle and buffalo, respectively. Multivariate regression models and receiver operating curve analysis suggest that the mRNA expression levels of X-linked genes may be useful in predicting bull fertility. The study indicates that sperm-expressed X-linked genes influence semen quality and field fertility rate in both cattle and buffalo.
SMAD family member 1 (SMAD1) is phosphorylated and activated by the BMP receptors, which help regulate ovulation rate, cell growth, apoptosis, and development. Previously, the genome-wide association ...study revealed that it has been associated with fecundity in sheep. However, its effect on litter size has not been investigated in goats. Therefore, this study aimed to determine the level of SMAD1 mRNA expression in various tissues and to identify its polymorphisms and their association with litter size in Shaanbei white cashmere goat (SBWC). As a result, RT-qPCR analysis showed that SMAD1 was expressed in various tissues in female SBWC goats, including the ovary (P < 0.05). Importantly, the mRNA expression level in the ovaries of mothers of multi-lambs had a higher level than the mothers of single lambs (P < 0.05). Moreover, two InDels (18-bp and 7-bp) in intron 1 of SMAD1 were polymorphic among ten potential loci. Both 18-bp and 7-bp InDels were significantly correlated with litter size (P = 0.014) and (P = 0.0001), respectively. As shown by the chi-squared test, genotypic distributions of 18-bp and 7-bp were significantly distinct between single-lamb (P = 0.02) and multi-lamb mothers (P = 0.002). Our findings confirm that two InDels in SMAD1 were significantly associated with litter size and suggest that they could be used to improve fertility traits in goat breeding strategies.
•SMAD1 mRNA was widely expressed in varied tissues and the ovary level of goats was significantly high (P < 0.05).•The expression of SMAD1 showed significant differences in ovaries in mothers of multi-lamb and mothers of single-lamb.•These InDel loci P1-Del-18-bp and P2-Del-7-bp were significantly associated with Shaanbei white cashmere goat litter size.
Previously, we showed that the methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii) could produce and secrete the beta-propeller phytase FTEII in an active form under the control of the ...AOX1 promoter and methanol as the inductor. In this work, we engineered P. pastoris strains to construct a constitutive P. pastoris expression system (GAP promoter) and extracellularly produce the phytase FTEII. We optimized the culture conditions to increase the extracellular volumetric phytase productivity (Qp) and evaluated the impact of the optimization process on the physiological response of the host. Moreover, we analyzed the expression levels of the FTEII gene and endogenous genes for P. pastoris cells in cultures with the lowest and highest Qp to understand which processes (from heterologous gene expression to protein secretion) might be responsible for the increase in Qp. The results indicate that a low specific growth rate and temperature in the fed-batch phase increases the Qp, which was correlated with an upregulation of the KAR2 and PSA1–1/MPG1 genes rather than increased heterologous gene transcription.
•A low specific growth rate and temperature increases extracellular volumetric productivity.•The increased extracellular volumetric productivity is correlated with an upregulation of KAR2 and PSA1-1 genes.•The increased secretion process was caused by an increase in the Kar2p/BiP chaperone and cell viability.
Schistosoma mansoni is a parasitic flatworm that causes a human disease called schistosomiasis, or bilharzia. At the genomic level, S. mansoni is AT-rich, but has some compositional heterogeneity. ...Indeed, some regions of its genome are GC-rich, mainly in the regions located near the extreme ends of the chromosomes. Recently, we showed that, despite the strong bias towards A/T ending codons, highly expressed genes tend to use GC-rich codons. Here, we address the following question: are highly expressed sequences biased in their amino acid frequencies? Our analyses show that these sequences in S. mansoni, as in species ranging from bacteria to human, are strongly biased in nucleotide composition. Highly expressed genes tend to use GC-rich codons (in the first and second codon positions), which code the energetically cheapest amino acids. Therefore, we conclude that amino acid usage, at least in highly expressed genes, is strongly shaped by natural selection to avoid energetically expensive residues. Whether this is an adaptation to the parasitic way of life of S. mansoni, is unclear since the same pattern occurs in free-living species.
•Amino acid frequencies in S. mansoni proteins change according to the expression levels.•Highly expressed S. mansoni genes tend to use smaller and energetically less expensive amino acids than lowly expressed genes.•There is an inverse correlation between overall protein expression and protein hydropathy levels.
•BjuSPL10c was expressed at a high level in flowers and up-regulated at reproductive stage.•Seven potential interactive proteins (BjuB025567, BjuA041065, BjuB033332, BjuA045694, BjuA027365, ...BjuA031237 and BjuA005619) were screened from B.juncea yeast library of flower buds at squaring stage.•Six (BjuB025567, BjuA041065, BjuB033332, BjuA045694, BjuA031237 and BjuA005619) of those proteins interacted with BjuSPL10c in vivo.•All of these six genes expressing interactive proteins were down-regulated in flowers.
Brassica juncea var. tumida Tsen et Lee (Tumorous stem mustard) is a specific vegetable in China. Its tumorous stem can be consumed as fresh vegetable or produced pickle. In practice, early-bolting happens in around 15%, which inhibits B. juncea industry development. SPL is a plant specific transcription factor, plays important roles in flowering and gibberellins (GA) signaling. qRT-PCR assay found that BjuSPL10c was expressed at a high level in flowers and reproductive stage. To explore interactive proteins, BjuSPL10c was used as bait, finally seven proteins were screened and they are BjuB025567, BjuA041065, BjuB033332, BjuA045694, BjuA027365, BjuA031237 and BjuA005619. Further study confirmed that six of those proteins interacted with BjuSPL10c in vivo. qRT-PCR was conducted to understand mRNA expression levels of these six proteins in different tissues and development stages. The results showed that compared with root, mRNAs for all of these six genes were down-regulated in flowers. For different developmental stages, BjuB025567 and BjuA005619 were up-regulated at vegetative stage, down-regulated at reproductive stage; BjuB033332, BjuA045694 and BjuA031237 were significantly up-regulated at both vegetative and reproductive stages; BjuA041065 was showed “down-up-down” expression pattern. Taking all results together, BjuB025567, BjuA041065, BjuB033332, BjuA045694 and BjuA031237 may participate in flowering time regulation through interacting with BjuSPL10c in B. juncea.
Phenotypic heterogeneity in bioprocesses is suspected to reduce performances, even in case of monoclonal cultures. Here, robustness of an engineered isopropanol-overproducing strain and heterogeneity ...of its plasmid expression level were evaluated in fed-batch cultures. Previously, eGFP was identified as a promising plasmid expression reporter for C. necator. Here, the behavior of 3 engineered strains (isopropanol overproducer, eGFP producer, and isopropanol/eGFP co-producers) was compared at the single-cell and population levels. Production yields and rates have been shown to be dependent on isopropanol/acetone tolerance. A link could be established between the variations in the fluorescence intensity distribution and isopropanol / acetone production using the eGFP-biosensor. Co-production of isopropanol and eGFP exhibited cumulative metabolic burden compared to single overexpression (isopropanol or eGFP). Expression of eGFP during isopropanol production resulted in lower isopropanol tolerance with a loss of membrane integrity resulting in protein leakage and reduced plasmid expression. The co-expression of heterologous isopropanol pathway and eGFP-biosensor enabled to demonstrate the heterogeneity of robustness and plasmid expression at the single cell level of C. necator. It highlighed the conflicting interactions between isopropanol overproduction and eGFP reporter system. Fluorescent reporter strains, a crucial tool for monitoring subpopulation heterogeneity although biases have to be considered.
•Co-expression of heterologous isopropanol pathway and eGFP-biosensor to evaluate plasmid expression stability at single-cell level.•The co-production of eGFP and Isopropanol impacts strain robustness and performances comparing to the single overexpression (Isopropanol or eGFP).•Increased cell permeabilization and plasmid loss with increasing isopropanol and acetone concentration.
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