Effects of larval density on gene regulation in C. elegans during routine L1 synchronization

ABSTRACTBleaching gravid C. elegans followed by a short period of starvation of the L1 larvae is a routine method performed by worm researchers for generating synchronous populations for experiments. During the process of investigating dietary effects on gene regulation in L1 stage worms by single-worm RNA-Seq, we found that the density of resuspended L1 larvae affects expression of many mRNAs. Specifically, a number of genes related to metabolism and signalling are highly expressed in worms arrested at low density, but are repressed at higher arrest densities. We generated a GFP reporter strain based on one of the most density-dependent genes in our dataset – lips-15 – and confirmed that this reporter was expressed specifically in worms arrested at relatively low density. Finally, we show that conditioned media from high density L1 cultures was able to downregulate lips-15 even in L1 animals arrested at low density, and experiments using daf-22 mutant animals demonstrated that this effect is not mediated by the ascaroside family of signalling pheromones. Together, our data implicate a soluble signalling molecule in density sensing by L1 stage C. elegans, and provide guidance for design of experiments focused on early developmental gene regulation.

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An unusually low density ultra-short period super-Earth and three mini-Neptunes around the old star TOI-561

Monthly Notices of the Royal Astronomical Society ◽

10.1093/mnras/staa3728 ◽

2020 ◽

Author(s):

G Lacedelli ◽

L Malavolta ◽

L Borsato ◽

G Piotto ◽

D Nardiello ◽

...

Keyword(s):

Transit Time ◽

Time Variation ◽

Planetary System ◽

Radial Velocities ◽

Low Density ◽

Outer Planets ◽

Short Period ◽

The Stability

Abstract Based on HARPS-N radial velocities (RVs) and TESS photometry, we present a full characterisation of the planetary system orbiting the late G dwarf After the identification of three transiting candidates by TESS, we discovered two additional external planets from RV analysis. RVs cannot confirm the outer TESS transiting candidate, which would also make the system dynamically unstable. We demonstrate that the two transits initially associated with this candidate are instead due to single transits of the two planets discovered using RVs. The four planets orbiting TOI-561 include an ultra-short period (USP) super-Earth (TOI-561 b) with period Pb = 0.45 d, mass Mb = 1.59 ± 0.36 M⊕ and radius Rb = 1.42 ± 0.07 R⊕, and three mini-Neptunes: TOI-561 c, with Pc = 10.78 d, Mc = 5.40 ± 0.98 M⊕, Rc = 2.88 ± 0.09 R⊕; TOI-561 d, with Pd = 25.6 d, Md = 11.9 ± 1.3 M⊕, Rd = 2.53 ± 0.13 R⊕; and TOI-561 e, with Pe = 77.2 d, Me = 16.0 ± 2.3 M⊕, Re = 2.67 ± 0.11 R⊕. Having a density of 3.0 ± 0.8 g cm−3, TOI-561 b is the lowest density USP planet known to date. Our N-body simulations confirm the stability of the system and predict a strong, anti-correlated, long-term transit time variation signal between planets d and e. The unusual density of the inner super-Earth and the dynamical interactions between the outer planets make TOI-561 an interesting follow-up target.

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Regulation of very-low-density-lipoprotein lipid secretion in hepatocyte cultures derived from diabetic animals

Biochemical Journal ◽

10.1042/bj2620313 ◽

1989 ◽

Vol 262 (1) ◽

pp. 313-319 ◽

Cited By ~ 14

Author(s):

J M Duerden ◽

S M Bartlett ◽

G F Gibbons

Keyword(s):

Low Density Lipoprotein ◽

Density Lipoprotein ◽

Inhibitory Effect ◽

Diabetic Rats ◽

Whole Body ◽

Very Low Density Lipoprotein ◽

Low Density ◽

Short Period ◽

Streptozotocin Diabetic Rats ◽

Cholesterol Secretion

Hepatocytes were derived from 2-3-day streptozotocin-diabetic rats and maintained in culture for up to 3 days. Compared with similar cultures from normal animals, these hepatocytes secreted less very-low-density-lipoprotein (VLDL) triacylglycerol, but the decrease in the secretion of VLDL non-esterified and esterified cholesterol was not so pronounced. This resulted in the secretion of relatively cholesterol-rich VLDL particles by the diabetic hepatocytes. Addition of insulin for a relatively short period (24 h) further decreased the low rates of VLDL triacylglycerol secretion from the diabetic hepatocytes. The secretion of VLDL esterified and non-esterified cholesterol also declined. These changes occurred irrespective of whether or not exogenous fatty acids were present in the culture medium. Little or no inhibitory effect of insulin was observed after longer-term (24-48 h) exposure to the hormone. Both dexamethasone and a mixture of lipogenic precursors (lactate plus pyruvate) stimulated VLDL triacylglycerol and cholesterol secretion, but not to the levels observed in hepatocytes from normal animals. The low rate of hepatic VLDL secretion in diabetes contrasts with the increase in whole-body VLDL production rate. This suggests that the intestine is a major source of plasma VLDL in insulin-deficient diabetes.

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The significance of biomass allocation to population growth of the invasive species Ambrosia artemisiifolia and Ambrosia trifida with different densities

BMC Ecology and Evolution ◽

10.1186/s12862-021-01908-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Wenxuan Zhao ◽

Tong Liu ◽

Yan Liu ◽

Hanyue Wang ◽

Ruili Wang ◽

...

Keyword(s):

Cluster Formation ◽

Ambrosia Artemisiifolia ◽

High Density ◽

High Population ◽

Leaf Biomass ◽

Total Biomass ◽

Low Density ◽

Population Densities ◽

Ambrosia Trifida ◽

Short Period

Abstract Background Ambrosia artemisiifolia and Ambrosia trifida are globally distributed harmful and invasive weeds. High density clusters play an important role in their invasion. For these two species, the early settled populations are distributed at low densities, but they can rapidly achieve high population densities in a short period of time. However, their response to intraspecific competition to improve the fitness for rapid growth and maintenance of high population densities remains unclear. Therefore, to determine how these species form and maintain high population densities, individual biomass allocations patterns between different population densities (low and high), and plasticity during seedling, vegetative, breeding and mature stages were compared. In 2019, we harvested seeds at different population densities and compared them, and in 2020, we compared the number of regenerated plants across the two population densities. Results Most biomass was invested in the stems of both species. Ambrosia trifida had the highest stem biomass distribution, of up to 78%, and the phenotypic plasticity of the stem was the highest. Path analysis demonstrated that at low-density, total biomass was the biggest contributor to seed production, but stem and leaf biomass was the biggest contributors to high-density populations. The number of seeds produced per plant was high in low-density populations, while the seed number per unit area was huge in high-density populations. In the second year, the number of low-density populations increased significantly. A. artemisiifolia and A. trifida accounted for 75.6% and 68.4% of the mature populations, respectively. Conclusions High input to the stem is an important means to regulate the growth of the two species to cope with different densities. These two species can ensure reproductive success and produce appropriate seed numbers. Therefore, they can maintain a stable population over time and quickly form cluster advantages. In the management, early detection of both species and prevention of successful reproduction by chemical and mechanical means are necessary to stop cluster formation and spread.

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Global accumulation of circRNAs during aging in Caenorhabditis elegans

10.1101/175026 ◽

2017 ◽

Author(s):

Mariela Cortés-López ◽

Matthew Gruner ◽

Daphne A. Cooper ◽

Hannah N. Gruner ◽

Alexandru-Ioan Voda ◽

...

Keyword(s):

Global Scale ◽

Circular Rnas ◽

Rna Seq ◽

Aging Research ◽

C Elegans ◽

Fourth Larval Stage ◽

Functional Consequences ◽

Exceptional Stability ◽

Massive Accumulation

SummaryCircular RNAs (CircRNAs) are a newly appreciated class of RNAs that lack free 5´ and 3´ ends, are expressed by the thousands in diverse forms of life, and are mostly of enigmatic function. Ostensibly due to their resistance to exonucleases, circRNAs are known to be exceptionally stable. Here, we examined the global profile of circRNAs in C. elegans during aging by performing ribo-depleted total RNA-seq from the fourth larval stage (L4) through 10-day old adults. Using stringent bioinformatic criteria and experimental validation, we annotated 1,166 circRNAs, including 575 newly discovered circRNAs. These circRNAs were derived from 797 genes with diverse functions, including genes involved in the determination of lifespan. A massive accumulation of circRNAs during aging was uncovered. Many hundreds of circRNAs were significantly increased among the aging time-points and increases of select circRNAs by over 40-fold during aging were quantified by qRT-PCR. The age-accumulation of circRNAs was not accompanied by increased expression of linear RNAs from the same host genes. We attribute the global scale of circRNA age-accumulation to the high composition of postmitotic cells in adult C. elegans, coupled with the high resistance of circRNAs to decay. These findings suggest that the exceptional stability of circRNAs might explain age-accumulation trends observed from neural tissues of other organisms, which also have a high composition of post-mitotic cells. Given the suitability of C. elegans for aging research, it is now poised as an excellent model system to determine if there are functional consequences of circRNA accumulation during aging.

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Small Molecule Stabilization of PINK-1/PINK1 Improves Neurodegenerative Disease

10.1101/2021.06.07.447442 ◽

2021 ◽

Author(s):

Elissa Tjahjono ◽

Jingqi Pei ◽

Alexey V Revtovich ◽

Terri-Jeanne E Liu ◽

Alisha Swadi ◽

...

Keyword(s):

Neurodegenerative Disease ◽

Dependent Manner ◽

Loss Of Function ◽

Mitochondrial Fragmentation ◽

Atp Production ◽

C Elegans ◽

Mitochondrial Homeostasis ◽

Phenotypic Screen ◽

Gfp Reporter ◽

Common Causes

Macroautophagic recycling of dysfunctional mitochondria, known as mitophagy, is essential for mitochondrial homeostasis and cell viability. Accumulation of defective mitochondria and impaired mitophagy have been widely implicated in many neurodegenerative diseases, and loss-of-function mutations of two regulators of mitophagy, PINK1 and Parkin, are amongst the most common causes of recessive Parkinson's disease. Activation of mitophagy via pharmacological treatments may be a feasible approach for combating neurodegeneration. In this effort, we screened ~45,000 small molecules for the ability to activate mitophagy. A high-throughput, whole-organism, phenotypic screen was conducted by monitoring stabilization of PINK-1/PINK1, a key event in mitophagy activation, in a Caenorhabditis elegans strain carrying a Ppink-1::PINK-1::GFP reporter. We obtained eight hits that induced mitophagy, as evidenced by increased mitochondrial fragmentation and autophagosome formation. Several of the compounds also reduced ATP production, oxygen consumption, mitochondrial mass, and/or mitochondrial membrane potential. Importantly, we found that treatment with two compounds, which we named PS83 and PS106 (more commonly known as sertraline) reduced neurodegenerative disease phenotypes (including delayed paralysis in a C. elegans Alzheimer's model) in a PINK-1/PINK1-dependent manner. This report presents a promising step toward the identification of compounds that will stimulate mitochondrial turnover.

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The IDR-containing protein PID-2 affects Z granules and is required for piRNA-induced silencing in the embryo

10.1101/2020.04.14.040584 ◽

2020 ◽

Author(s):

Maria Placentino ◽

António Miguel de Jesus Domingues ◽

Jan Schreier ◽

Sabrina Dietz ◽

Svenja Hellmann ◽

...

Keyword(s):

Gene Regulation ◽

Caenorhabditis Elegans ◽

Rna Polymerase ◽

Small Rna ◽

Rna Silencing ◽

Rna Dependent Rna Polymerase ◽

Prolyl Aminopeptidase ◽

C Elegans

AbstractIn Caenorhabditis elegans, the piRNA (21U RNA) pathway is required to establish proper gene regulation and an immortal germline. To achieve this, PRG-1-bound 21U RNAs trigger silencing mechanisms mediated by RNA-dependent RNA polymerase (RdRP)-synthetized 22G RNAs. This silencing can become PRG-1-independent, and heritable over many generations. This state is named RNAe. It is unknown how and when RNAe is established, and how it is maintained. We show that maternally provided 21U RNAs can be sufficient to trigger RNAe in embryos. Additionally, we identify the IDR-containing protein PID-2, as a factor required to establish and maintain RNAe. PID-2 interacts with two novel, partially redundant, eTudor domain proteins, PID-4 and PID-5. Additionally, PID-5 has a domain related to the X-prolyl aminopeptidase protein APP-1, and binds APP-1, implicating N-terminal proteolysis in RNAe. All three proteins are required for germline immortality, localize to perinuclear foci, affect Z granules, and are required for balancing of 22G RNA populations. Overall, our study identifies three new proteins with crucial functions in the C. elegans small RNA silencing network.

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Creation of Low-Copy Integrated Transgenic Lines in Caenorhabditis elegans

Genetics ◽

10.1093/genetics/157.3.1217 ◽

2001 ◽

Vol 157 (3) ◽

pp. 1217-1226 ◽

Cited By ~ 1

Author(s):

Vida Praitis ◽

Elizabeth Casey ◽

David Collar ◽

Judith Austin

Keyword(s):

Caenorhabditis Elegans ◽

Expression Level ◽

Dna Arrays ◽

Extrachromosomal Dna ◽

C Elegans ◽

Microparticle Bombardment ◽

Alternative Method ◽

Extrachromosomal Array ◽

Gfp Reporter ◽

Transgenic Lines

Abstract In Caenorhabditis elegans, transgenic lines are typically created by injecting DNA into the hermaphrodite germline to form multicopy extrachromosomal DNA arrays. This technique is a reliable means of expressing transgenes in C. elegans, but its use has limitations. Because extrachromosomal arrays are semistable, only a fraction of the animals in a transgenic extrachromosomal array line are transformed. In addition, because extrachromosomal arrays can contain hundreds of copies of the transforming DNA, transgenes may be overexpressed, misexpressed, or silenced. We have developed an alternative method for C. elegans transformation, using microparticle bombardment, that produces single- and low-copy chromosomal insertions. Using this method, we find that it is possible to create integrated transgenic lines that reproducibly express GFP reporter constructs without the variations in expression level and pattern frequently exhibited by extrachromosomal array lines. In addition, we find that low-copy integrated lines can also be used to express transgenes in the C. elegans germline, where conventional extrachromosomal arrays typically fail to express due to germline silencing.

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Broad oxygen tolerance in the nematode Caenorhabditis elegans

Journal of Experimental Biology ◽

10.1242/jeb.203.16.2467 ◽

2000 ◽

Vol 203 (16) ◽

pp. 2467-2478 ◽

Cited By ~ 5

Author(s):

W.A. Van Voorhies ◽

S. Ward

Keyword(s):

Caenorhabditis Elegans ◽

Metabolic Rate ◽

Developmental Stages ◽

Small Body ◽

Metabolic Cost ◽

Soil Nematode ◽

Nematode Caenorhabditis Elegans ◽

Oxygen Levels ◽

C Elegans ◽

Short Period

This study examined the effects of oxygen tensions ranging from 0 to 90 kPa on the metabolic rate (rate of carbon dioxide production), movement and survivorship of the free-living soil nematode Caenorhabditis elegans. C. elegans requires oxygen to develop and survive. However, it can maintain a normal metabolic rate at oxygen levels of 3.6 kPa and has near-normal metabolic rates at oxygen levels as low as 2 kPa. The ability to withstand low ambient oxygen levels appears to be a consequence of the small body size of C. elegans, which allows diffusion to supply oxygen readily to the cells without requiring any specialized respiratory or metabolic adaptations. Thus, the small size of this organism pre-adapts C. elegans to living in soil environments that commonly become hypoxic. Movement in C. elegans appears to have a relatively minor metabolic cost. Several developmental stages of C. elegans were able to withstand up to 24 h of anoxia without major mortality. Longer periods of anoxia significantly increased mortality, particularly for eggs. Remarkably, long-term exposure to 100 % oxygen had no effect on the metabolic rate of C. elegans, and populations were able to survive for a least 50 generations in 100 % (90 kPa) oxygen. Such hyperoxic conditions are fatal to most organisms within a short period.

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Regulation of ectodermal and excretory function by the C. elegans POU homeobox gene ceh-6

Development ◽

10.1242/dev.128.5.779 ◽

2001 ◽

Vol 128 (5) ◽

pp. 779-790 ◽

Cited By ~ 2

Author(s):

T.R. Burglin ◽

G. Ruvkun

Keyword(s):

Transcription Factor ◽

Epithelial Cells ◽

Homeobox Genes ◽

Homeobox Gene ◽

Null Mutant ◽

Reporter Construct ◽

Excretory Function ◽

C Elegans ◽

Gfp Reporter ◽

Excretory Cell

Caenorhabditis elegans has three POU homeobox genes, unc-86, ceh-6 and ceh-18. ceh-6 is the ortholog of vertebrate Brn1, Brn2, SCIP/Oct6 and Brn4 and fly Cf1a/drifter/ventral veinless. Comparison of C. elegans and C. briggsae CEH-6 shows that it is highly conserved. C. elegans has only three POU homeobox genes, while Drosophila has five that fall into four families. Immunofluorescent detection of the CEH-6 protein reveals that it is expressed in particular head and ventral cord neurons, as well as in rectal epithelial cells, and in the excretory cell, which is required for osmoregulation. A deletion of the ceh-6 locus causes 80% embryonic lethality. During morphogenesis, embryos extrude cells in the rectal region of the tail or rupture, indicative of a defect in the rectal epithelial cells that express ceh-6. Those embryos that hatch are sick and develop vacuoles, a phenotype similar to that caused by laser ablation of the excretory cell. A GFP reporter construct expressed in the excretory cell reveals inappropriate canal structures in the ceh-6 null mutant. Members of the POU-III family are expressed in tissues involved in osmoregulation and secretion in a number of species. We propose that one evolutionary conserved function of the POU-III transcription factor class could be the regulation of genes that mediate secretion/osmoregulation.

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Transcriptome Response to Drought, Rehydration and Re-Dehydration in Potato

International Journal of Molecular Sciences ◽

10.3390/ijms21010159 ◽

2019 ◽

Vol 21 (1) ◽

pp. 159 ◽

Cited By ~ 2

Author(s):

Yongkun Chen ◽

Canhui Li ◽

Jing Yi ◽

Yu Yang ◽

Chunxia Lei ◽

...

Keyword(s):

Signal Transduction ◽

Gene Regulation ◽

Lipid Metabolism ◽

Drought Stress ◽

Sugar Metabolism ◽

Rna Seq ◽

Drought Tolerant ◽

Cell Components ◽

Drought Hardening

Potato is an important food crop and its production is susceptible to drought. Drought stress in crop growth is usually multiple- or long-term. In this study, the drought tolerant potato landrace Jancko Sisu Yari was treated with drought stress, rehydration and re-dehydration, and RNA-seq was applied to analyze the characteristics of gene regulation during these treatments. The results showed that drought-responsive genes mainly involved photosynthesis, signal transduction, lipid metabolism, sugar metabolism, wax synthesis, cell wall regulation, osmotic adjustment. Potato also can be recovered well in the re-emergence of water through gene regulation. The recovery of rehydration mainly related to patatin, lipid metabolism, sugar metabolism, flavonoids metabolism and detoxification besides the reverse expression of the most of drought-responsive genes. The previous drought stress can produce a positive responsive ability to the subsequent drought by drought hardening. Drought hardening was not only reflected in the drought-responsive genes related to the modified structure and cell components, but also in the hardening of gene expression or the “memory” of drought-responsive genes. Abundant genes involved photosynthesis, signal transduction, sugar metabolism, protease and protease inhibitors, flavonoids metabolism, transporters and transcription factors were subject to drought hardening or memorized drought in potato.

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