Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: In human preimplantation embryos, it has been shown that the reduced expression of X chromosomes in females ensures the dosage compensation [41]. expression activates the X‐chromosome inactivation by engaging proteins functioning in chromatin remodelling [3, 42]. With the advanced technologies, including single‐cell RNA sequencing, it has emerged that lncand XIST are expressed on the active X chromosome in the early human preimplantation embryos [43]. Furthermore, the expression of these two RNAs has never been shown to overlap. Introducing XACT into heterologous systems caused the accumulation of Xist RNA in cis and therefore it may be involved in the control of XIST association to chromosome in cis and may temper its ability of silencing. It is also possible that XACT functions in balancing the X‐chromosome inactivation at the early stages of preimplantation embryo development [43, 44]. Recently, the dosage compensation was shown to be driven by a CAG promoter of a new Xist allele (Xist(CAG)) [45]. Furthermore, Xist(CAG) upregulation in preimplantation embryos showed variation depending on the parental origin and the paternal expression was suggested to be preferentially inactivated with the paternal Xist(CAG) transmission [45]. 2. 2. Epigenetic modification of the gametesIn germ cells, methylation is maintained in a sex‐specific manner. Methylation in PGCs diminishes as they migrate to the gonads. Studies suggest that in females, remethylation occurs after birth when the oocytes are in the process of development. When demethylation is completed, the PGCs either enter mitosis in males or arrest at meiosis in females [46]. Reprogramming of the methylation in the embryo is necessary for parent‐specific expression of genes [14]. Gene expression varies during preimplantation embryo development due to these reprogramming events and appropriate gene expression determines the survival of the embryo [6]. Recently, short noncoding RNAs, microRNAs (miRNAs) and long noncoding RNAs (lncRNA) have gained importance in their potential function to affect numerous pathways by targeting multiple genes [47, 48]. Advertisement 3.

Output: corroborate


Input: Claim: Ocean carbon capture may mitigate climate change but requires further study for safety. [SEP] Text: Large-scale CCUS projects currently online or in development are expected to capture more than 400 megatons of CO2 per year by 2030. That’s far short of the more than 1 gigaton of CO2 per year CCUS projects would need to capture by then in order to stay on track with the Agency’s scenario for achieving net-zero emissions by 2050. A recent analysis suggests that at least 5 billion tons annually is achievable. The research, not yet published, limits CCUS growth to an average of 20 percent per year until 2050 for most cases. “That’s a major contribution to climate mitigation,” says Samuel Krevor, an environmental engineer at London and a lead author of the research. Krevor, like many researchers in the field, receives some funding from fossil fuel companies. says the contribution is likely to be minor relative to other climate solutions, including shifting to renewable energy and planting and maintaining forests to help store away CO2 from the atmosphere. Using data from the IPCC, Hauber and colleagues calculate that by 2030, CCUS will provide just 2. 4 percent of all emissions reductions. What’s more, projects rarely meet their stated goals. An analysis by the Institute for of 13 key CCUS projects, published in 2022, found that most failed to reach their targets. Relying on publicly available data, the analysis found, for example, that the facility has underperformed by 36 percent over its lifetime. When there were fewer customers for the captured CO2, the analysis finds, the facility released it into the atmosphere. A facility in Decatur, Illinois, run by Midland, an agribusiness based in Chicago, was nearly 50 percent off its annual target at the end of 2020. An ExxonMobil spokesperson said the company has made progress since the report, noting that the company has expanded CO2 storage capacity at its facility by over 1 million metric tons annually. And a spokesperson for Midland said that how much CO2 it captures and stores depends on how much biofuel it produces. The company’s Decatur facility is looking at different strategies to decarbonize its operations including capturing CO2 produced by a new gas power plant that will provide energy for the company’s biofuel facility. It’s also unclear how much CO2 capacity underground storage sites possess.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Metabolic analysis and key metabolite identification To investigate the metabolic pathways involved in zigzag-shaped stem formation, the metabolites in the stems of and MZ were detected using UPLC-ESI-TOF-MS/MS. In total, 752 metabolites clustered into 97 KEGG pathways were identified from and MZ, and among these metabolites, 75, 84 and 86 metabolites showed significantly different levels in the MZ-vs-QQ, MZ-vs-LYQQ and QQ-vs-LYQQ comparisons, respectively (Additional file 1: Fig. S5). diagram analysis showed that 13 metabolites overlapped between MZ-vs-QQ and MZ-vs-LYQQ, which were our metabolites of interest (Fig. 6a), and the results indicated that these differential metabolites might be associated with zigzag-shaped stem formation in tea plants. Based on their log2 fold change values, these differential metabolites were visualized as a heat map in Fig. 6b. Quercetin O-acetylhexoside, methyl gallate, D-pantothenic acid and L-glutamic acid were upregulated in both QQ and LYQQ, whereas the remaining metabolites, including fustin, 10-formyl-THF, skimmin, LysoPC 20:4, LysoPC 18:1 (2n isomer), LysoPC 18:3 (2n isomer), 2-methylsuccinic acid, 2-isopropylmalate, and caffeine, were significantly downregulated in tea plants with zigzag-shaped shoots. DiscussionPlants are sessile and cannot move freely from their habitat, even if they encounter adverse environments. Generally, plant shoots grow upward, whereas roots grow downward; therefore, shoot architecture is a determinant of plant morphology. In tea plants, the shoots play a substantial role in determining the horticultural characteristics and tea yield, and almost all tea plant cultivars exhibit straight stems. The two tea plants QQ and LYQQ, with zigzag-shaped shoots, were identified and planted previously; however, with advances in research, there is increasing interest in the mechanism by which QQ and LYQQ develop their zigzag-shaped shoots.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Expression of miRNAs in preimplantation embryosThe expression of miRNAs in preimplantation embryos has been mainly studied by knock‐out experiments, by cloning experiments and by identifying individual miRNAs by microarray analysis and real‐time polymerase chain reaction [93]. The expression studies have been carried out using animal models and tissues, cultured cells; that is, cancer cells and human embryonic stem cells; and mouse/bovine/human gametes and embryos. Human embryonic stem cells, which are derived from the inner cell mass of an embryo at the blastocyst stage and are characterised by their ability of self‐renewal and multipotency, are the key in gene expression research since the access of human embryos is difficult and these cells are one of the closest representations of human embryos. Studying miRNA expression in stem cells not only gives insight into potential miRNAs expressed in human embryos but also may show the important role of miRNAs in the stem cell functioning [94]. MiRNA expression has been observed as early as oogenesis and spermatogenesis in mouse, bovine and human [95, 96]. Differences in the miRNA expression have been observed between immature and mature oocytes that may represent the natural turnover and indicate that each embryonic stage is defined by a specific miRNA. Similar miRNA expression profiles in mature mouse oocytes and early developing embryos indicate that at these stages the zygote has maternally inherited miRNAs [50]. Similar to oocyte, sperm carries a range of miRNAs. Approximately 20% of these miRNAs are located in the nuclear or perinuclear part of the sperm indicating that these miRNAs are transferred to the zygote at the time of fertilisation [97]. It was suggested that the sperm‐borne miRNAs may down‐regulate the maternal transcripts in mammals. However, when this hypothesis was tested using microarray analysis, it was shown that none of these miRNAs in the sperm have significant importance since all of them were already present in the oocytes (meiosis II) [98]. Multiple miRNAs were involved in the formation of germ cell layers. MiR‐290, which was expressed at different levels during preimplantation embryo development of mouse embryos, had a negative effect on the germ cell and mesoderm differentiation in the mouse ES cells via targeting Nodal inhibitors [99].

Output: pass


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: & & & & &Aa : español español& & caption full caption right caption left caption center &A expert &A expert 1 Slide 2 Slides 3 Slides 4 Slides 5 Slides 6 Slides 7 full width center : capture, utilization and storage technologies are expected to play a role in cutting CO2 emissions and limiting global warming, but some critics say they are costly and divert attention from more effective strategies. help with climate change, carbon capture will have to evolve The technologies are a useful tool to reduce CO2 levels but have yet to move us away from fossil fuels Gilbert 07. 09. 2024 sound science and smart storiesHelp us make scientific knowledge accessible to allDonate today More than 200 kilometers off Norway’s coast in the sits the world’s first offshore carbon-capture-and-storage project. Built in 1996, the Sleipner project strips carbon dioxide from natural gas — largely made up of methane — to make it marketable. But instead of releasing the CO2 into the atmosphere, the greenhouse gas is buried. The effort stores around 1 million metric tons of CO2 per year — and is praised by many as a pioneering success in global attempts to cut greenhouse gas emissions. Last year, total global CO2 emissions hit an all-time high of around 35. 8 billion tons, or gigatons. At these levels, scientists estimate, we have roughly six years left before we emit so much CO2 that global warming will consistently exceed 1. 5 degrees Celsius above average preindustrial temperatures, an internationally agreed-upon limit. (Notably, the global average temperature for the past 12 months has exceeded this threshold. )Phasing out fossil fuels is key to cutting emissions and fighting climate change. But a suite of technologies collectively known as carbon capture, utilization and storage, or CCUS, are among the tools available to help meet global targets to cut CO2 emissions in half by 2030 and to reach net-zero emissions by 2050. These technologies capture, use or store away CO2 emitted by power generation or industrial processes, or suck it directly out of the air. Panel on (IPCC), the body charged with assessing climate change science, includes carbon capture and storage among the actions needed to slash emissions and meet temperature targets. Carbon capture, utilization and storage technologies often capture CO2 from coal or natural gas power generation or industrial processes, such as steel manufacturing.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Zigzag-shaped shoots, which occasionally appear in garden plants, are an unusual trait in woody plants, but there is relatively little information regarding this feature. Similarly, in Arabidopsis, zig mutant stems elongate in a zigzag fashion, curve upward at the internodes and, interestingly, exhibit abnormal gravitropism in hypocotyls and shoots [8-11]. To understand the cause of this anomalous zigzag-shaped morphology, we observed stem sections using optical microscopy. There were no aberrations in the main tissue structures (Fig. 1). However, differences in cell arrangement and shape were observed between the zigzag-shaped stems of QQ and LYQQ and the MZ stems, including the arrangement of cortex cells, which were disordered and loosely arranged, and the cells in the cortex and pith exhibited aberrant shapes (Fig. 1). Consistent with our findings, similar cell shapes and arrangements were found in the zig-1 mutant stems of Arabidopsis [8]; however, different cell shapes and arrangements were observed in the epidermal layer and pith of Arabidopsis than in the cortex and pith of tea plants; this may represent a difference between woody plants and Arabidopsis. Thus, zigzag-shaped stems might be caused by the anomalous shape, arrangement and expansion of cells in tea plants. To investigate the molecular mechanism of zigzag-shaped stem formation in tea plants, shoots were collected, and transcriptome sequence analysis was performed. In total, 46. 06 million clean reads were generated, and 6232, 7212 and 6930 DEGs were identified from MZ-vs-QQ, MZ-vs-LYQQ and QQ-vs-LYQQ, respectively (Additional file 2: Table S1 and Fig. 3b). These DEGs were mainly enriched in several pathways, such as ‘Biosynthesis of secondary metabolites’, ‘Plant-pathogen interaction’, and ‘Stilbenoid, diarylheptanoid and gingerol biosynthesis’, indicating that these pathways might be associated with differences among cultivars (Fig. 3b).

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Furthermore, HPAT5 was shown to interact with let‐7 family of miRNAs [110]. Implantation of embryos involves complex mechanisms and many different genetic and physiological factors are involved during the process. Developing preimplantation embryo must have a good coordinated interaction with the maternal uterine endometrium. LncRNAs were shown to be differentially expressed in endometrial tissues obtained from pigs with pregnancy and non‐pregnancy with two lnc_01729386 and TCONS_01325501, with potential roles in implantation [111]. Advertisement 5. Gene expression and assisted reproductive technologiesworld, approximately 1% of children are born with assisted reproductive technology (ART) treatments. The infertile couples have the best possibility to conceive a child with these treatments. Although these techniques have been considered to be safe in terms of foetal and post‐natal development [112, 113], there is an increased risk for morbidities, especially imprinting disorders [114]. Furthermore, the global gene expression profiles vary due to in vitro culture of zygotes [115, 116] and in vitro fertilisation processes [117]. Following in vitro culture, apoptotic and morphogenetic pathways have shown to be altered [118]. Intra‐cytoplasmic sperm injection (ICSI), one of the widely used ART techniques, provides infertile couples with sperm motility problems a great chance to have a baby. ICSI is a unique process in which the sperm is injected into the ooplasm [119]. However, ICSI bypasses a number of physiological processes that would normally take place. These embryos derived from ICSI were shown to be cleaved at a slower rate. Furthermore, a reduced number of embryos become hatched with a fewer number of cells and the calcium oscillations are shorter with different patterns [120]. Mice embryos generated by ICSI were shown to be obese and have anomalies of the organs [121]. Advertisement 6. ConclusionNormal development of preimplantation embryos involves complex mechanisms. For a normal developing embryo, the expression of both maternal and paternal genes is required. Several factors are involved in the regulation of parental genes in preimplantation embryos. Epigenetic modifications are one of the most important factors that are involved in the regulation of gene expression during preimplantation embryos. Extensive research studies have been performed throughout the years to establish the methylation profiles of the mammalian gametes and embryos.

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: The CO2 is compressed into a liquid under high pressure and transported through pipelines to sites where it may be stored, in porous sedimentary rock formations containing saltwater, for example, or used for other purposes. The captured CO2 can be injected into the ground to extract oil dregs or used to produce cement and other products. Governments and industry are betting big on such projects. Last year, for example, the British government announced £20 billion (more than $25 billion) in funding for CCUS, often shortened to CCS. States allocated more than $5 billion between 2011 and 2023 and committed an additional $8. 2 billion from 2022 to 2026. Globally, public funding for CCUS projects rose to $20 billion in 2023, according to the Agency (IEA), which works with countries around the world to forge energy policy. Given the urgency of the situation, many people argue that CCUS is necessary to move society toward climate goals. But critics don’t see the technology, in its current form, shifting the world away from oil and gas: In a lot of cases, they point out, the captured CO2 is used to extract more fossil fuels in a process known as enhanced oil recovery. They contend that other existing solutions such as renewable energy offer deeper and quicker CO2 emissions cuts. “It’s better not to emit in the first place,” says Grant Hauber, an energy finance adviser at the Institute for a nonpartisan organization in Lakewood, Ohio. greening of planes, trains and automobiles power heats up Food & to overcome political polarization on climate change What’s more, fossil fuel companies provide funds to universities and researchers — which some say could shape what is studied and what is not, even if the work of individual scientists is legitimate. For these reasons, some critics say CCUS shouldn’t be pursued at all. “Carbon capture and storage essentially perpetuates fossil fuel reliance. It’s a distraction and a delay tactic,” says Jennie Stephens, a climate justice researcher at in Boston. She adds that there is little focus on understanding the psychological, social, economic and political barriers that prevent communities from shifting away from fossil fuels and forging solutions to those obstacles.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: To gain insights into the DEGs that specifically regulate zigzag-shaped stem development, we made a Venn diagram of cultivar comparisons and identified 2175 overlapping DEGs between MZ-vs-QQ and MZ-vs-LYQQ, which were mainly enriched in the “Plant-pathogen interaction”, “Phenylpropanoid biosynthesis”, “Flavonoid biosynthesis” and “Linoleic acid metabolism” pathways (Fig. 4). Among these pathways, the “Phenylpropanoid biosynthesis” pathway serves as a source of metabolites in plants, is involved in the biosynthesis of lignin, flavonoids, coumarins and lignans, and plays a fundamental role in plant structural support [29, 30]. It has been found that, in Arabidopsis, mutation of the genes encoding cinnamate 4-hydroxylase (C4H) and hydroxycinnamoyl-coenzyme A shikimate:quinate hydroxycinnamoyl-transferase (HCT) involved in this pathway resulted in changes in the structural, developmental, and reproductive phenotypes of Arabidopsis plants [31-33]. Interestingly, the flavonols quercetin and kaempferol have been shown to inhibit polar auxin transport and to enhance consequent localized auxin accumulation [34-36]. Recently, Kuhn, et al. [34] suggested that flavonols could modulate auxin transport by modifying the antagonistic kinase/phosphatase equilibrium. Therefore, flavonols could affect auxin transport in zigzag-shaped shoots. On the other hand, Ramos, et al. [37] found that the concentration of quercetin in the upper half of longitudinally dissected 45-degree-inclined radiata pine seedlings was higher than that in the lower half and than that in non-inclined seedlings when seedlings were inclined for one month, indicating that quercetin can accumulate in inclined shoots such as the internodes of zigzag-shaped shoots. Consistently, we observed that a C4H gene (TEA016772.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: CpGs were classified as unmethylated (below the first quartile of the total distribution; CpGs, dark red) or methylated (above the third quartile of the total distribution; me-CpGs, light blue) for muscle and for testis. The expression of genes measured as log2-transformed count per million (cpm) values is shown in the upper panel depending on the type of CpGs these genes contained in their first intron. In the lower panel, the relative distance of the CpGs and me-CpGs from the first exon-first intron boundary was calculated as distance from nucleotide 0 (bp)/width of the intron (bp). The sequences of the four enriched TF-binding motifs that contained CpGs are also shown. rank sum test with continuity correction was used to test for statistical differences of gene expression and relative distance between CpGs and me-CpGs, which are reported with the following equivalence: ***p < 0. 001; *p < 0. 05Full size image Table 1 Effects on gene expression of the methylation status and the relative distance of the CpGs inside the four transcription factor binding motifs enriched in the first intronsFull size table The DNA methylation of the first intron associates with the upstream features and is independent of its lengthIn order to test whether there is association of the methylation state of two gene features, we calculated the odds ratio (OR) as representative of the odds that a gene feature A is also methylated when gene feature B is methylated. In both tissues, there was strong evidence for statistically significant association of the DNA methylation of the promoter, the first exon and the first intron (Fig. 5), since the 99. 9% confidence intervals (CIs) were far from overlapping the value 1. The gene body methylation, including all exons and introns of a gene, showed strong association with the DNA methylation of all gene features tested, while the methylation of the rest of exons and the rest of introns was also associated. In testis, the methylation of the first intron was associated with the methylation of the rest of exons as well. Fig. 5Association of DNA methylation between pairs of gene features as measured by odds ratio.

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: According to the Global CCS Institute, an industry-led think tank headquartered in Melbourne, Australia, of the 41 commercial projects operational as of July 2023, most were part of efforts that produce, extract or burn fossil fuels, such as coal- and gas-fired power plants. That’s true of the Sleipner project, run by the energy company Equinor. It’s the case, too, with the world’s largest CCUS facility, operated by ExxonMobil in Wyoming, in the United States, which also captures CO2 as part of the production of methane. Granted, not all CCUS efforts further fossil fuel production, and many projects now in the works have the sole goal of capturing and locking up CO2. Still, some critics doubt whether these greener approaches could ever lock away enough CO2 to meaningfully contribute to climate mitigation, and they are concerned about the costs. Others are more circumspect. Sally Benson, an energy researcher at Stanford University, doesn’t want to see CCUS used as an excuse to carry on with fossil fuels. But she says the technology is essential for capturing some of the CO2 from fossil fuel production and usage, as well as from industrial processes, as society transitions to new energy sources. “If we can get rid of those emissions with carbon capture and sequestration, that sounds like success to me,” says Benson, who codirects an institute that receives funding from fossil fuel companies. Annual global carbon dioxide emissions need to be cut in half by 2030, or by about 20 gigatons, to achieve net-zero emissions by 2050. Carbon capture, utilization and storage technologies, called CCUS or CCS, are estimated to contribute less to emissions reductions than some other climate mitigation strategies, including shifting to renewable energy or restoring ecosystems. CCUS can also be more expensive; costs here are expressed as additional costs relative to the existing technology or status quo effort. Born from the oil industryCCUS technology was not conceived as a climate solution. It dates to the 1970s and 1980s, when oil production in the began to decline. Oil companies started using a process called enhanced oil recovery that injects CO2 (or water) into sedimentary rocks to recover hard-to-reach dregs of oil, a precursor to today’s CCUS.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1) was significantly differentially expressed between MZ-vs-QQ and MZ-vs-LYQQ; moreover, we found that skimmin (pmf0295) expression was reduced in the MZ-vs-QQ (log2 FC: -0. 995) and MZ-vs-LYQQ (log2 FC: -3. 52) comparisons. Therefore, the zigzag-shaped stems of tea plants might be partially related to flavonoids, especially flavonol-mediated auxin transport. It is well recognized that a zigzag-shaped inflorescence stem results from the mutation of zig (zigzag)/sgr4, which encodes VPS10 interacting 11 (VTI11), a Qb-SNARE involved in vesicle transport between the trans-Golgi network and vacuole that causes abnormal gravitropism in Arabidopsis when mutated [8, 10, 11, 38, 39]. SNAREs play an important role in membrane fusion at the vacuole and are involved in the regulation of amyloplast sedimentation in response to gravity and in cell shape development [11, 39]. ZIG can form a complex with other types of SNARE proteins, including SYP22/SGR3/VAM3, SYP5, and VAMP727, most likely at the prevacuolar compartment and vacuole [11, 40-42]. Although ZIG and the other SGR genes were not significantly expressed, 11 genes mainly involved in vesicular trafficking were identified (Fig. 5d and Additional file 3: Table S3). Among these genes, both vacuolar protein sorting-associated protein genes (VPS18 and VPS41) were repressed in QQ and LYQQ, whereas the expression levels of vesicle-associated membrane protein 714 (VAMP714) and vacuolar-sorting receptor 6 (VSR6) were increased in QQ and LYQQ. It has been established that the phenotype of zig-1 could be partially suppressed by mutations in the zig suppressor1 (ZIP1), ZIP2, ZIP3 and ZIP4 genes in Arabidopsis [38, 43, 44]. Niihama, et al.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: The vast majority of the highest expressed genes in both tissues had DNA methylation below 10% (89. 5% of genes in muscle and 84. 9% in testis). However, in the lowest expressed genes, DNA methylation was more equally distributed to the two extremes, with the 75. 2% of genes in the muscle and the 48. 2% of genes in the testis having less than 10% methylation, and the 24. 8% of genes in the muscle and the 51. 8% of genes in the muscle having more than 90% methylation. More genes contain tDMRs in their first intron than in other gene featuresIn general, there were distinct patterns between the tissue-specific genes and the non-tissue-specific genes that were obvious from the gene expression data. Therefore, we focused on tDMRs between testis and muscle and explored the relationships between differential DNA methylation and differences in gene expression. Both directions of correlation were evident between DNA methylation and gene expression. There was strong negative correlation (ρ = − 0. 73, p < 0. 001) for up-regulated genes, in either testis or muscle that contained hypo-methylated tDMRs inside their gene body or 4 kb upstream of the TSS or downstream of the 3′ UTR (squares in Fig. 6). Nonetheless, there was also weaker positive correlation (ρ = 0. 26, p < 0. 001) for up-regulated genes, in either testis or muscle that contained hyper-methylated tDMRs (circles in Fig. 6). The same two categories of genes showing either negative or positive correlation between DNA methylation and gene expression were obvious in genes that contained tDMRs only in the promoter, first exon or first intron (Fig. 6). There were 187 genes that contained tDMRs in their first intron, while there were fewer genes that contained tDMRs in their promoter (47) and the first exon (75). The majority of the tDMRs in the first intron were located in proximity to the first exon-first intron boundary (Additional file 1: Fig. S7). Fig. 6Differentially expressed genes with differentially methylated regions (tDMRs) between tissues.

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: CCUS technologies are now capturing CO2 from a variety of operations — including at traditional power plants that burn coal or other fossil fuels; in nontraditional plants where energy is produced from biofuels such as ethanol; and during the production of ammonia, which is used in fertilizer. All such efforts complement other practices that turn to natural processes to remove carbon from the atmosphere to help reach net zero, such as planting forests or locking CO2 in soils using sustainable farming practices. The strongest criticisms are lobbed at using CCUS to extract fossil fuels. Today nearly three-quarters of the carbon captured through CCUS projects is used to extract more oil from dregs. The largest CCUS operation, ExxonMobil’s $656 million facility in Wyoming, aims to capture around 8 million tons of CO2 each year from methane extracted from the nearby LaBarge gas fields. ExxonMobil sells the captured CO2 for enhanced oil recovery. Though the effort cuts emissions because some of the CO2 remains in the ground, the burning of the additional fossil fuels it helps extract still releases CO2. Just 12 of the 41 existing projects included in the Global CCS Institute database inject CO2 with the exclusive aim of storing it underground, thus keeping its climate-warming effects at bay. Half of those 12, including the Sleipner project, are involved in methane production — and methane releases carbon dioxide into the atmosphere when burned. Cement manufacturing and iron and steel manufacturing are also desirable targets for CCUS, because each produces around 6 percent to 9 percent of global CO2 emissions, and both processes are difficult to clean up in other ways. Only one project, run by the Company, is capturing CO2 emissions from iron and steelmaking. There are no projects up and running to capture CO2 from cement manufacturing. ’s database includes just a single fully operational, large-scale project that is currently sucking CO2 directly from the air and storing it underground. That project, in Hellisheiði, Iceland, is run by the Swiss company Climeworks. Another, bigger Climeworks project recently started operations but is not yet completed. But the database omits direct air capture projects that are doing other things with the CO2, including one that is sealing it in concrete, and omits smaller-scale and pilot projects that are online or coming online.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: [44] reported that ZIP2, which encodes an AtVPS41/AtVAM2 protein, is involved in protein sorting to the vacuole in Arabidopsis, and the zip2 mutation is a missense mutation. These results indicate that zigzag-shaped stem formation is mainly related to abnormal gravitropism responses mediated by membrane trafficking. Additionally, we also found that six SEC family genes were significantly expressed in the MZ-vs-QQ and MZ-vs-LYQQ comparisons (Fig. 5d and Additional file 3: Table S3); these genes are crucial for SNARE complex assembly and preprotein translocation [45, 46]. Interestingly, we found that both LAZY genes (TEA031847. 1, TEA001744. 1) were markedly repressed in QQ and LYQQ (Fig. 5d and Additional file 3: Table S3). It is well known that loss-of-function mutation of LAZY1 enhances polar indole-3-acetic acid (IAA) transport and reduces shoot gravitropism and therefore regulates the growth angle of lateral branches in rice, Arabidopsis and maize [17-19, 21, 47]; however, the function of LAZY in woody plants remains to be elucidated. Therefore, we propose that the development of zigzag-shaped stems in tea plants might be associated with a change in the shoot gravitropism response, especially one affecting the disruption of membrane trafficking to vacuoles, although the ZIG/SGR4 gene did not exhibit a significant change in expression. The plant hormone auxin is important for organ growth and cell morphogenesis. In this study, seven DEGs involved in auxin metabolism, transport and signalling were identified by comparison of the MZ-vs-QQ and MZ-vs-LYQQ sets, and all of the genes were downregulated in QQ and LYQQ (Fig. 5c and Additional file 3: Table S3). Numerous studies have suggested that polar auxin transport, which is primarily determined by polar localization of PIN auxin efflux carriers, controls plant tropism in roots and shoots and plays essential roles in plant growth [13, 48, 49]. Gerttula, et al.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: DiscussionIn this study, we present an inverse correlation of the DNA methylation in the first intron and gene expression, which is conserved in tissues with different levels of cellular complexity and across vertebrates. Furthermore, we detect CpGs in enriched TF-binding sites close to the first exon–first intron boundary indicative of gene expression and tDMRs the methylation of which correlates with gene expression. Recent studies on the relationship between DNA methylation and gene expression have revealed a key role for the region from + 0. 5 to + 2. 5 kb downstream of the TSS in transcriptional regulation of different human tissues [37, 38]. In addition, the methylation of the first exon was shown in mammalian cell lines to be negatively correlated to gene expression, in a more pronounced way than the promoter region [9]. In parallel, the methylation of the first intron has been shown by functional studies to have both positive and negative correlation with gene expression in specific genes in cancer cell lines, fetal and adult tissues [39], CD4+ cell lines isolated from mice [40], during lineage specification in T cells [41], in multiple myeloma cell lines [42], in leukocytes of patients with schizophrenia [43] and in blood samples isolated from children [44]. Furthermore, it has been suggested that the first intron contains distinct properties from the rest of introns and that is linked to transcriptional regulation [45, 46]. These properties may be linked to the closer proximity of the first intron to the TSS, since in many species the CpG-rich regions expand from the CGI promoter to the surrounding sequences [47]. Other active chromatin marks are enriched in conserved parts of the human first intron [48]. However, to the best of our knowledge, an association at the genome-wide scale of the methylation of the first intron as an outlined gene feature has not been demonstrated to date. In two complex tissues of a phylogenetically distant species, we present the same pattern previously observed in humans. In the European sea bass genome, the median methylation of the first intron showed, consistently in both tissues, the most clear inverse relationship with gene expression among all gene features.

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: A decade ago in a paper in the of Environment and Resources, Benson and Heleen de Coninck, a climate change researcher at the of Technology and in the Netherlands, wrote that, to help mitigate climate change, CCUS needs to serve more than fossil fuel companies seeking to extract oil. In the decade since, Benson notes, CCUS has been slow to expand into other areas largely because of a lack of public policies supporting the technologies, such as government subsidies for new projects or a tax on CO2 emissions that would make it cheaper to sequester than to emit it. However, she notes, this is now changing. When it is fully operational, Climeworks’ Mammoth project will be the world’s largest facility pulling CO2 directly from the air and burying it underground. The project, in Hellisheiði, Iceland, follows another, smaller Climeworks project called Orca. : © 2024 to the futureCCUS may be poised to turn a corner. As of July 2023, 351 new commercial-scale CCUS projects were in the works, according to the Global CCS Institute. Many of these forthcoming projects will capture CO2 with the exclusive goal of burying it underground rather than using it to squeeze out more oil. Around 22 of the projects are aimed at capturing CO2 at cement plants and five will capture CO2 directly from the air and store it underground. Still, a connection with fossil fuels remains: Around 30 will serve methane production, and others are planned for carbon capture at coal- and gas-fired power plants. Even with this new bloom of projects, it’s not clear that the technology has a large part to play in solving our climate woes, says Sean O’Leary, a senior researcher in energy and economics at the Valley Institute, a clean-energy think tank based in Johnstown, Pennsylvania. Current and future projects are unlikely to capture carbon in sufficient quantities to make much of a dent on global emissions, O’Leary says. Estimates suggest that existing projects could capture around 50 million tons of CO2 annually — cutting the more than 35 billion tons of gross global carbon emissions by around 0. 14 percent. Once all 392 projects are online, they could capture a few hundred million tons — about 1 percent of carbon emissions. Estimates of how much carbon CCUS needs to capture to help achieve climate goals vary widely between 1 billion and 30 billion tons annually by 2050.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: [50] proposed that PIN expression in different cambium cells results in auxin transport towards the cambium in the top and bottom of the stem to trigger wood formation in response to gravity in woody stems. Consistent with this finding, we found that the expression of was repressed in QQ and LYQQ (Fig. 5c and Additional file 3: Table S3); these changes in expression in QQ and LYQQ might alter the polar transport of auxin and then affect the auxin gradients between stem sides; therefore, the shoots exhibit bending. Wu, et al. [51] reported that rice VLN2, a type of actin-binding protein involved in microfilament regulation, affects the recycling of PIN2 and polar auxin transport, and vln2-defective mutant plants exhibited a hypersensitive gravitropic response and twisted roots and shoots at the seedling stage. In this study, we also found that VLN2 (TEA030753. 1) was markedly repressed in QQ and LYQQ (Fig. 5e and Additional file 3: Table S3), suggesting that zigzag-shaped stems in tea plants might be related to polar auxin transport and the gravitropism response. Moreover, cell expansion might exert a compressive force, leading to bending of the stem. Our results showed that genes involved in cell expansion and cell wall synthesis, such as expansin, and xyloglucan endotransglucosylase/hydrolase protein, were differentially expressed (Fig. 5a and Additional file 3: Table S3), resulting in alteration of cell expansion and elongation. In addition, wall-associated kinase (WAK) genes were also differentially expressed in MZ-vs-QQ and MZ-vs-LYQQ, suggesting that WAK-mediated cell expansion and signalling pathways might be required for zigzag-shaped stem formation in tea plants. It is possible that cell expansion in the stems can produce a force that can lead to zigzag-shaped shoots. Importantly, cell expansion and differentiation predominantly rely on auxin [12, 52, 53]; thus, the mechanism of auxin regulation in zigzag-shaped shoot development needs to be studied precisely in the different tissue sides of zigzag-shaped stems.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: We further show that the inverse relationship between DNA methylation of the first intron and gene expression is conserved across vertebrate species, since it is evident in the model fish Tetraodon, in the model frog Xenopus and two healthy human tissues. This does not seem to hold in invertebrates, which actually exhibit distinct mechanisms of DNA methylation and extreme diversity [49, 50]. In general, across vertebrates, several characteristics of the sequences related to DNA methylation, like the CpG density, are conserved around the TSSs. These characteristics slightly differ for fish, where there is higher CpG density, but still signatures of CGI promoters [47]. Nevertheless, even though the CpG density differs, conserved mechanisms of regulation are present as reflected in this study. Overall, there seems to be a conserved role for the DNA methylation of the first intron across tissues, vertebrates and developmental stages. The classic promoter methylation–gene expression model seems to hold only in extreme cases and specific genes, while a “triple-inverse” model was suggested, where the methylation of the promoter and the gene body exerts separate influences on gene expression [51]. The variability of DNA methylation in the first intron from 0 to 100% independently of the expression level could be linked to the more variable and larger length of the intron and suggestive of a more complex role of this methylation. In our case, a general pattern would be a negative association of the methylation of the first intron with gene expression in the majority of genes, which is clearest at the extremes of the gene expression range. Nevertheless, subclasses of genes escape this rule and exhibit positive correlations. Indeed, at the genome-wide level there are clusters of genes, each one showing different DNA methylation patterns associated with gene expression [38, 52]. DNA methylation in positive correlation with gene expression has been suggested to appear either as cause or consequence of transcription [53]. Our results also suggest a permissive state of gene expression linked with low methylation, but not a linear inhibitory link with high methylation. These observations are in support of the increasing evidence of a far more complex relationship of the epigenetic modifications—including histone and DNA modifications and noncoding RNAs—with gene expression at a spatiotemporal scale [52].

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: Large-scale CCUS projects currently online or in development are expected to capture more than 400 megatons of CO2 per year by 2030. That’s far short of the more than 1 gigaton of CO2 per year CCUS projects would need to capture by then in order to stay on track with the Agency’s scenario for achieving net-zero emissions by 2050. A recent analysis suggests that at least 5 billion tons annually is achievable. The research, not yet published, limits CCUS growth to an average of 20 percent per year until 2050 for most cases. “That’s a major contribution to climate mitigation,” says Samuel Krevor, an environmental engineer at London and a lead author of the research. Krevor, like many researchers in the field, receives some funding from fossil fuel companies. says the contribution is likely to be minor relative to other climate solutions, including shifting to renewable energy and planting and maintaining forests to help store away CO2 from the atmosphere. Using data from the IPCC, Hauber and colleagues calculate that by 2030, CCUS will provide just 2. 4 percent of all emissions reductions. What’s more, projects rarely meet their stated goals. An analysis by the Institute for of 13 key CCUS projects, published in 2022, found that most failed to reach their targets. Relying on publicly available data, the analysis found, for example, that the facility has underperformed by 36 percent over its lifetime. When there were fewer customers for the captured CO2, the analysis finds, the facility released it into the atmosphere. A facility in Decatur, Illinois, run by Midland, an agribusiness based in Chicago, was nearly 50 percent off its annual target at the end of 2020. An ExxonMobil spokesperson said the company has made progress since the report, noting that the company has expanded CO2 storage capacity at its facility by over 1 million metric tons annually. And a spokesperson for Midland said that how much CO2 it captures and stores depends on how much biofuel it produces. The company’s Decatur facility is looking at different strategies to decarbonize its operations including capturing CO2 produced by a new gas power plant that will provide energy for the company’s biofuel facility. It’s also unclear how much CO2 capacity underground storage sites possess.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: In this study, 20 transcription factors (TFs) belonging to different TF families, including two ARFs, were differentially expressed in MZ-vs-QQ and MZ-vs-LYQQ, and most of these TFs were significantly repressed in QQ and LYQQ (Fig. 5b and Additional file 3: Table S3). Almost all of these genes had homologues associated with plant growth and developmental regulation in other plants. For instance, (TEA031729. 1), a MYB-type TF, could interact with WOX to control wood formation in poplar [54]; overexpression of IBH1 causes erect leaves in rice and dwarfism in Arabidopsis [55]; and HEC1 coordinates with WUS to promote stem cell proliferation in the shoot meristem [56, 57]. kawakamii, antisense suppression of PkMADS1, a regulator of shoot morphogenesis, resulted in zigzag-shaped shoots [58]. Interestingly, in some transformants of antisense PkMADS1, the main shoot apex appeared to be used up early during leaf formation, and then, the axillary bud of the youngest leaf took over the function of the apical meristem, resulting in the formation of one leaf per node and the zigzag-shaped growth habit for the stem, indicating that central and lateral meristem fates regulated by a variety of TFs may relate to zigzag-shaped shoot formation. Recently, several genes that regulate architectural phenotypes in woody plants, such as 2 (ARK2) in Populus [50] and 1C (GID1C), Control 1 (TAC1) and WEEP in peach [23, 59, 60], have been isolated; however, most of these genes are related to the plant gravitropic response, and none of these genes encode TFs. Additionally, among the nine SGR genes, SGR1 and SGR7 encode scarecrow (SCR) and GRAS family TFs, respectively. We found that the SCR gene (TEA030046. 1) was markedly repressed in QQ and LYQQ (Fig. 5b and Additional file 3: Table S3).

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: The function of the inverse relationship between DNA methylation of the first intron and gene expression could be partially explained by the presence of intronic enhancers interacting with the promoters of their corresponding genes. Indeed, the intron-mediated enhancement is a well-described phenomenon [48, 54, 55]. Silencing of intragenic enhancers is considered to play a role even more significant than promoter methylation in the silencing of their target genes [7]. In addition, intronic enhancers present tissue-specific methylation status associated with gene expression [56, 57]. Our results also revealed enriched TF-binding motifs common between tissues. Moreover, the unmethylated CpGs tend to be located closer to the beginning of the first intron and associated with higher gene expression levels, while the methylated CpGs tend to be further downstream and associated with lower gene expression levels. Therefore, the methylation status of the CpGs at shorter or greater distances from the beginning of the first intron which belong to a TF-binding motif is indicative of the gene expression level. Taken together, these results further support a regulatory role for the DNA methylation in the first intron region, although further experiments are needed to demonstrate the mechanistic relationships at the functional level. tDMRs located in the whole gene showed both positive and negative correlation with gene expression as in human tissues [11]. Here, in addition to confirm this in a phylogenetically distant species, we partition the genomic localization of tDMRs in three important gene features: promoter, first exon and first intron. tDMRs are distributed across all these gene features and exhibit both directions of correlation, but no enrichment of positive or negative correlation depending on the location. This is in accordance with the latest findings in human tissues [11] and in contrast to the standard model of gene regulation by DNA methylation. However, in the first intron, there are more tDMRs, in agreement with our finding of the importance of the first intron in the regulation of gene expression by DNA methylation. In human macrophages after bacterial infection, the majority of gene body DMRs were also located in the first introns of genes [58]. Taken together, these results suggest an overlooked role for the DNA methylation of the first intron in the tissue-specific regulation of gene expression.

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: Most global estimates suggest that between 10,000 billion and 30,000 billion tons of underground storage is available. Some estimates put it as a high as 55,000 billion tons. Greig, a chemical engineer at who previously worked on a CCUS project for the fossil fuel industry, notes that those volumes could be way off. Assessments are based on estimates of the pore space in different geologic formations — those pores provide open spaces that can hold CO2 — which gives only a rough picture, he says: “Subsurface storage is by nature uncertain. ”Such uncertainties have caused projects to veer off course, including a $2. 7 billion project to separate CO2 from methane in gas fields in In Salah, Algeria, and store it 1. 9 kilometers underground. The energy company Equinor and its partners started injecting CO2 there in 2004 with the aim of storing 1. 1 million tons annually. But it suspended operations because of limits in underground capacity, according to an Equinor spokesperson. There were concerns that the gas was escaping up toward the cap rock, which acts as a final safety net sealing the CO2 in place. On top of the uncertainty, money is a problem. Some skeptics say that the costs of building and operating CCUS projects ultimately make them unviable. According to 2019 data from the IEA, the costs of capturing CO2 range from $15 to $120 per ton, depending on how dilute the gas stream is. Cost estimates for capturing CO2 directly from the air, where it is very dilute, typically vary between $225 and $500 per ton, with some estimates as high as $1,000 per ton. Multiply that price tag by even a small portion of the 1 billion tons of CO2 that the IPCC says needs to be removed from the atmosphere by 2050, and the costs quickly add up. Stay in the KnowSign up for the newsletter todaySome experts point out that these costs will likely go down as the technologies mature and if the market increases, though not necessarily on the same scale as the dramatic costs reductions seen for solar and wind power technology. For example, the IEA notes that costs for CO2 capture from coal-fired power plants dropped from over $100 per ton in 2014 to $65 per ton in 2017, and it estimates that in projects built from 2025 to 2027, the cost will be around $45 per ton.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Plant growth and development are directed by a TF-mediated complex network integrated with plant hormones, enzymes and other cellular components; therefore, as-yet-unknown TFs may be involved in the regulation of plant architectural phenotypes. ConclusionIn the current study, we investigated the mechanism of zigzag-shaped shoot formation in tea plants using comparative transcriptomics and metabolomic analysis. The results showed that zigzag-shaped stem development in tea plants might be regulated by a complex network involving vesicular trafficking, phytohormones, cell expansion, secondary metabolism, and diverse transcription factors. Importantly, zigzag-shaped shoot formation might be closely related to alterations in the gravitropic response and polar auxin transport in tea plants. Our findings provide insights into zigzag-shaped shoot formation in tea plants and serve as a valuable foundation for further investigations of architecture formation in woody plants. MethodsPlant materials The tender stems (between the first and third leaves from the apical bud) of tea plants with erect (C. sinensis var. Meizhan, MZ) and zigzag-shaped (C. sinensis var. Qiqu, QQ; C. sinensis var. Lianyuanqiqu, LYQQ) shoots were collected from the germplasm resource garden of in October 2018. A portion of each sample was immediately frozen in liquid nitrogen and then stored at -80°C until use for transcriptome sequencing and metabolite analysis. The remaining samples were fixed in cold fixative solution (4°C) for section observation. All samples were examined in triplicate and used as biological replicates. Tissue section observation Longitudinal stem sections were sliced and stained as previously described by Ile, et al. [61] with minor modifications. At least seven stems from each tea plant cultivar were cut into fragments (<0. 5 cm) and fixed in fixative solution over 72 h at 4°C.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: We used RRBS to assess DNA methylation and RNA-seq to measure the gene expression levels in the European sea bass genome which is one of the best annotated teleost genomes [31]. Nevertheless, the precision of the annotation of genes and their regulatory elements is not comparable to model species, like human or mouse. Therefore, we defined promoters as the region − 1000 kb upstream the predicted TSSs, as commonly arbitrarily defined [59,60,61,62,63,64], but without excluding the possibility of alternative TSSs or variable promoter lengths. The limitations of the sea bass genome annotation may influence also the gene expression data, where the analysis could only be performed at the gene level, based on the current annotation. RRBS allows for enrichment of the standard relevant parts of the genome for DNA methylation, e. g. , promoters and CpG islands, and requires only a modest amount of sequencing [65, 66], making it a cost-effective alternative to WGBS which is considered generally inefficient since only 20–30% of the reads provide relevant information [67, 68]. Our RRBS results, including the genome representation and the actual methylation values, are comparable to other teleost fish, like the stickleback [69], the Atlantic salmon [70] and the zebrafish [71]. Regardless of the limitations of this study related to the main species in question and the techniques used, our key results were confirmed in other vertebrate species, corroborating the general trends shown in the sea bass, even accepting the possibility that some genes may be not well annotated. ConclusionsOur integrative analyses clearly reveal the important and conserved role of the methylation level of the first intron and its inverse association with gene expression regardless of tissue and species. Notably, the first intron exhibits a tissue-independent enrichment for TF-binding motifs and the methylation of the CpGs they contain is indicative of the gene expression level. Furthermore, the first intron presents a higher number of tDMRs than other gene features, suggestive of a regulatory role in tissue-specific expression. These findings not only contribute to our basic understanding of the epigenetic regulation of gene expression but also identify the first intron as an informative gene feature regarding the relationship between DNA methylation and gene expression where future studies could be focused, e. g.

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: Partly because of the costs, CCUS should be prioritized for cases where there are no other reasonable approaches to reducing CO2 emissions, says Sabine Fuss, a climate economist at the Institute on and at of Berlin. She does, though, see a potential role for direct air capture despite its expense. And while researchers are divided on the feasibility of direct air capture, Fuss thinks it needs to be funded regardless. If the world overshoots its climate targets, she says, we will likely need this technology to reach net-zero emissions and forestall even worse effects of climate change. How big a role CCUS will eventually need to play is up to us and what we do now, Fuss says. But given the uncertainties, we can’t continue to burn fossil fuels and release carbon and count on CCUS to clean it up afterward. “We have to do all that we can to reduce emissions in the short to medium term rather than rely on CO2 removals in the longer run,” she says. 10. 1146/knowable-070924-2 is a freelance reporter based in Washington, DC, who covers the environment, agriculture and sustainability. She’s a good listener, a keen observer and a bit of a cynic. Check out her work at bynatashagilbert. com or @ngreports.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: The stems were dehydrated by transferring them sequentially through a series of increasing concentrations of ethanol (75 to 100% absolute ethanol), followed by 100% ethanol, ethanol:xylene (2:1), ethanol:xylene (1:1), ethanol:xylene (1:2), pure xylene, pure xylene (each for 1 h), xylene:Paraplast (1:1) for 24 h, and molten Paraplast (melting point 65°C) for 48 h and finally embedded in freshly molten Paraplast. Central longitudinal sections of 5 μm thickness per stem were cut using a disposable-blade rotary microtome (RM2016, Leica, Shanghai, China), allowed to stand overnight and dried at 40°C for 4 h. Sections were dewaxed in xylene, hydrated gradually in decreasing concentrations of ethanol (from 100 to 70%) and stained with safranine (1. 0% for 2. 5 h) followed by (1. 0% for 8 s) in ethanol. After staining, the stem sections were observed under a Leica DMi8 inverted microscope (Leica, Shanghai, China). UPLC-ESI-MS/MS analysis and differential metabolite identification A total of 100 mg of powder from crushed freeze-dried samples was weighed and extracted overnight at 4°C with 1. 0 ml of 70% aqueous methanol containing 0. 1 mg/L lidocaine as an internal standard. Following centrifugation at 10,000 ×g for 10 min, the supernatant was absorbed and filtered (SCAA-104, 0. 22-μm pore size; ) before liquid chromatography-tandem mass chromatography (LC-MS/MS) analysis. Quality control samples were mixed with all the samples to ensure the reproducibility of the entire experiment. The extracted compounds were analysed using an ultra performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) system (UPLC, Shim-pack 30A; MS/MS, 6500 QTRAP) [62]. For compounds separation, column, mobile phases, and operation parameters were chosen or set following the description by Xu et al. [63].

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Each library was sequenced using the v3-HS, in 76-bp paired-end mode on an Illumina HiSeq 2000 instrument following the manufacturer’s protocol. Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files. RNA-seq analysisRNA-seq reads were aligned with the -seq pipeline v1. 7 ( which is based on the GEM mapper [73]. The pipeline aligns the reads in a sample in three phases, mapping against the reference genome (dicLab v1. 0c, Jul. 2012), against a reference transcriptome (track) and against a de novo transcriptome, generated from the input data to detect new junction sites. The sea bass genome used here is one of the best in silico annotated fish genomes [31]. After mapping, all alignments were filtered to increase the number of uniquely mapped reads. The filtering criteria included a minimum intron length of 20 bp, a maximum exon overlap of 5 bp and a filter step against a reference annotation checking for consistent pairs and junctions where both sites align to the same annotated gene. The libraries’ statistics including the number of raw reads and the average reads aligned can be found in Additional file 2. The same pipeline was used to quantify expression at the gene level. Similarity across RNA-seq samples was investigated with principal component analysis (PCA; Additional file 1: Fig. S8A), where the first principal component separated the samples by tissue type and explained almost 96% of the variance. One muscle sample was excluded from further analysis since it was clearly an outlier in the quality clustering. The variation in gene expression values was higher and with more extreme values in muscle (Levene’s test; p < 0. 001), whereas the testis had higher expression median (Mood’s median test; χ2 = 3372. 7, p < 0. 001; Additional file 1: Fig. S9A). Subsequently, the TMM method [74] was used for gene expression normalization, which takes into account not only library size (sequencing depth) of the samples but also the composition of the RNA population. The EdgeR robust method [75] was used for differential expression analysis. Genes with p adjusted < 0. 05 were considered significant.

Output: pass


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: September 01 2018 Can carbon capture from air shift the climate change equation? Critics dismiss the idea of scrubbing meaningful amounts of carbon dioxide from the air, but proponents say the approach could be scaled up for the job. Search for other works by this author on: PubMed 10. 1063/PT. 3. 4018 Open the PDF for in another window and Can carbon capture from air shift the climate change equation? . 1 September 2018; 71 (9): 26–29. Download citation file: Ris (Zotero) toolbar search Menu toolbar search search input Search input auto suggest filter your search plants, Synthetic fuel, Energy policy, Energy storage, Petroleum, Renewable energy, Climate change, Chemical elements, Chemical compounds, News and events Of all the schemes for rescuing the world from the worst effects of climate change, perhaps none seems more quixotic than extracting carbon dioxide directly from the air. Yet at least three companies have developed working capture systems and lined up serious investments to deploy them. All plan to make money on the venture, by selling the gas for production of chemicals, fertilizers, and synthetic fuels and even for desalination, but they say their real goal is to alter the climate change equation. Although CO2 removal is conceptually straightforward, using it to address the climate change problem is an enormous challenge. Yet dramatically reducing or eliminating net global carbon emissions is vital if the world is to stay below the 2 °C temperature increase from preindustrial levels that scientists say is the threshold for the direst impacts of climate change. That task is formidable: 37 gigatons of CO2 were emitted in 2017, according to a projection by the Project. The sum is likely to grow in coming years as developing countries use more energy. View largeDownload slideClimeworks’ direct-air capture plant supplies 900 tons of carbon dioxide a year to a commercial greenhouse in Hinwil, Switzerland. View largeDownload slideClimeworks’ direct-air capture plant supplies 900 tons of carbon dioxide a year to a commercial greenhouse in Hinwil, Switzerland. Close modal Trying to counter such massive emissions with direct-air capture (DAC) seems incredible to some. The atmospheric concentration of the gas is just over 400 ppm, up from around 277 in the preindustrial era. At 100% capture efficiency, 2500 molecules of air must be scrubbed to capture one molecule of CO2.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: The effluent was further transported to an ESI-triple quadrupole-linear ion trap (QTRAP)-MS. Analyst 1. 6. 1 software was employed for metabolite identification. Details on data filtering, peak detection, alignment, calculations, and differential metabolite identification were described by Tang et al. [64]. Particularly, metabolites with T-test P values <0. 05 and VIP ≥ 1 were considered as differential metabolites and mapped to KEGG metabolic pathways for pathway enrichment analysis (FDR ≤ 0. 05)[65]. RNA isolation, library construction, Illumina sequencing, and data processing The total RNA from each sample, which consisted of at least 30 shoots collected from over 10 tea individuals, was extracted using the (). The total RNA quantity and integrity were evaluated and estimated using an 2100 system () and a NanoDropTM ultraviolet spectrophotometer (), respectively. cDNA libraries were constructed using the kit (Gene, Beijing, China) and sequenced using an Illumina HiSeq TM 2500 instrument (Co. , Guangzhou, China). High-quality clean reads were acquired by removing adaptor sequences, reads containing more than 10% unknown nucleotides (N), and low-quality reads containing more than 50% low-quality (Q value≤20) bases; then, the Q20 and Q30 values, GC content, and sequence duplication levels of the clean reads were calculated. The clean reads of each sample were then mapped to the tea plant genome by TopHat2 [66] (version 2. 0. 3. 12). Gene abundances were quantified with RSEM software, and the unigene expression levels were quantified using fragments per kilobase of transcript per million mapped reads (FPKM) values [67]. To identify DEGs across samples or groups, the edgeR package ( was used, and genes with |log2FC| ≥1 and FDR <0. 05 were identified as DEGs. DEGs were then subjected to enrichment analysis of GO functions and KEGG pathways using the Gpackage [68] and KOBAS software [69], respectively. Quantitative real-time PCR validation To validate the reliability of the gene expression analysis in this study, 16 genes were selected for real-time qPCR analysis. Total RNA samples were used for cDNA synthesis according to the method recommended by the SuperScript® III kit manufacturer.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Non-genomic transmission of longevity between generations: potential mechanisms and evidence across species access Published: 27 July 2017 Non-genomic transmission of longevity between generations: potential mechanisms and evidence across species Alexander M. Vaiserman1, Alexander K. Koliada1 & Randy L. Jirtle2,3 Epigenetics & Chromatin 1. Fig. 1Distinction between intergenerational and transgenerational inheritance in mammals. In the case of intergenerational inheritance, parental exposures directly influence not only embryos and/or fetuses (F1 generation), but also already developing germ cells, giving rise to the F2 generation. Thus, F1 and F2 phenotypes may be directly exposed to external developmental cues, and F3 generation is the first one where the phenotype is not through primary triggering exposure. Therefore, true transgenerational effects include those that persist into the F3 generation [8]Full size image Many recent papers highlight the role of epigenetic mechanisms in mediating these effects. These processes include modified patterns of DNA methylation and histone posttranslational modifications, replacement of canonical histones with histone variants, as well as altered noncoding RNA expression causing changed local accessibility to the genetic material and modified gene expression [9]. In a number of papers, the possibility of persistence of epigenetic modifications across multiple generations was reviewed and thoroughly discussed [10,11,12,13,14]. A good example of epigenetic intergenerational inheritance comes from the viable yellow agouti (A vy) mouse model where maternal supplementation with methyl donors was shown to influence not only the affected dams, but also their F2-generation progeny via epigenetic modifications in the germline [15, 16]. In several recent studies, the potential importance of non-genomic transgenerational effects in the inheritance of age-related characteristics has been highlighted [6]. In particular, the evidence for transgenerational effects of maternal diet on reproductive and metabolic aging in offspring has been obtained in various mammalian species such as guinea pigs, rodents, and sheep [17]; however, the transgenerational effects on longevity have been reported only rarely to date. Most of the papers reviewing and discussing such effects are focused solely on data obtained from the nematode Caenorabditis elegans [18,19,20,21], although similar findings were obtained in other species as well (see subsections below).

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: “In order to remove CO2 from an ambient airstream, you need a device whose physical proportions are immense,” says MIT physicist Robert Jaffe, who poses DAC as a problem in his book of Energy (2018). “If we walk through a simple calculation, the results are daunting. ” For example, a coal-fired power plant that meets the needs of a city the size of Cambridge, Massachusetts, would emit 1. 6 million tons of CO2. Regardless of the specific removal process, Jaffe says, simply moving the volume of air necessary to capture that amount would require a DAC plant 100 meters high by 600 meters long, with its fans blowing constantly day and night at 2 meters per second. Jaffe assumed a capture efficiency of 50% and an atmospheric CO2 concentration of 500 ppm, perhaps an ambient level at which solutions such as DAC are seriously considered, he says. (Jaffe’s hypothetical power plant produces 150 MW of electricity; a typical US coal-fired power plant produces about 1 GW. ) Direct-air capture is not to be confused with capturing CO2 post-combustion at the source of fossil fuel emissions, a technology that has been deployed in a few places around the world. (Today, May 2013, page 23. ) The concentration of CO2 in flue gas is far higher—up to 15% for coal plants—than in the atmosphere. Even so, thermodynamics requires that the capture and compression of the gas will consume about 16% of the power plant’s useful energy output, says Jaffe. Post-combustion capture from flue gas isn’t expected to become viable unless governments impose a substantial price on CO2 emissions. In its influential 2011 report Capture of CO2 with Chemicals, the Society estimated it would cost $600 to capture a ton of CO2 directly from the air and require erecting 30-km-long plants for every gigawatt-size coal plant. DAC advocates say the report did a disservice by dismissing DAC as a viable option for mitigating climate change. Among the DAC advocates is Peter Eisenberger, a physicist and cofounder of Global Thermostat. His company, based in City, is one of three startups that claim they can or soon will be able to capture CO2 with DAC at a cost well below half of APS’s figure.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Information about the primers used for qRT-PCR analysis is listed in Additional file 4: Table S4. qRT-PCR was performed using ™ II (TaKaRa, Dalian, China) in a CFX96 Touch real-time PCR system (BIO-) according to the manufacturer’s protocol, and amplification was performed as previously reported [70]. The results were calculated using the 2−ΔΔCT method [71] with the CsPTB1 gene as a control [72]. Each sample was examined in triplicate. AbbreviationsDEGs: differentially expressed genes; FDR: false discovery rate; FPKM: fragments per kilobase of transcript per million mapped reads; LC-MS/MS: liquid chromatography-tandem mass chromatography; LYQQ: Lianyuanqiqu; MZ: Meizhan; PIN: PIN-; QQ: Qiqu; qRT-PCR: quantitative real-time PCR; SGR: shoot gravitropism; UPLC-ESI-MS/MS: ultra performance liquid chromatography-electrospray ionization-tandem mass spectrometry; ZIG: zigzag; ZIP: zig suppressor1DeclarationsEthics approval and consent to participate The tea cultivars ‘Meizhan’, ‘Qiqu’ and ‘Lianyuanqiqu’ used in this study were planted and grown at. No specific permits were required for plant collection. The study did not require ethical approval or consent, as no endangered or protected plant species were involved. Consent for publication Not applicable. Availability of data and materials The datasets generated and analysed during the current study are available in the (SRA), with the link of under the accession number PRJNA559220. Competing interest The authors declare that they have no competing interests. work was supported by the of China (31800587, 31600555), the Foundation of (2017J01616), the for (CARS-19), the Construction of of (102/71201801101), and the “2011 Center”, (Cultivation) special project (J2015-75). The funding bodies were not involved in the design of the study, collection, analysis, and interpretation of data, and in writing the manuscript.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: In this review, evidence from various taxa demonstrating that lifespan and longevity-associated characteristics can be transmitted across generations is described and discussed. Basic mechanisms of epigenetic regulationEpigenetic modifications refer to both mitotically and meiotically heritable alterations in gene expression that occur without changes in underlying DNA sequence [22]. While DNA is relatively static throughout ontogenesis, the epigenetic code changes dramatically during the embryonic development of the organism to initiate differential gene expression patterns between various developing tissues. This code consists of chemical modifications of DNA and histone proteins that play a crucial role in packing the DNA by forming nucleosomes. In many species including mammals, DNA methylation, consisting of the addition of a methyl group at the fifth position of cytosine followed by a guanine nucleotide (a CpG dinucleotide), is one of the most important mechanisms of epigenetic regulation [23, 24]. This process mostly occurs within so-called CpG islands, i. e. , regions of the genome that are rich in cytosine followed by guanine nucleotides. CpG islands are typically common near transcription start sites often associated with promoter regions. Methylation of CpG islands in promoter regions of various genes usually leads to their transcriptional silencing, although several transcription factors important for cell reprogramming during development were recently identified that prefer to bind to CpG-methylated sequences [25]. Posttranslational modification of core histone proteins, including the acetylation, phosphorylation, methylation, phosphorylation, sumoylation, and ubiquitination of histone tails, is another key mechanism of epigenetic regulation [26]. Various combinations of histone modifications form the histone code for an organism which mark the functional units of chromatin, recruiting transcription factors, and coactivators/cosuppressors that regulate chromatin structure and gene activity. Among all histone modifications, methylation and acetylation of histone tails appear to be the most important modifications linked to gene expression. Transcriptional activity can be affected by histone modifications through two major mechanisms. Firstly, they can change the structure and conformation of chromatin. Secondly, they can provide signals for particular enzymes to recruit transcriptional activators or suppressors.

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: To date, however, the Swiss company Climeworks is the only one that can document cost in a commercial setting. Its plant supplies a greenhouse with 900 tons of CO2 annually to boost crop yields by accelerating photosynthesis. Coincidentally, the cost comes to $600 a ton. For comparison, CO2 used by the US oil and gas industry for enhanced oil recovery can be purchased from naturally occurring underground reservoirs for $30–$40 per ton. All the companies’ cost estimates include only the cost of capturing the CO2 and not the cost of permanent underground storage. A 2015 of Sciences, Engineering, and Medicine report estimated the cost of sequestration will be $10–$20 per ton of CO2. Proponents of DAC say it will be a far more efficient method of CO2 removal and far less land-intensive than another alternative, reforestation. Although other methods of CO2 removal have been proposed, the UN on Climate Change, in its most recent assessment, judged those to have “biogeochemical or technological limitations to their potential on the global scale. ” By one estimate, by of the Research Center, more than 2 × 106 km2 would have to be reforested to have a significant effect on climate change. The state of Alaska is 1. 7 × 106 km2. And the world loses about 100 000 km2 each year to deforestation. From CO2 to fuels All DAC systems work by forcing huge volumes of air through devices called contactors, where the CO2 molecules are adsorbed by chemical compounds. The chemicals are either hydroxides or amines. All require heat to release the concentrated CO2, with far higher temperatures needed for hydroxide systems. Electricity is required for the large fans; natural gas or electricity can provide the heat. In the case of amines, waste heat from industrial processes can be used. (CE) is a Canadian firm founded by physicist David Keith. The company has been operating a pilot-scale DAC plant in Squamish, British Columbia, since 2015; it captures 1 ton of CO2 a day. In CE’s two-chemical-loop process, the air is passed through contactors containing an aqueous potassium hydroxide. When CO2 is captured, it forms potassium carbonate, which is sent to a fluidized bed reactor, where it reacts with calcium hydroxide.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Author information Affiliations 1 College of Horticulture,of in Universities of 2 College of Tea and and HC initiated and designed the research. and NY conducted the experiment, and and JL analysed the data. HC and CY wrote the paper. CY revised and approved the final manuscript. All authors read and approved the manuscript. Corresponding author Correspondence to are grateful to thank Biotechnology Co. , Ltd for assisting in sequencing and bioinformatics analysis. 289. Roychoudhry S,Kepinski S. Shoot and root branch growth angle control—the wonderfulness of lateralness. Plant Biol. 2015;23:124-131. Morita MT. Directional gravity sensing in gravitropism. Plant Biol. 2010;61:705-720. . Arabidopsis thaliana: A model for the study of root and shoot gravitropism. Arabidopsis Book. 2002;1:e0043. . Growth-mediated plant movements: hidden in plain sight. Plant Biol. 2018;41:89-94. . Input and signal conversion of gravity in plant gravitropism. J Exp Bot. 2019;70(14):3495-3506. . Plant responses to gravity. Dev Biol. 2019;92:122-125. . SGR2, a phospholipase-like protein, and ZIG/SGR4, a SNARE, are involved in the shoot gravitropism of Arabidopsis. Plant Cell. 2002;14(1):33-46. . Role of endodermal cell vacuoles in shoot gravitropism. J Regul. 2002;21(2):113-119. . Involvement of the vacuoles of the endodermis in the early process of shoot gravitropism in Arabidopsis. Plant Cell. 2002;14(1):47-56. . complex containing SGR3/AtVAM3 and ZIG/VTI11 in gravity-sensing cells is important for Arabidopsis shoot gravitropism. . 2003;100(14):8589-8594. Weijers D,Wagner D. Transcriptional responses to the auxin hormone. Plant Biol. 2016;67:539-574. Zhao Y. Auxin biosynthesis and its role in plant development.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: The dynamic “writing” and “erasing” of histone modifications are conducted by specific enzymes that catalyze the processes of the addition or removal of acetyl groups from lysine residues on the histone N-terminal tails. The main “writers” include histone acetyltransferases and methyltransferases, while “erasers” include histone deacetylases and lysine demethylases [26, 27]. More specifically, histone acetyltransferases acetylate lysine residuals by transferring acetyl groups from acetyl coenzyme A (acetyl-CoA) to form ε-N-acetyl lysine. This modification leads to the neutralization of the positive charge of lysine and can consequently disrupt the interactions between the DNA and the histone tails. Acetylated histones are commonly associated with euchromatin and active transcription. In contrast, deacetylation of histones results in restriction of DNA accessibility through revealing the positive charge of lysine. This permits interactions between the DNA and the histone tails and results in chromatin compaction. Similarly, the phosphorylation of threonine, serine, and tyrosine by kinases and phosphatases alters histone’s net charge, thereby contributing to the modification of the chromatin structure. The processes of DNA methylation and histone modification are closely interconnected with each other. DNA methylation can affect the histone modification and vice versa, thereby collectively influencing chromatin accessibility to RNA polymerase and transcription factors. Recently, one more key component of epigenetic control of gene expression by noncoding RNAs has been discovered. Noncoding RNAs can regulate gene activity at both the transcriptional and posttranscriptional levels [28, 29]. They are functional RNA molecules that are transcribed from DNA but not translated into proteins. Several noncoding RNAs may interfere with the functionality of messenger RNAs (mRNAs) through a mechanism of RNA interference. By this mechanism, gene expression is regulated in a sequence-specific way without changing target sequences. The microRNAs (miRNAs), small (18–22 nucleotides in length) RNA molecules that may negatively regulate posttranscriptionally the expression of their target genes, are the most thoroughly studied class of noncoding RNAs involved in epigenetic regulation.

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: The resulting potassium hydroxide returns to the contactors, and solid pellets of calcium carbonate are moved to a calciner and heated to 900 °C to release the CO2. The lime that’s left is hydrated and returned to the bed reactor. A June 2. The highest-cost DAC plants would supply pressurized CO2 for shipment or geologic sequestration. The lowest-cost plant would serve as the front end of a gas-to-liquids plant that would produce synthetic fuels to replace or be blended with gasoline, diesel, or aviation fuels. Keith says CE’s board will decide in the next several months whether to build a combined DAC and synthetic fuels plant to validate all the steps in the process. The plant would produce 100 barrels or so a day. It’s possible that the Canadian or US government might put up some funding. The next step, a commercial plant producing 2000 barrels a day of fuels and capturing 300 000 tons of CO2 per year, will cost roughly $300 million, Keith says. Financing depends on finding both a buyer for the fuels and a supplier of low-cost renewable energy, preferably one that will take an ownership stake in CE. The economics of CE’s fuels venture and how carbon-neutral the fuels will be depend mostly on the price and carbon content of the electricity needed to produce the fuels’ hydrogen component. CE plans to use mainly renewable energy in splitting water for hydrogen. Keith says CE will produce fuels for about $1 a liter: $0. 70 for splitting water and $0. 15 apiece for the DAC and fuels-synthesis processes. Petroleum products cost about $0. 60 a liter. Keith acknowledges that synthetic fuels can’t compete with petroleum products in unregulated environments. But in niche markets, notably California, a low-carbon fuel standard (LCFS) sets limits on the carbon-intensity of fuels sold there. Measured in grams of CO2 per megajoule, the current limit will be gradually tightened so that increasing numbers of electric vehicles and a growing fraction of renewable fuels such as biodiesel and ethanol will be in the mix. The federal renewable fuel standard, on which the corn ethanol industry depends, provides further incentive for low-carbon synthetic fuels. And a new federal tax credit taking effect this year provides incentives for capturing and storing or reselling CO2.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Plant Biol. 2010;61:49-64. Adamowski M,Friml J. PIN-dependent auxin transport: action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. Haswell ES. Gravity perception: How plants stand up for themselves. Curr Biol. 2003;13(19):R761-R763. . Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Curr Biol. 2016;26(22):3026-3032. . A core regulatory pathway controlling rice tiller angle mediated by the LAZY1-dependent asymmetric distribution of auxin. Plant Cell. 2018;30(7):1461-1475. . 1 family plays a key role in gravity signaling within statocytes and in branch angle control of roots and shoots. Plant Cell. 2017;29(8):1984-1999. . AtLAZY1 is a signaling component required for gravitropism of the Arabidopsis thaliana inflorescence. Plant J. 2013;74(2):267-279. . Architecture1, an protein involved in shoot gravitropism, regulates plant architecture in rice. Plant Physiol. 2013;161(1):317-329. . Maize LAZY1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling, and light response. Plant Physiol. 2013;163(3):1306-1322. Yoshihara T,Iino M. Identification of the gravitropism-related rice gene LAZY1 and elucidation of LAZY1-dependent and -independent gravity signaling pathways. Physiol. 2007;48(5):678-688. . Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees. . 2018;115(20):E4690-E4699. . Genetic divergence between Camellia sinensis and its wild relatives revealed via genome-wide SNPs from RAD sequencing. PloS One. 2016;11(3):e0151424. Chen L,Yamaguchi S. RAPD markers for discriminating tea germplasms at the inter-specific level in China. Plant Breeding.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: The miRNA “seed sequences” (nucleotides 2–8 at the 5′ end) bind to complementary sites in the 3′ untranslated region of the target mRNA and inhibit the translation of this mRNA or cause its degradation. This results in the premature degradation or in the stop of translation due to the formation of so-called RNA-induced silencing complexes (RISCs). The miRNAs commonly have multiple targets, and a particular gene may be targeted by different miRNAs. Thus, signaling pathways regulated by these molecules may be exceptionally complex. Importantly, the expression of miRNAs can be modulated by DNA methylation or histone modifications and vice versa, thereby leading to regulatory feedback loops in epigenetic regulation. Recently, the crucial role of noncoding RNAs in transgenerational epigenetic inheritance has been highlighted [3]. An important point in terms of transgenerational epigenetics is that, in mammals, epigenetic marks such as DNA methylation are nearly globally erased and then re-established through two waves of demethylation followed by de novo methylation during the stages of preimplantation and primordial germ cell (PGC) maturation [30, 31]. It is traditionally believed that such re-establishment of epigenetic signatures encompasses the entire genome, except for imprinted genes [30], and prevents the transmission of acquired epigenetic information across generations. Nevertheless, some methylation marks are, in fact, not fully erased, and persist throughout these periods. For example, in the Guo et al. study [32], 7. 8 and 6. 0% of the methylation marks in male and female PGCs, respectively, were shown to be still not erased 10–11 weeks after gestation (i. e. , a time of minimal DNA methylation). It has been repeatedly shown that the epigenome (i. e. , the totality of epigenetic marks across the entire genome) demonstrates its highest sensitivity to environmental cues during specific windows of sensitivity in early development when the process of re-establishment of epigenetic marks takes place [33], and that epigenetic transgenerational inheritance operates during these same periods [4].

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: Adapting catalytic converters A different chemical process, using amine sorbents, is being deployed by two companies: Climeworks and Global Thermostat. In GT’s process, 2 m2 arrays of contactors laden with CO2 are physically transferred to a second stage, where the gas is driven out under partial vacuum by 85 °C steam. The relatively low temperature lowers energy costs by using waste heat generated by electricity plants and other industrial processes. GT has operated a 1000-ton-per-year CO2 DAC pilot plant since 2010. says he expects to achieve a cost of $100 per ton at the company’s first commercial facility, nearing completion in Huntsville, Alabama. The plant doesn’t use waste heat; if it were available there, he says, CO2 could be captured at $75 per ton. The 3000-ton-per-year machine, housed in two shipping containers, is for a major beverage bottler. Eisenberger expects his process to drop to $50 a ton in a few years. The savings would result from incremental improvements as more devices are built and from further refinements to the contactors. The cost could be cut in half again as the price of solar electricity falls. GT has adapted vehicle catalytic converters to serve as contactors. The converters’ narrow channels entrain flow at 5 meters per second parallel to the contacting surface, minimizing turbulence, Eisenberger says. That’s more than twice the flow rate of 2 meters per second that Jaffe used in his calculations, he notes, and at least double what’s possible with CE’s and Climeworks’ contactors. Eisenberger says other projects with end users in plastics, fertilizers, and fuel are at various stages of commercialization. GT’s process also works for flue gas, and deals are in the works for flue-gas capture plants in the 100 000-ton-per-year range, he says. Climeworks, based in Zurich, Switzerland, with 60 employees, is the sole company to date with a commercial plant in operation. Valentin Gutknecht, director of business development, says it was the first to produce fuels from DAC. It has sold several plants with capacities up to 50 tons of CO2 per year to the automaker Audi for synthetic fuels R&D and demonstration.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 2005;124(4):404-409. . Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. . 2018;115(18):4151-4158. . The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Mol Plant. 2017;10(6):866-877. Yao M,Chen L: Tea germplasm and breeding in China. In: Breeding. Edited by. Berlin, Heidelberg: Springer; 2012: 13-68. Vogt T. Phenylpropanoid biosynthesis. Mol Plant. 2010;3(1):2-20. Fraser CM,Chapple C. The phenylpropanoid pathway in Arabidopsis. Arabidopsis Book. 2011;9:e0152-e0152. . Flavonoid accumulation in Arabidopsis repressed in lignin synthesis affects auxin transport and plant growth. Plant Cell. 2007;19(1):148-162. . Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis. Plant J. 2009;60(5):771-782. . The growth reduction associated with repressed lignin biosynthesis in Arabidopsis thaliana is independent of flavonoids. Plant Cell. 2010;22(5):1620-1632. . Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Sci Rep. 2017;7:41906. . Flavonols accumulate asymmetrically and affect auxin transport in Arabidopsis. Plant Physiol. 2011;156(2):585-595. Hernandez I,Munne-Bosch S. Naringenin inhibits seed germination and seedling root growth through a salicylic acid-independent mechanism in Arabidopsis thaliana. Biochem. 2012;61:24-28. Ramos P, Guajardo J, Moya-León MA,Herrera R. A differential distribution of auxin and flavonols in radiata pine stem seedlings exposed to inclination. Genomes. 2016;12(3):42. .

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Moreover, the obvious distinction between epigenetic (‘soft’) and genetic (‘hard’) inheritance is that epigenetic changes, unlike the genetic ones, are reversible and can persist for only a few generations in the absence of the inducing trigger [10]. Therefore, it is commonly believed that attenuation of epigenetic memory over a multiple generations is a passive process attributable to dilution of particular inherited factors [34]. It can be speculated that preservation of these marks might be limited not only to imprinted regulatory elements referred to as imprintome [35], but also to several non-imprinted genes [36]. Moreover, the imprinted loci are environmentally sensitive as well, especially during early developmental stages. Thus, imprinted gene expression is not only parent-of-origin dependent, but is also influenced by environmental exposures early in life [37]. The retention of methylation marks in both imprinted and non-imprinted genes would allow for the transmission of epigenetically acquired memory to the later germ cells, thereby being one of the mechanisms potentially involved in the process of transgenerational epigenetic inheritance. A schematic representation of the dynamics of genome-wide DNA methylation reprogramming during the early mammalian development is presented in Fig. 2. Other mechanisms potentially contributing to this process are presented in Fig. 3. Fig. 2Genome-wide demethylation and de novo DNA methylation processes in the mammalian germline and in preimplantation embryos. The levels of global DNA methylation are indicated on the y-axis and are shown by a blue line for the paternal genome and a pink line for the maternal genome. The top bar schematically presents waves of demethylation followed by de novo methylation in F0–F3 generationsFull size image Fig. 3Potential mechanisms of transgenerational transmission of environmentally induced effects through both maternal and paternal lines (black letters) or only the maternal line (red letters). The figure is based on hypothetical mechanisms suggested by Heard and Martienssen [90] to explain transgenerational inheritance of acquired informationFull size image Findings from animal studiesSeveral recent findings indicate a resistance of epigenetic marks to complete erasure during these developmental periods, allowing their transmission across generations [13, 38]. Examples of inter- or transgenerational transmission of epigenetic marks have been reported for many taxa from microorganisms to humans [5].

Output: corroborate


Input: Claim: Ocean carbon capture will soon solve all problems related to climate change. [SEP] Text: Climeworks is commissioning a commercial system for a carbonated beverage producer. Unlike GT’s versions, Climeworks’ amine-based contactors aren’t moved once they’re loaded with CO2. Instead, the fans are stopped after several hours and the amine solution is heated in place to 100 °C to release the captured gas. Climeworks is supplying the CO2 for a collaboration in Iceland known as Carbfix. Union–funded project injects concentrated CO2 into a basaltic geologic formation. There it reacts with the rock to form a calcite mineral. Drawing on the country’s plentiful geothermal heat, the project boasts carbon-negative status. The company is supplying some of the CO2 needed for the Crude air-to-fuels plant to be completed in 2020. Carbfix will tap Norway’s abundant hydroelectric power to produce about 56 000 barrels of synthetic fuels a year. The system from Climeworks is modular, and any number of its 50-ton-per-year, self-contained contactor units can be combined. From its current $600 per ton, cost will decline further with technology improvements and mass production, Gutknecht says. “We know this isn’t a cost level that will have a significant effect on global climate. For that we are working on a rigorous roadmap to achieve a cost level of $100 per ton by 2030. ” He’s confident that $200 per ton can be achieved within two to three years. Altruistic motives View largeDownload slideGlobal Thermostat’s pilot plant captures 1000 tons of CO2 per year using modified automotive catalytic converters. View largeDownload slideGlobal Thermostat’s pilot plant captures 1000 tons of CO2 per year using modified automotive catalytic converters. Close modal Climeworks, GT, and CE are all finalists for the Challenge, a $25 million prize offered by UK billionaire to the first company that can demonstrate for 10 years an economically viable method for DAC and permanent removal of CO2. Each company is pursuing parallel commercial and altruistic paths. “We absolutely think we can finance plants and make money,” says Keith of his fuels venture. “I’m not saying it’s easy; there’s a lot of ways to fail. do think it’s possible.

Output: contrast