Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: Bioinformatics and Genomics CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms Artem Nedoluzhko1, Fedor Sharko2,3, Md. Golam Rbbani1, Anton Teslyuk2, Ioannis Konstantinidis1, Jorge M. O. Fernandes1 1Faculty of Biosciences and Aquaculture, Nord University, Bodø, Bodø, Norway 2Complex of “Kurchatov Institute”, Moscow, Russia 3Institute of Bioengineering, of Biotechnology of the of 10. 7717/peerj. 8757 Published 2020-03-16 Accepted 2020-02-16 Received 2019-12-04 gene, Prediction, Annotation, Structural components Copyright © 2020 Nedoluzhko et al. is an open access 2020. CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. PeerJ 8:e8757 The authors have chosen to make the review history of this 1. 12) (Marcel, 2011). tilapia reference genome (ASM185804v2) and its gene-annotation (ref_O_niloticus_UMD_NMBU_top_level. gff3) were used in the following analysis. CircRNA prediction was performed for each ribosomal RNA depleted RNA-seq library using the circRNA in silico prediction tools (i) CIRI (Gao, Wang & Zhao, 2015) that is linked to miARma-Seq pipeline (Andres-Leon & Rojas, 2019), (ii) CIRI2 (Gao, Zhang & Zhao, 2018), (iii) CircExplorer2 (Zhang et al. , 2016), (iv) find_circ (Memczak et al. , 2013), and (v) circFinder (Westholm et al. , 2014). Prediction output files from all libraries were converted separately to coordinate file format. After sorting, these coordinate files (from different prediction algorithms, but for each library) were merged using bedtools multiinter (Quinlan & Hall, 2010) to determine a joint prediction output from 2, CircExplorer2, find_circ, and circFinder (see Table S1).

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: These compounds affect the viability of some microorganisms used for biotransformation of 2G substrates [20, 58, 59]. In this context, P. putida DOT-T1E has been shown to grow in the presence of > 50, 25 and 25 mM of furfural, 3-hydroxymethylfurfural and syringic acid, respectively, in agreement with the high tolerance of this strain to toxic compounds, although their combination enhanced toxicity. DOT-T1E and its derivatives thrive at maximal rate with up to 3% (w/v) of lignocellulose substrates, and adaptative evolution assays (ALE) in our lab ended with evolved clones adapted to tolerate up to 11% (w/v) lignocellulosic substrates (Juan L. Ramos, unpublished results). We are focusing our efforts on enhancing the intracellular production of l-Phe as a primary substrate for the synthesis of aromatic compounds and the evolution of the strain to thrive with a wide range of C-sources and tolerance to substrates, products and possible toxicants in industrial wastes to further identify and engineer possible bottlenecks for 2-PE production. We strongly support the idea that P. putida DOT-T1E could become an efficient microbial cell factory for the production of aromatic compounds from agro-industrial waste material. ConclusionsPetrochemicals exacerbate environmental issues by necessitating substantial energy inputs for their production, contributing to carbon emissions, and directly or indirectly causing pollution. In contrast, we have identified P. putida DOT-T1E as a promising biorefinery for the sustainable and environmentally friendly production of aromatic compounds, specifically 2-PE, from various sugars. This approach stands in contrast to conventional chemical methods. The strains CM12-5 and CM12-5Δgcd, designed to overproduce l-phenylalanine, demonstrated the capability to convert this amino acid into 2-PE upon the expression of Ehrlich pathway genes from plasmid pPE-1. The intracellular concentration of l-phenylalanine was identified as a critical limiting factor in 2-PE production.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: collected biocrusts from the Negev and analyzed bacterial metagenomes in the biocrusts to evaluate the distribution of metabolic potential among bacterial populations. To compare functional potential between various bacterial phyla, they selected metabolic genes encoded in the metagenomic-assembled genomes and grouped them into 10 function categories. ” Citation: RC2: 'Comment on egusphere-2022-1510', #2, 04 Mar 2023 This study is interesting as it identifies which bacteria proliferate in biocrusts from natural and postmining areas and examines functional gene abundances unlike previous studies that have focused on characterizing the microbial community composition of natural and post-mining biocrusts. This, I consider the approach novel. Nonetheless, I have a few comments that should be addressed:AbstractL19-23. I recommend deleting this sentence because it refers to a previous study, and the abstract should focus on the objectives and results of the present study. Then, in the Introduction or the Discussion, it is fine if mention to previous results is done. M&ML103-105. It is not clear the predominant p109. Add a short description of the biocrust sampled (thickness, cover, composition, …. ). Were there differences in the biocrust from natural and post-mining sites? ResultsRegarding the results of the proliferated bacterial community composition, it would be nice to include a figure with the relative abundances of the different bacteria phylum for natural and post-mining biocrusts to make the results clearer. DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonizacion by cyanobacteria can be faster than thought. L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. L379-381.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: We developed CircParser, as a streamlined pipeline, which makes use output files from the most popular circRNAs in silico predictors. CircParser works under Linux/Unix system and its parameters are presented in Table 1. Table 1: CircParser. pl usage. Required and optional parameters. description -h, –help Show this help message and exit -b CircRNA input file (required) -g, –genome Reference genome file (required) -t, –tax (optional) -a Genome annotation file, gff/gff3 file (optional) –np Prohibition for coordinate merging (optional) -c, –ciri Input circRNA from CIRI—CIRI2 in silico predictors, (default: input from CircExplorer2, find_circ, circFinder, and BED files) –threads Number of threads (CPUs) for BLAST search (optional) -v, –version Current CircParser version DOI: 10. 7717/peerj. 8757/table-1 Usage: perl CircParser. pl [-h] -b INPUT_FILE—genome REF_can merge overlapped circRNAs coordinates from circRNAs predictor outputs using bedtools merge (Quinlan & Hall, 2010) at the first stage of the pipeline; this ensures that they are related to the same host gene and creates separate coordinates files (bed file) with overlapped circRNAs coordinates. In addition, it is optionally possible to merge circRNA without overlapping coordinates but located in the contiguous genome locus using the special option. The separate coordinate files (bed file) are converted to fasta files using bedtools getfasta (Quinlan & Hall, 2010). Finally, CircParser uses fasta files for host gene prediction using a NCBI database (the longest stage of pipeline) for circRNAs (Fig. 1A). CircParser works by default with the NCBI online database, but it can optionally use a custom database or a pre-compiled NCBI database installed locally. CircParser includes the following blast parameters, which are necessary for host gene prediction, and assigns sequences to the respective circRNA: -perc_identity 90; -max_target_seqs 1000; -max_hsps 1; the maximum number of aligned sequences to keep is 1000; the minimum percent identity of matches to report is 90%.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: The sustainable harvest residuals and thinnings alone are estimated at about 75 million tons/year accordingly to the DOE biomass report [1]. These forest residuals and thinnings could produce the equivalent of 5 billion gallons of lignocellulosic ethanol annually. Woody biomass feedstocks include softwood and hardwood. Various pretreatment methods have been developed for pretreating biomass before an enzymatic conversion of pretreated biomass into monomeric sugars for a biofuel or a bioproduct conversion process. An overview on lignocellulosic biomass pretreatment methods well described that most of the pretreating methods worked well on herbaceous biomass and hardwood biomass while not working well with high lignin content softwood biomass [2]. Thus, softwood biomass is the most recalcitrant biomass to pretreat for enzymatic hydrolysis. To utilize the most recalcitrant lignocellulosic materials, an efficient, scalable and cost effective pretreatment method is needed. Bisulfite pulping was a widely used industrial method for pretreating woody biomass for papermaking industries. In 1867, Tilghman invented the use of calcium bisulfite to pulp wood [3, 4]. The first commercial sulfite process for sulfite pulp production was built in 1874 in Bergvik, Sweden [5]. Due to its effectiveness in lignin sulfonation and lignin removal from wood, bisulfite or sulfite pulping has been used for almost 14 decades in the papermaking industry. In addition, spent sulfite pulping liquor is rich in hemicellulose sugars, such as arabinose, galactose, mannose and xylose. However, the spent sulfite liquor also contains some glucose. Spent sulfite liquor has been a source of hemicellulosic sugar for renewable biofuel fermentation, as demonstrated by Tembec for over two decades [6]. Sulfite pulping sludge has been found highly digestible by enzymes and suitable for producing lignocellulosic ethanol [7–9]. The cost that goes into producing a bleached sulfite pulp, however, is high compared to the price of the sugar that it could replace.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: Response: Added a bar plot of Phyla relative abundances to the PCoA ordination in figure 5 (labeled ‘a’ and ‘b’) and statistical data in the supplementary file (Table S4). DiscussionL354-357. Can you remind here when was the sampled post-mining site restored? Was it at 2007? I wonder if one reason for the lack of photosynthetic potential difference between post-mining and natural biocrusts is because the biocrust in the post-mining site has been already recovered. For example, soil colonization by cyanobacteria can be faster than thought. Response: I mentioned the restoration year in L375. I agree that it is likely that the biocrusts we sampled have a significant cyanobacterial community, however we hypothesize that the recovery of the biocrust differs even within the mining site, emphasizing the importance of microenvironments, where certain areas have more developed biocrusts and others have less developed biocrust even within the same post-mining plot. I referenced this in the discussion (L376 – L383): “…However, in the current study, we sampled post-mining biocrusts at a different location in the Gov mining site (~500 m away from the original plot) due to technical constraints. In the new location we found that the photosynthetic potential of the biocrust in the post-mining plots did not differ from the natural biocrust. These results highlight the importance of microenvironments in shaping the functionality of biocrusts (Garcia-Pichel and Belnap, 1996). The similarities in active communities and photosynthetic potential could be due to more developed biocrusts in the new sampling locations compared to the previous ones. ”L369-370. There is little discussion on the results of the Picrust analysis. It would be nice to compare the results of this study with other studies that have also examined functional genes in biocrusts to see if abundances of the functional genes at this site greatly differ from those of biocrusts of other regions. Response: I added a paragraph addressing the analysis with reference and comparison to a previous study that used to infer functional potential (L395 – L405):“…analysis revealed no significant differences in the abundances of genes within any of the function categories examined (Fig. 6).

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: CircParser also filters out non-informative blast results, such as “uncharacterized”, “clone”, “linkage group” and others from the output table. Figure 1: An overview of the CircParser pipeline. (A) The pipeline includes merging of the circRNAs with overlapping genome coordinates and presents the number of different circRNAs originating from one host gene. (B) CircParser includes the prediction of circRNA structural components using a genome annotation gff/gff3 file. Download full-size image DOI: 10. 7717/peerj. 8757/fig-1 CircParser can also discriminate circular RNAs by their structural components: exonic, intronic, exon-intronic or intergenic using genome annotation gff/gff3 file (-a parameter). In this case, the user should avoid circRNAs coordinate merging (using –np parameter) during the pipeline implementation for correct results (Fig. 1B). Usage: perl CircParser. pl -np -b INPUT_FILE –genome REF_-a. gff However, poor quality of annotation file can lead to errors in the circRNAs structure analysis. implementation of CircParser is available at applied CircParser to twelve merged coordinate files that contained information about joint coordinates for circRNAs predicted using CircExplorer2, miARma-Seq (with CIRI predictor), CIRI2, find_circ, and circFinder. The five different algorithms predicted on average ∼131 (CircExplorer2); ∼501 (CIRI); ∼706 (CIRI2); ∼257 (find_circ), and ∼398 (circFinder) circRNAs per sample, with an insignificant overlap ∼37 circRNAs (Fig. 2; Table S1), similarly to previously published comparisons (Hansen, 2018; Hansen et al. , 2016). Figure 2: Number of circular RNAs that have been predicted by 2, CircExplorer2, find_circ, circFinder, and that are common between all prediction algorithms. Download full-size image DOI: 10. 7717/peerj. 8757/fig-2 To access the host gene of circular RNAs and to reduce false-positive rates, only overlapping circRNAs (Fig. 2) were used in CircParser.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: Blastobotrys adeninivorans and B. raffinosifermentans, two sibling yeast species which accumulate lipids at elevated temperatures and from diverse sugars access Published: 20 June 2019 Blastobotrys adeninivorans and B. raffinosifermentans, two sibling yeast species which accumulate lipids at elevated temperatures and from diverse sugars Stéphane Thomas1 na1, Daniel R. A. Sanya1 na1, Florian Fouchard1, Huu-Vang Nguyen1, Gotthard Kunze2, Cécile Neuvéglise1 & …Anne-Marie Crutz-: orcid. org/0000-0001-9111-51851 Show authors Biotechnology for Biofuels 38. 1 ± 1. 6% of its dry-cell weight, and synthesize lipids from various sugar substrates, up to 36. 6 ± 0. 5% when growing in cellobiose. Both species, represented by LS3 and CBS 8244T, could grow with little filamentation in the lipogenic medium from 28 to 45 °C and reached lipid titers ranging from 1. 76 ± 0. 28 to 3. 08 ± 0. 49 g/L in flasks. Under these conditions, the maximum bioconversion yield (YFA/S = 0. 093 ± 0. 017) was obtained with LS3 at 37 °C. The presence of genes for predicted subunits of an ATP citrate lyase in the genome of LS3 reinforces its oleaginous character. ConclusionsBlastobotrys adeninivorans and B. raffinosifermentans, which are known to be xerotolerant and genetically-tractable, are promising biotechnological yeasts of the Saccharomycotina that could be further developed through genetic engineering for the production of microbial oil. To our knowledge, this is the first report of efficient lipid storage in yeast when cultivated at a temperature above 40 °C. This paves the way to help reducing costs through consolidated bioprocessing. BackgroundThe use of renewable feedstocks to produce microbial oil for biodiesel or other applications has become a scientific and environmental issue over the last two decades.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: In contrast, a previous study conducted in the Highlands, examined active bacterial communities during a rain and subsequent drying (Baubin et al. , 2021). The results indicated an increase in genes related to photosynthesis, light, and sensing following the rain, while the other function categories did not vary significantly. We note that the identity and abundances of the functional genes in the dry biocrusts detected by Baubin et al. , (2021) and here (Fig. 6) are similar. Therefore, we propose that the similarity between the post-mining and natural biocrust communities (Fig. 5) reflect similar functional potential (Fig. 6). However, low abundance of active ASVs were used to infer the abundances of functional genes (Fig. 6), and large variance between samples in post-mining biocrusts could mask significant differences (Table S5). ”L379-381. It is hypothesized that the low bacterial growth in harsh environments like this one could be because biocrusts prioritize activation and preparation for desiccation over growth. However, this hypothesis cannot be fully demonstrated with the reported results. Could you add 401. Is there any practical experience of the application of cyanobacteria inoculation to restore this mining site in Israel? If so, it would be nice to add a few sentences regarding the potential of this technique to restore biocrust in the current mining site. Response: No, there have not been any active restoration measures in Zin mining sites and no previous scientific studies regarding the mining practices of ICL mining company. I address the need for active restoration measures in Zin mining sites (including cyanobacteria inoculation) in L439 – L444:“…Our results further emphasize the need for active restoration measures in the Zin mines. Such measures include soil inoculation with local cyanobacterial propagules (Acea, 2003, Wang et al. , 2009, Zhao et al. , 2016, et al. , 2017) and increased hydration (Morillas & Gallardo, 2015, Zhang et al. , 2018), which were effective in enhancing biocrust establishment and recovery following disturbances (Antoninka et al. , 2020). ”Table 1. Values should also include the standard deviation. Response: I added SD values to the table (L254 – L254).

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: This pipeline allows the elimination of non-informative outputs (e. g. , contains only chromosome/contig name, number of uncharacterized loci, or name of BAC clone, and etc. ), while keeping more the relevant blast results and retrieving the likely host gene name for the circular RNAs; in the case of impossibility to find identical sequences in the database, this tool mark these sequences as ). CircParser results also allow us to determine the number of circRNA types from one host gene and their minimum and maximum size in base pairs (bp). We showed that our algorithm detected presumable host gene names for the vast majority of predicted circRNAs. Moreover, most of them were related to muscle functions (e. g. , calcium/calmodulin-dependent protein kinase, troponin T3, myocyte-specific enhancer factor 2C, and others), and immune-related genes (MHC class IA antigen), which were consistently found among different individuals (Table S2), despite the relatively low coverage for circRNAs analysis of the sequencing data used (Mahmoudi & Cairns, 2019). An example of circRNA structure analysis for 2, CircExplorer2, find_circ, and circFinder outputs is presented in S3. To estimate the capacity of our pipeline we compared a number of host genes that were predicted by CircExplorer2 and CircParser (CircExplorer2 outputs were used as input files) for the same O. niloticus fast muscle datasets used earlier. As a result, CircParser shows greater efficiency for Nile tilapia, improving the number of predicted host genes up to two-fold (Fig. 3). Figure 3: CircParser capacity: number of host genes that were predicted by CircExplorer2 and CircParser. Download full-size image DOI: 10. 7717/peerj. 8757/fig-3 Another equally important aspect of CircParser concerned the accuracy of this pipeline. The most well-annotated reference genome of zebrafish (assembly GRCz11) and zebrafish muscle transcriptomic dataset (ERR145655) were used for accuracy estimation, i. e. , the agreement between the annotation file and CircParser output. We showed that in this case, CircParser host gene prediction was confirmed in 82. 4% cases.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: [17] reported the relative fatty acid (FA) composition of two strains of this species, without however mentioning the total amount of lipid. Several yeast species are well-known lipid producers. Three have attracted most of the research efforts in recent years [18]: Yarrowia lipolytica and Lipomyces starkeyi, belonging to the Saccharomycotina, and Rhodotorula (Rhodosporidium) toruloides, belonging to the Basidiomycota. All three species exhibit a genome size of over 20 Mb [19,20,21]. L. starkeyi and R. toruloides are known for their utilization of a wide range of substrates and their outstanding lipogenic capabilities (up to 70% DCW as lipids) [22,23,24]. L. starkeyi is particularly well suited for rapid and simultaneous utilization of sugar mixtures, reaching a lipid content of 52% DCW and a lipid titer of 13. 3 g/L in a mixture of cellobiose and glucose [25]. Strain diversity or culture conditions may alter lipid production; to maximize lipid production, the synthesis of endopolysaccharides under nitrogen limitation should be avoided [26]. Although progress has been made in recent years, the genetic engineering of these yeasts is still a shortcoming [18]. B. adeninivorans is phylogenetically close to Y. lipolytica [27]. Some strains of Y. lipolytica, as well as other species in the genus, are naturally more prone to store lipids from exogenous hydrophobic compounds than to turn glucose into lipids. Lipid content can easily reach 30% DCW [28] in the former case and generally 6 to 15% DCW in the latter [28, 29]. Metabolic engineering and/or process optimization, as well as strain screening, have been successfully used to increase lipid content above 35% DCW and reportedly up to 90%. Y. lipolytica has also required genetic engineering or specific culture conditions to utilize xylose, cellobiose, or cellulose polymers, which are major components of lignocellulosic materials.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: of for to & Inclusion Statement/Code of News and this journal Search all journals of for to & Inclusion Statement/Code of News and this journal Search all journals HortDate: 01 Dec 2014 Online ISSN: 2327-9834 Advertisement 10. 21273/. 49. 12. 1506 Free access Download PDF Cite this 0. 05; t test) in biomass production between the plants grown aeroponically and hydroponically. Aeroponically grown plants produced an average of 49. 8 g dried aerial plant material (DW) (sd 20. 7) per plant, whereas hydroponically grown plants produced an average of 57. 6 g DW (sd 16. 0). In contrast, withaferin A content was statistically higher in plants grown hydroponically. These plants contained an average of 7. 8 mg·g−1 DW (sd 0. 3), whereas the aeroponically grown plants contained an average of 5. 9 mg·g−1 DW (sd 0. 6). These results demonstrate that hydroponic techniques are optimal in reproducibly and efficiently generating withaferin A. These findings may be of importance to the natural products industry in seeking to maximize production of biologically active compounds from medicinal plants. Keywords: optimization of plant secondary metabolites synthesis; plant pharmaceuticals; soilless plant culture; natural productsIntensified interest in plant secondary metabolites for anticancer and other disease treatments has led to recent exploration of medicinal plant growth conditions to optimize biomass production and metabolite synthesis (Cragg et al. , 2009; Nagella and Murthy, 2011). Our study compares these variables for Withania somnifera when grown under soilless hydroponic and aeroponic conditions. W. somnifera (L. ) Dunal (Solanaceae) has been used for over 3000 years in the Ayurvedic medical tradition of India (Dalavayi et al. , 2006). Preparations of dried root powder called “ashwagandha” have been administered as a general tonic to increase energy, improve overall health and longevity, and to prevent diseases (Xu et al. , 2009). Currently, considerable attention is focused on the anticancer properties of one of the secondary metabolites, withaferin A (WA), of this medicinal plant (Mishra et al. , 2000).

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: Conclusions Thus, we conclude that CircParser represents a reproducible workflow that enables researchers to effectively predict the host genes for circular RNAs, even in non-model organisms with poorly annotated genome assemblies. Sequencing and quality trimming statistics Number of circular RNAs have been predicted by CircExplorer2, CIRI/ miARma-Seq, CIRI2, find_circ, and circFinder software. The number of common circular RNAs predicted by all methods is also indicated. DOI: 10. 7717/peerj. 8757/supp-1 CircParser pipeline output table for overlapping circRNAas (without structural component analysis) DOI: 10. 7717/peerj. 8757/supp-2 CircParser pipeline output table for overlapping circRNAs (with structural component analysis) DOI: 10. 7717/peerj. 8757/supp-3 We would like to acknowledge Jorge Galindo-Villegas from (Norway) and Tomas B. Hansen from the (Denmark) for their valuable advice. M. O. Fernandes is an for PeerJ. The authors declare there are no competing interests. conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft. conceived and designed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft. Md. analyzed the data, authored or reviewed drafts of the paper, and approved the final draft. analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft. performed the experiments, authored or reviewed drafts of the paper, and approved the final draft. Jorge M. O. Fernandes conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. DNA following information was supplied regarding the deposition of DNA sequences: Data is available at the database: GSE135811. The following information was supplied regarding data availability: CircParser is available at Github.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: 5 g/L NH4Cl in YNB medium with 30 g/L carbon source, leading to a mass carbon-to-nitrogen ratio (C/N) of 60 and 90, respectively). Under these conditions, lipogenesis began at the start of growth for all strains. The highest amount of lipids in the cells was reached after 72 h and ranged from 14 to 29% DCW (Figs. 3, 4). Lipogenesis was negligibly better at C/N 90 than C/N 60 (up to 10% better) but it lowered growth and global sugar consumption. Fig. 3Bioconversion of sugars into lipids during the growth of two strains of B. raffinosifermentans in nitrogen-limited YNB-based media. Glucose and xylose were each used as the C source (30 g/L) at two different C/N ratios. Average values and the standard deviation (n = 3) for OD600 (blue line), residual sugar in the medium (g/L, plain green line), cumulative organic acids (g/L, dotted green line), and lipid content (% DCW, orange line) were plotted over time (h)Full size image Fig. 4Bioconversion of sugars to lipids during growth of two strains of B. adeninivorans in nitrogen-limited YNB-based media. Glucose and xylose were each used as the C source (30 g/L)at two different C/N ratios. Average values and the standard deviation (n = 3) for OD600 (blue line), residual sugar in the medium (g/L, plain green line), cumulative organic acids (g/L, dotted green line), and lipid content (% DCW, orange line) were plotted over time (h)Full size image The four strains exhibited different behaviors in terms of growth and metabolism, lipid accumulation, organic acid excretion, and sugar consumption. There were no strict species-specific correlations. CBS 7377 was the slowest and least efficient strain for lipid accumulation, whereas LS3 (of the same species) reached the highest lipid content. Conversely, the OD reached by LS3 in stationary phase was the lowest of all strains. However, different OD may reflect morphological differences between strains rather than differences in biomass production. The results of the strains of B. adeninivorans were more similar to each other.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: It is therefore important to determine how to increase plant biomass and WA production by comparing outcomes from traditional, in-soil growing conditions with soilless hydroponic and aeroponic conditions in controlled greenhouse environments. Growing plants in controlled environments (greenhouses), using hydroponic and aeroponic conditions, reduces exposure to pests, permits application of reproducible growth conditions, and allows for year-round biomass production (Muro et al. , 1997). These benefits are then associated with increased yield and quality of secondary metabolites used as potential pharmaceuticals. Because biomass production and especially secondary metabolites (like WA) may be related to the plant's defense mechanisms, it is possible that “over”-controlling the growing conditions in the greenhouse may actually reduce the plant's synthesis of these parameters. In future studies, we plan to include stressors such as heat, salt load, and partial dehydration to test how these stressors affect WA synthesis. Controlling other factors (in the greenhouse) would therefore allow us to isolate the particular stressor that specifically improves secondary metabolite (WA) production while optimizing other growth conditions. In hydroponics, the roots of the plants are maintained in a static, continuously aerated, or discontinuously flowing nutrient liquid solution (Jones, 2004; Souret and Weathers, 2000). In aeroponics, water and nutrients are supplied through a fine mist that deposits droplets of nutrient solution on the roots (Souret and Weathers, 2000; Zobel et al. , 1976). These soilless methods are optimal for medicinal plant research and production because they eliminate soilborne pests, prevent contamination through field-grown plant species, and afford a more rigorously controlled, year-round growing environment. Materials and MethodsSeeds of Withania somnifera were obtained from the Center (NPC; University of Arizona) stock collection (6 months old, stored at 4 °C). They were germinated in 1-inch Grodan rockwool cubes in a germination chamber kept at 28 °C with 16 h of fluorescent lighting. After ≈5 weeks (late summer), seedlings with an aerial length of ≈5 cm were transferred to a float system [deep water culture containing 50% modified Medium (Hoagland and Arnon, 1950); see composition in Table 1] in the greenhouse [25 °C, 45% relative humidity (RH) and a light shadecloth to protect from direct sunlight].

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: Availability and implementation: implementation of CircParser is available at study has received funding from the Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 683210) and from the of Norway under the Toppforsk programme (grant agreement no 250548/F20). was supported by the RFBR (for Basic Research) Grant no 19-54-54004. This work was partially carried out in for and supported by Ministry of Science and of Russian Federation, grant #075-15-2019-1659. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 2019. miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data. Methods 152:31-40. 2019. circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. Bioinformatics 36(2):539-545. 2012. Transcriptome-wide discovery of circular RNAs in Archaea. Research 40:3131-3142 Ekblom R, Wolf JB. 2014. A field guide to whole-genome sequencing, assembly and annotation. 7:1026-1042. 2018. CircView: a visualization and exploration tool for circular RNAs. Briefings in Bioinformatics 19:1310-1316. 2015. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. 16:4. 2018. Circular RNA identification based on multiple seed matching. Briefings in Bioinformatics 19:803-810 Hansen TB. 2018. Improved circRNA identification by combining prediction algorithms. Frontiers in Cell and 6:20. 2016. Comparison of circular RNA prediction tools. Research 44:e58. 2018. Molecular roles and function of circular RNAs in eukaryotic cells. Cellular and Science 75:1071-1098. 2019. Identification of virus-encoded circular RNA. Virology 529:144-151 -. 2016. salmon genome provides insights into rediploidization. Nature 533:200-205 Mahmoudi E, Cairns MJ. 2019. Circular RNAs are temporospatially regulated throughout development and ageing in the rat. 9:2564 Marcel M. 2011.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: Overall, both species cultivated in low-nitrogen medium reached a lipid content above 20%. Sugar uptake was more efficient for LS3 than for other strains in all media (Figs. 3, 4). With few exceptions, < 75% of the initial sugar was consumed by the end of experiment, leaving room for optimization of the medium and culture conditions. Within the time of the experiment, B. raffinosifermentans LS3 reached the highest lipid content among all four strains, whereas B. adeninivorans CBS 8244T accumulated lipid more slowly and probably did not reach its maximum. The excretion of organic compounds is a well-known competing sink for lipid production, particularly that of citric acid, both an intermediate of the TCA cycle and a precursor for acetyl-CoA in oleaginous yeasts. In our shake-flask experiments, we found two different organic acids to be excreted into the medium: citric acid and acetic acid. Globally, their cumulative concentration in the medium (Figs. 3, 4) tended to steadily rise over time and reached 3. 4 ± 0. 2 g/L (CBS 7766 cultivated in xylose C/N 90) to 10. 1 ± 0. 6 g/L (LS3 cultivated in xylose C/N 90) by the end of experiment. LS3 was unique concerning the excretion of organic acids, both in terms of their total concentration, which did not increase after 50 to 60 h of cultivation in some media, and the relative proportion of acetic to citric acid. Although acetic acid was the most abundant organic acid excreted by all other strains, excretions of citric acid was equivalent or more abundant in LS3 (Additional file 1: Figure S3). In glucose media, in particular, the final concentration of acetic acid was no more than half that of citric acid for this strain. This lower final concentration of acetic acid was due to reaching the plateau early (C/N 90, Additional file 1: Figure S3) or clear reuptake of this compound (C/N 60, Additional file 1: Figure S3), whereas glucose was not exhausted.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: The nutrient medium (NM) was stone-aerated using an air pressure pump (EcoAir 5) for 1 min every 5 min to promote aerial plant and root growth. When the plants reached an aerial height of 10 to 15 cm (≈6 weeks) (in early fall), they were transferred to an aeroponics box measured 1. 0 m × 1. 0 m × 1. 5 m (width × length × height) or to a hydroponic system (nutrient film technique with drip irrigation using a 5″ × 5″ × 10″ polyvinyl chloride pipe). Both systems were located in the same greenhouse. There were seven plants in the aeroponics box and seven plants in the hydroponics system. In both environments, the interplant distance was the same at 20 cm. In the aeroponics system, plants were arranged on the periphery of a square platform, whereas in the hydroponic system, the plants were arranged linearly. Therefore, in both systems, the plant density was similar. Plants in the aeroponics system were irrigated with NM for 1 min every 4 min and in the hydroponics system for 1 min every 10 min. The hydroponic system contained a small volume of nutrient film in the pipe so that the roots were exposed to nutrients even when irrigation was off. For both systems, the NM was sourced from the same reservoir containing the NM with a pH of 5. 9 and electroconductivity (EC) of 1. 85 dS·m−1. Table 1. Composition of nutrient medium (NM). z Plant growth was assessed by measuring the height of all plants and calculating the weekly averages for both systems. In addition, the surface area of one average-sized leaf of six randomly chosen plants per system was measured every week and weekly averages were calculated. This was done by tracing the leaf (while remaining on the plant) on a plain paper and cutting it out on paper. This paper was weighed and the surface area determined by using a predetermined surface area of paper-to-weight ratio. To measure plant biomass production, all plants were harvested at the flowering stage (8 weeks after transfer to the two growth conditions), and both wet and dry weights were recorded for aerial and root segments. The aerial parts were weighed individually per plant and the roots were measured as a total for each system.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: Skip to Content eLife home page your research Search by keyword or author Reset form my search to Genetics and 10. 7554/eLife. 46922 Open access Copyright information Version of RecordSeptember 24, 2019 Open annotations (there are currently 0 annotations on this page). 12,314 views 1,028 downloads 124 6922. Copy to clipboard Download BibTeX Download. RIS Full text Figures and data Peer review Side by side Additional files 10 figures, 2 tables and 6 additional files 1 with 2 supplements Download asset Open asset Estimating the rate of germline mutation using multigenerational CEPH/Utah pedigrees. (a) The CEPH/Utah dataset comprises 33 three-generation families. Summaries of sequencing coverage for CEPH/Utah individuals are presented in Figure 1—figure supplement 1. After identifying candidate de novo mutations in the second generation (e. g. , the de novo ‘T’ mutation shown in the second-generation father), it is possible to assess their validity both by their absence in the parental (first) generation and by transmission to one or more offspring in the third generation. (b) Total numbers of DNMs (both SNVs and indels) identified across second-generation CEPH/Utah individuals and stratified by parental gamete-of-origin. Boxes indicate the interquartile range (IQR), and whiskers indicate 1. 5 times the IQR. Diagrams of phasing strategies for germline DNMs are presented in Figure 1—figure supplement 2. Figure 1—figure supplement 1 Download asset Open asset Distribution of sequencing coverage in CEPH/Utah samples (a) The fraction of bases greater than or equal to the specified coverage in the second generation, (b) third generation, (c) first-generation parents sequenced to 30X coverage, and (d) first-generation parents re-sequenced to 60X coverage. Figure 1—figure supplement 2 Download asset Open asset Determining the parent-of-origin for de novo mutations using transmission. (a) We phased de novo mutations observed in the second generation by transmission to a third generation. We first searched ±200 kilobase pairs from the de novo allele (shown in red) for informative sites (shown in blue) present in one of the two first-generation parents of the second-generation individual.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: In terms of their FA composition, Blastobotrys strains synthesized and stored four main FAs during the 96 h of cultivation, accounting for more than 96% of total FA content: C18:1 (43 to 52%, depending on the strain and medium), C16:0 (23 to 27%), C18:2 (11 to 20%), and C18:0 (4 to 11%) (Additional file 1: Figure S4). C16 and C18 FAs are typically the most abundant FAs in a wide range of yeasts and fungi [60, 61]. However, the relative proportion varies depending on the yeast and culture/media conditions. The FA fraction was particularly poor in mono unsaturated C16:1. This feature was also noted for B. adeninivorans CBS 8244T in a comparative study of the FA composition of Saccharomycotina yeasts cultivated in YPD [62]. We found consistent but only very low levels of C17 chain-length FA (< 4 mg/g DCW). Indeed, yeast are not known to naturally synthesize large amounts of such odd-chain FAs, unless provided, for example, with odd-carbon precursors or benzoate [63,64,65]. Olstorpe et al. [17] reported FA profiles for CBS 8244T and CBS 7377 cultured in YPD medium, which were unexpectedly poor in oleic acid (3 to 11% of total FA at 30 °C) and rich in C17:1 (20 to 29% of total FA at 30 °C). The reason for these uncommon profiles is unknown, especially since Froissard et al. [62] reported the same four main FAs in B. adeninivorans CBS 8244T cultivated in YPD at 28 °C as those observed here. Lipid synthesis from various carbon sourcesSugars found in plants as reserve sugars or constituting lignocellulosic fibers, as well as the industrial by-product glycerol, are attractive substrates for microbial oil production. We tested the LS3 strain, our best lipid producer, for its ability to accumulate lipids while growing in various hexoses, polysaccharides, or glycerol.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: The plants were dried in a dark and warm drying room (39 °C, 17% RH) for 14 d. All data were statistically analyzed to determine the mean, sd, and statistical parameters (t test) using Microsoft ExcelTM (Microsoft Inc. , Redmond, WA). We are aware that there is a division of opinion in the plant science research community concerning the validity of using statistical analysis in studies such as ours, where true sample replication was not undertaken and where, instead, the process of pseudoreplication of samples was used (South and Somers, 2009; Wilson, 2007). As far as costs, timing, and inherent additional concerns resulting from replication in the greenhouse, we chose not to repeat the experiments described here but to rely on the strength of differences in the various parameters which we measured (biomass, WA production), especially as evidenced from statistical analysis. Air-dried foliage was combined for each growing condition and pulverized (Wiley Mill, Model No. 2). Three representative samples of 1. 0 g each were extracted with 10. 0 mL 60% aqueous methanol and subjected to 2 h of ultrasonic vibration and stored at room temperature for 1 week. The extracts were then filtered and washed twice with 2 mL of 60% aqueous methanol (MeOH). The solvent was evaporated to dryness using a Buchi rotavapor (water bath at 40 °C). The remaining residues were re-dissolved in 2. 0 mL MeOH and filtered through cotton. Each solution was diluted 1:10 with MeOH and subjected to HPLC on a Kromasil C18 RP column (250 × 4. 6 mm, 5 μm, 0. 7 mL·min−1 flow rate) with gradient elution using 40% to 100% aqueous MeOH and ultraviolet-Vis detection at 229 nm. An external standard curve method was used to calculate the concentrations of WA in all samples. ResultsSeed germination rate was 34% (data not shown). Plant growth analysis showed trends but no statistically significant differences between the aeroponically and hydroponically grown plants (Figs. 1 and 2), although during the first 3 weeks, aeroponically grown plants developed faster.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: If the second-generation individual’s spouse does not possess these informative alleles, we can look in the children of the second-generation individual to see if they have inherited both the de novo allele and the nearby informative alleles. This pattern of inheritance is only possible if the de novo allele and informative alleles are on the same haplotype; thus, in this example, we see that the de novo allele is on the maternal grandfather’s haplotype, and is paternal in origin. (b) A toy sample of paired-end sequencing reads is shown for each member of a trio (mother, father, and child). In this strategy, we identify informative alleles (shown in blue) that are present in one of the two parents, and within a read length (500 bp) of the de novo allele in the child (shown in red). Then, we identify individual sequencing reads that span the de novo and informative alleles. If the de novo allele is always present in the same read as the informative allele, then we can phase the de novo allele to the parent with the informative allele, and vice versa. Figure 2 with 2 supplements Download asset Open asset Effects of parental age and sex on autosomal DNM counts and mutation types in the second generation. (a) Numbers of phased paternal and maternal de novo variants as a function of parental age at birth. Poisson regressions (with 95% confidence bands, calculated as 1. 96 times the standard error) were fit for mothers and fathers separately using an identity link. Germline mutation rates, as a function of both paternal and maternal ages, are presented in Figure 2—figure supplement 1. (b) Mutation spectra in autosomal DNMs phased to the paternal (n = 3,584) and maternal (n = 880) haplotypes. Asterisks indicate significant differences between paternal and maternal fractions at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. P-values for each comparison are: C > G: 0. 719, T > G: 4. 93e-3, T > A: 8. 60e-2, T > C: 8. 02e-2, C > A: 0. 159, C > T: 7. 65e-6, indel: 8.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: The FA fraction of the cells was characterized after 72 and 96 h of culture at 28 °C in YNB-based medium with the C source at 30 g/L and 0. 75 g/L NH4Cl. After 96 h, lipids accumulated to above 30% DCW in all substrates, except galactose, starch, and glycerol (Fig. 5). Maximum lipid synthesis and storage was obtained for some of the sugars (i. e. , cellobiose, glucose, sucrose, or fructose), likely rapidly assimilated, after 96 h in our shake-flask cultures since the rise between 72 and 96 h was less than 5. 5% (Additional file 2: Table S1). In contrast, glycerol appeared to be the least favorable substrate for bioconversion into lipids (total FAs reached only 16. 1 ± 0. 4% DCW), probably because of its slow assimilation, which also affected the OD reached at 96 h: 11. 4 ± 1. 0% in glycerol instead of 16. 8 ± 0. 4% in cellobiose. We also observed small differences in the composition of FA profiles relative to that obtained in glucose, especially when LS3 was grown in starch or glycerol (Additional file 2: Table S1). Such variations that depend on the culture conditions have already been reported for other oleaginous yeasts [66]. In all cases, however, C18:1 was the main FA, followed in decreasing proportion by C16:0, C18:2, and C18:0 (Additional file 2: Table S1). In conclusion, all tested substrates, from simple to complex, could be turned into lipids by strain LS3, although with varying efficiency. Fig. 5Bioconversion of various sugars into lipids. LS3 was cultivated for 72 h in nitrogen-limited YNB-based medium (0. 75 g/L NH4Cl) supplemented with the indicated sugars at 30 g/L. a Lipid content (% DCW) is presented as a bar with the average value and mean deviation (n = 2) and a color code indicating the nature of the carbon source: green, C5 monosaccharide; light blue, C6 monosaccharide; blue, disaccharide; gray, polysaccharide; red, polyol.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: A power outage occurred 30 d after the plants had been transplanted to their systems (during Week 5) resulting in a temperature rise to 50 °C and disabling the pumps supplying NM to both systems for ≈4 h. As a result of this event, the growth rate of aeroponically grown plants decreased to less than 1 cm/week and the growth rate of hydroponically grown plants reduced to ≈3 cm/week. 1, the effect of the power outage is seen in Week 5, because plant heights remained almost the same. The trend lines show aeroponic plants with a slightly steeper growth slope, signifying a faster growth rate on average. Additionally, the surface area of the leaves in each system varied largely and yielded only weak trends without statistically significant differences. This can be seen in Figure 3, where the leaves of the aeroponically grown plants were somewhat larger than in the hydroponically grown plants. Size Fig. 1. Aerial plant size grown aeroponically and hydroponically. Vertical bars represent 95% confidence interval. Diamonds and squares represent weekly averages (n = 7) and lines represent linear best fit. Citation: HortScience horts 49, 12; 10. 21273/. 49. 12. 1506Download FigureDownload figure as PowerPoint slide Size Fig. 2. Plant growth rates in aeroponics and hydroponics. Vertical bars represent 95% confidence interval. Diamonds and squares represent weekly averages (n = 7). Citation: HortScience horts 49, 12; 10. 21273/. 49. 12. 1506Download FigureDownload figure as PowerPoint slide Size Fig. 3. Leaf surface areas for aeroponics and hydroponics. Vertical bars represent 95% confidence interval. Diamonds and squares represent weekly averages (n = 6). Citation: HortScience horts 49, 12; 10. 21273/. 49. 12. 1506Download FigureDownload figure as PowerPoint slideAs shown in Table 2, aeroponically grown plants produced an average of 49. 8 g DW (sd 20. 7). Hydroponically grown plants produced an average of 57. 6 g DW (sd 16. 0). Therefore, there was no significant difference (P > 0. 05) in aerial biomass production between the two growing methods. The percent DW column (Table 2) indicates what percentage of the wet weight corresponds to actual plant material.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: 01e-2, CpG >TpG: 0. 835. Mutation spectra stratified by parental ages are presented in Figure 2—figure supplement 2. Figure 2—figure supplement 1 Download asset Open asset Contribution of maternal and paternal age to de novo mutation rates. For (a) second- and (b) third-generation individuals in the CEPH/Utah cohort, plotted points show the relationship between paternal and maternal age at birth. Each point is colored by the autosomal SNV mutation rate in the individual; these rates were calculated by dividing the autosomal count in each child by that child’s autosomal callable fraction. Colors indicate the magnitude of the mutation rate (blue = lower, red = higher). Black lines indicate the trend for a 1:1 relationship between paternal and maternal age. Figure 2—figure supplement 2 Download asset Open asset Comparison of mutation spectra in children born to older or younger parents. Second-generation children were divided into two groups based on the ages of their parents at birth, and autosomal mutation spectra were compared between the two groups. In all panels, no significant differences were found at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. (a) Comparison of DNMs in children born to fathers younger (n = 2,182) or older (n = 2,360) than the median paternal age of 29. 2 years. P-values for each comparison are: C > G: 0. 304, T > G: 0. 140, T > A: 0. 306, T > C: 0. 248, C > A: 0. 8. 81e-2, C > T: 0. 444, indel: 6. 89e-2, CpG >TpG: 0. 810. (b) Comparison of DNMs in children born to mothers younger (n = 2,225) or older (n = 2,317) than the median maternal age of 25. 7 years. P-values for each comparison are: C > G: 0. 580, T > G: 0. 659, T > A: 0. 554, T > C: 0. 697, C > A: 0. 918, C > T: 0. 990, indel: 0.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: toruloides thermotolerant mutant, a temperature increase from 30 to 37 °C, while stimulating lipid production, drastically raised the relative proportion of C18:1, which reached 86% of total FA [32]. In conclusion, lipid metabolism of the LS3 and CBS 8244T strains was robust at temperatures from 28 to 45 °C. Temperature had a moderate impact on the final amount and nature of total cellular FAs, although LS3 showed optimal lipid production at 37 °C. Such robustness of lipid metabolism to differences in temperature is not shared across all yeasts. For example, the lipid content of L. starkeyi DSM 70295 reportedly decreased by 57% when the culture temperature was raised from 10 to 20 °C [70]. In the thermophilic species Kluyveromyces marxianus, 11 wild-type strains recently screened for lipogenesis (the best strain reportedly reached 10% DCW, mainly stored as free FAs) had a much lower FA content at 30 than 42 °C [42]. ConclusionsHarnessing microbial lipid metabolism to produce oils or other chemicals of interest is a promising alternative to petroleum or plant oil. However, limitations in the use of yeast have been encountered, such as the poor utilization of certain types of substrates, weak xerotolerance, limited yields for lipid conversion in competition with other metabolic pathways, or difficult culturing in bioreactors (filamentation, foaming). We believe that the availability of a set of various oleaginous microorganisms adapted to different types of applications could be useful. Elevated temperatures may help reduce the costs of the process and participate in the solubilization of substrates. B. adeninivorans and B. raffinosifermentans exhibit many advantageous traits for biotechnological processes and, as reported here, were able to synthesize and store lipids at high temperatures, up to 45 °C. Among four tested strains, LS3 was the best lipid-producing one. Although it showed a temperature dependence for growth, glucose consumption, and lipid storage, its native performance in the tested range of 28 to 45 °C is a good starting point (24 to 30% DCW from glucose). As for other oleaginous yeasts, strain screening, process optimization, and/or metabolic engineering is likely to be successful.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: Data in this column show that all plant materials were dried to the same extent. Table 2. Measured plant biomass for aeroponics and hydroponics. z Chemical analysis of the plant materials indicated that the hydroponically grown plants contained significantly higher concentrations of WA (P < 0. 05). As shown in Table 3, hydroponically and aeroponically grown plants contained an average of 7. 8 mg·g−1 DW (sd 0. 3) and 5. 9 mg·g−1 DW (sd 0. 6) WA, respectively. Table 3. content in dried plant materials for aeroponics and hydroponics. z DiscussionBecause multiple factors influence plant biomass production, we controlled all feasible environmental conditions (timing of transplanting, temperature, light, nutrient medium, RH, location in the greenhouse, etc. ) to reduce variability and to allow more precise comparison of plant growth under the two specified conditions. Additionally, the experiment comprised seven pesudoreplicates in each growing condition to attain accurate results. In previous studies, Solanum lycopersicum (tomatoes) have been found to produce higher yield in hydroponics and aeroponics than in traditional soil culture (Gysi and Von Allmen, 1997). Additionally, Solanum lycopersicum var. cerasiforme (cherry tomatoes), grown aeroponically, produced higher yields when compared with plants grown hydroponically. The improved yield was attributed to enhanced root aeration (Cho et al. , 1996; Soffer and Burger, 1988). In a recent study (Kindscher et al. , 2014) the authors discuss the effects of experimental manipulations of nutrients in the soil in which Physalis longifolia were grown. The authors found negligible differences in WA and other withanolides production as a function of these manipulations. However, the authors stress the importance of using genetic isolates of plants to provide for homogeneity so as to reduce secondary metabolite variability. In our study we used seeds from an isolated stock previously grown for several generations at NPC. We suggest, therefore, that genetic variability contributed minimally to the differences in secondary metabolite production in this study such that the differences we found can be more strongly attributed to the growing conditions. In this study, similar growth patterns and biomass yields of Withania somnifera were observed for both growing conditions.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: 371, CpG >TpG: 0. 678. (c) Comparison of DNMs in children born to fathers in the 25th percentile of youngest (n = 1,120) or oldest (n = 1,165) paternal ages (26. 4 or 34 years). P-values for each comparison are: C > G: 1. 73e-2, T > G: 0. 428, T > A: 0. 872, T > C: 0. 979, C > A: 0. 943, C > T: 7. 77e-2, indel: 0. 788, CpG >TpG: 0. 706. (d) Comparison of DNMs in children born to mothers in the 25th percentile of youngest (n = 1,169) or oldest (n = 1,121) maternal ages (22. 5 or 31. 4 years). P-values for each comparison are: C > G: 0. 327, T > G: 9. 92e-2, T > A: 0. 841, T > C: 0. 975, C > A: 0. 963, C > T: 0. 940, indel: 0. 598, CpG >TpG: 0. 780. Figure 3 with 2 supplements Download asset Open asset Parental age effects on autosomal germline mutation counts vary significantly among CEPH/Utah families. Illustrations of pedigrees exhibiting the smallest (family 24_C, panel a) and largest (family 16, panel b) paternal age effects on third-generation DNM counts demonstrate the extremes of inter-family variability. Diamonds are used to anonymize the sex of each third-generation individual. The method used to separate CEPH/Utah pedigrees into unique groups of second-generation parents and third-generation children is presented in Figure 3—figure supplement 1. Third-generation individuals are arranged by birth order from left to right. The number of autosomal DNMs observed in each third-generation individual is shown within the diamonds, and the age of the father at the third-generation individual’s birth is shown below the diamond. The coloring for these two families is used to identify them in panels c and d.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: AbstractIn 2010, our group announced the discovery of two cellodextrin transporter families from the cellulolytic fungus, Neurospora crassa. Furthermore, we demonstrated the utility of these transporters in the production of lignocellulosic biofuels. This discovery was made possible by a decision to systematically study cell wall degradation by N. crassa. The identified transport pathway has opened up a new way of thinking about microbial fermentation of hexoses as well as pentoses derived from plant cell walls. Integrating this pathway with the endogenous metabolism and signaling networks of S. cerevisiae is now a major goal of our group. Developing methods to convert the sugar-rich cell walls of plants to fuel is a major societal goal,Citation1 and has become the focus of intense research. Citation2 Present methods for conversion are limited by the evolved recalcitrance of plant cell walls to depolymerization into constituent sugars, and deficiencies in the traits of microbes used to ferment these sugars to fuels such as ethanol. Citation3 It is our philosophy that fundamental breakthroughs addressing both of these limitations will be made through the study of model organisms. Hence, we study the mechanisms by which the filamentous fungus, Neurospora crassa, degrades and metabolizes plant cell walls. N. crassa has been studied since the 1920s,Citation4 and features a wealth of resources including a high quality genome,Citation5 facile methods for genetic manipulation,Citation6 an almost complete set of gene knockouts,Citation7 and an international community of researchers. In the wild, N. crassa is commonly found growing upon recently burned plant matter,Citation8 and in 1977 was reported to secrete cellulases in response to specific inducers. Citation9 However, until 2009 N. crassa was largely ignored as a model biomass degrader; research focused instead on the related fungus, Trichoderma reesei (Hypocrea jecorina). T. reesei is now favored by industry for its ability to secrete large quantities of cellulases used to deconstruct plant biomass. Citation10Biomass degradation by N. crassa was revisited in 2009, with the report of a systematic study of plant cell wall degradation by this fungus.

Output: pass


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: Initially, aeroponically grown plants showed a growth rate that was statistically not different from hydroponically grown plants. As mentioned, a power outage causing a sharp rise in greenhouse temperature combined with irrigation pump failure resulted in reduced plant growth rates in both systems. As expected, this reduction, accompanied by partial wilting, was initially more pronounced in aeroponically grown plants whose roots did not receive any moisture or nutrients during the outage. All plants recovered in both conditions (Figs. 1 to 3) and resumed growth within 1 week. The pump failure, which was experienced in our study, may be considered a plant stressor, which therefore may have contributed to an increase in secondary metabolites (WA) production. Because this stress (lack of fertigation) would have been more pronounced in the aeroponics system, one would expect WA synthesis to be higher than in the hydroponic system because in the latter, some nutrient medium continued to bathe the plant roots. Because we found that WA production was larger in hydroponics, it amplifies the significance of our results. Plants generally display variations in biomass production (likely as a result of genetics and uncontrolled “hidden” environmental factors). To take such variations into account, we removed apparent outlier plants (H4 and A5) from the data analysis (not shown), which resulted in identical statistical results as data analysis, which included the outliers. These analyses showed that both soilless growing conditions yielded the same biomass per plant. In contrast, however, WA content analysis showed statistically significant differences. Plants growing in their natural habitat showed large variations of WA content (Kumar et al. , 2007; Mirjalili et al. , 2009). For example, naturally occurring plants in Iran were found to contain concentrations of WA ranging from 2. 2 to 32. 5 μg·g−1 DW (corresponding to 0. 0002% to 0. 00325%) (Mirjalili et al. , 2009), whereas in India, the leaves of naturally occurring plants were reported to contain 0. 192 to 1. 312 g/100 g DW (corresponding to 0. 192% to 1. 312%, but mostly less than 1%) WA (Kumar et al. , 2007). We report here that the aerial parts of our plants grown hydroponically contained an average of 7. 8 mg·g−1 DW (0.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: (c) The total number of autosomal DNMs is plotted versus paternal age at birth for third-generation individuals from all CEPH/Utah families. Regression lines and 95% confidence bands indicate the predicted number of DNMs as a function of paternal age using a Poisson regression (identity link). Families are sorted in order of increasing slope, and families with the least and greatest paternal age effects are highlighted in blue and red, respectively. (d) A Poisson regression (predicting autosomal DNMs as a function of paternal age) was fit to each family separately; the slope of each family’s regression is plotted, as well as the 95% confidence interval of the regression coefficient estimate. The same two families are highlighted as in (a). A dashed black line indicates the overall paternal age effect (estimated using all third-generation samples). Families are ordered from top to bottom in order of increasing slope, as in (c). A random sampling approach was used to assess the robustness of the per-family regressions to possible outliers; the results of these simulations are shown in Figure 3—figure supplement 2. Figure 3—figure supplement 1 Download asset Open asset Defining unique families in the CEPH/Utah dataset. The pedigree for a single family (family ID 19) is depicted. In this family, the third-generation individuals are first cousins and share a pair of grandparents. However, for the purposes of the inter-family variability presented in Figure 3, we defined ‘families’ as the unique groups of second-generation parents and their third-generation children. Thus, family ID 19 would be split into two unique families (19_A and 19_B), designated by the red boxes. Figure 3—figure supplement 2 Download asset Open asset Paternal age effect ranks of CEPH/Utah families are robust to outlier samples. For each CEPH/Utah family (i. e. , unique set of second-generation and third-generation individuals), we randomly sampled 75% of the third-generation individuals in the family, fit a regression predicting autosomal DNM counts as a function of paternal age at birth, and calculated the ‘rank’ of that family’s paternal age effect (out of 40 total families). We then plotted the distribution of ranks across 100 trials for each family.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: Citation11 Transcriptomic, proteomic and phenotypic data showed: (1) that the core cellulases of N. crassa are similar to those of T. reesei; (2) that N. crassa transcriptionally upregulates ∼2% of genes in response to pure cellulose or plant cell walls; (3) that there is a large amount of functional redundancy to the cellulase system of N. crassa, as only a cellobiohydrolase(I) deletion strain had a significant deficiency in its capacity to degrade pure cellulose. Interestingly, the set of cellulose-induced genes identified in this study included 10 major facilitator superfamily transporters. The strong induction of these transporters during biomass degradation led to a hypothesis that they have a key role in this process. In addition to the transporters, we noticed that N. crassa induced the expression of a putative intracellular β-glucosidase, an enzyme that cleaves the β (1 → 4) glycosidic bond in short cellodextrin chains. Cellodextrins are β (1 → 4) linked oligosaccharides of glucose, and are the product of cellulose depolymerization by fungal cellulases. Citation12 We therefore reasoned that a likely substrate for some of these transporters were cellodextrins. In 2010, we showed that two transporters, CDT-1 and CDT-2, indeed mediate the uptake of cellodextrins by N. crassa, and that following uptake cellodextrins are hydrolyzed intracellularly to glucose by a β-glucosidase. Citation13 A number of transcriptomic studies have shown that orthologs of these transporters are transcriptionally upregulated in response to plant cell wall material or cellobiose in diverse fungi, suggesting they are fundamental to the strategies used by fungi to interact with plants. Citation14–Citation16 The identification of these genes confirmed reports of cellodextrin permeasesCitation17 and intracellular β-glucosidasesCitation18 in T. reesei. The importance of these transporters to biomass degradation by N. crassa and other fungi inspired us to engineer the transport pathway into the yeast, Saccharomyces cerevisiae. S.

Output: corroborate


Input: Claim: Plants can only grow in soil and cannot thrive in alternative methods like hydroponics or aeroponics. [SEP] Text: 78%), whereas the aeroponic plants contained an average of 5. 9 mg·g−1 DW (0. 59%). These results show that hydroponically grown plants contained a significantly higher concentration of WA than plants grown aeroponically. As noted in “Methods,” our study does not comprise true replication (repeating the same experiment) but rather relies on analysis from pseudoreplicates. There is an almost equal division of opinion as to the validity of the latter approach with the conclusion that mitigating circumstances often prevent true replication in plant science research. Being aware of this situation, and using the results of our statistical analysis conservatively, we suggest that our findings indicate that WA synthesis using hydroponics is a more efficient system than using aeroponics (Hurlbert, 1984). Further research is needed to explore the mechanism(s) responsible for the increase in WA production we report here. Still, our findings are likely to have implications for the growing conditions of other medicinal plants where a secondary metabolite is the target compound. Our results indicate that hydroponics (NFT system) is the more effective method for growing Withania somnifera with the goal of reproducibly generating withaferin A. In addition, hydroponics is more suitable for commercial applications because it is less susceptible to problems (e. g. , resulting from pump failure). Plants grown hydroponically are also more economically grown and harvested as a result of the ability to customize the layouts of the systems compared with traditional field culture. The soilless conditions also eliminate soilborne pests and prevent contamination by field-growing plants. The results we report in this study suggest that other medicinal plants may also synthesize higher concentrations of metabolites in hydroponic conditions, which may be of pharmaceutical interest. Further studies should be undertaken to find the most effective nutrient medium composition, including adjustments to the sources of nutrients as well as changes to pH and EC, all known to affect biomass production and secondary metabolite synthesis (Hoagland and Arnon, 1950; Nagella and Murthy, 2011). Literature & Shin, G. H. 1996 Effects of culture systems on growth and yield of cherry tomatoes in hydroponics RDA J. Agr. Sci. 38 563 5671996Effects of culture systems on growth and yield of cherry tomatoes in hydroponicsRDA J. Agr. Sci. 38563567)| falseSearch 347.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: Families’ density plots are ordered along the y-axis by the original ranks of each family (as determined using the full dataset, and originally shown in Figure 3d, where a rank of 1 corresponds to the smallest age effect, and a rank of 40 corresponds to the largest). Figure 4 Download asset Open asset Identification of post-PGCS germline mosaicism in the second generation. (a) Mosaic variants occurring during or after primordial germ cell specification (PGCS) were defined as DNMs present in multiple third-generation siblings, and absent from progenitors in the family. (b) Comparison of mutation spectra in autosomal single-nucleotide germline mosaic variants (red, n = 288) and germline de novo variants observed in the third generation (non-shared) (blue, n = 22,644). Asterisks indicate significant differences at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. P-values for each comparison are: C > G: 6. 84e-2, T > G: 0. 169, T > A: 0. 236, T > C: 1. 51e-2, C > A: 4. 31e-3, C > T: 0. 385, CpG >TpG: 2. 26e-6. (c) For each third-generation individual, we calculated the number of their DNMs that was shared with at least one sibling, and plotted this number against the individual’s paternal age at birth. The red line shows a Poisson regression (identity link) predicting the mosaic number as a function of paternal age at birth. (d) We fit a Poisson regression predicting the total number of germline single-nucleotide DNMs observed in the third-generation individuals as a function of paternal age at birth, and plotted the regression line (with 95% CI) in blue. In red, we plotted the line of best fit (with 95% CI) produced by the regression detailed in (c). (e) For each third-generation individual, we divided the number of their DNMs that occurred during or post-PGCS in a parent (i. e.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: cerevisiae is the current organism of choice for fermenting glucose and sucrose to ethanol, but lacks the capacity to ferment cellodextrins. Citation19 Strains engineered to express cdt-1 or cdt-2 along with an intracellular β-glucosidase (gh1-1) grew with cellodextrins as a sole carbon source, and fermented cellobiose to ethanol efficiently. Multiple reports preceded ours in describing cellodextrin consumption or fermentation by engineered strains of S. cerevisiae. As early as 1986, Kohchi and Toh-e reported the consumption of cellobiose by S. cerevisiae expressing a secreted β-glucosidase from Candida pelliculosa. Citation20 They did not measure its fermentative capacity, however. Then, in 1988 Machida et al. reported cellobiose fermentation by S. cerevisiae expressing secreted β-glucosidases from Saccharomycopsis fibuligera. Citation21 Subsequent studies have repeated this feat both in labCitation22–Citation29 and industrial strains of S. cerevisiae,Citation30,Citation31 and in other yeast species. Citation32 All of these strains rely on extracellular hydrolysis of cellobiose to glucose by secreted β-glucosidases followed by uptake via the endogenous S. cerevisiae hexose transporters. In contrast, the first step in the pathway we described is the import of cellodextrins into the cytosol of S. cerevisiae, only then does hydrolysis to glucose occur. Other yeasts in nature have been shown to ferment cellobiose, but the molecular basis for this capability was not determined. Citation33–Citation36There are two main distinctions between cellodextrin fermentation mediated by transport and one mediated by extracellular hydrolysis to glucose: (1) cellodextrin transporters have a relatively high affinity for cellodextrins; (2) cellodextrins are hydrolyzed intracellularly. Both may be important during the fermentation of plant cell wall derived sugars.

Output: corroborate


Input: Claim: Modern agriculture can function without water or sunlight as long as the right technology is used. [SEP] Text: , Watanabe, H. , Cho, J. , An, N. , & Lee, B. (2014). Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight. of Environmental Agriculture, 33(2), 134-137. 2014, “Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight”, of Environmental Agriculture, vol. 33, no. 2, 137. Available from: doi:10. 5338/KJEA. 2014. 33. 2. 134 Ok, Junghun et al. “Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight. ” of 33. 2 (2014): 134-137. 1. . Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight. of [Internet]. 2014;33(2): 134-137. Available from: doi:10. 5338/KJEA. 2014. 33. 2. 134. and Byungmo Lee. “Photodegradation of Butachlor and Pyrazosulfuron-ethyl in Water under Natural Sunlight. ” of 33, no. 2 (2014): 134-137. doi: 10. 5338/KJEA. 2014. 33. 2. 134. Journal of p-ISSN 1225-3537e-ISSN 2233-4173 > Archives > 10. 7585/kjps. 2022. 26. 4. 330 Close 2014. Vol. 33. No. 2. 10. 5338/KJEA. 2014. 33. 2.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: , that were shared with a sibling) by their total number of DNMs (germline +germline mosaic), and plotted this fraction of shared germline mosaic DNMs against their paternal age at birth. Figure 5 with 1 supplement Download asset Open asset Identification of gonosomal mutations in the second generation. (a) Gonosomal post-zygotic variants were identified as DNMs in a second-generation individual that were inherited by one or more third-generation individuals, but exhibited incomplete linkage to informative heterozygous sites nearby. (b) Comparison of mutation spectra in single-nucleotide gonosomal DNMs that occurred on the paternal (n = 249) or maternal (n = 226) haplotypes. No significant differences were found at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. P-values for each comparison are: C > G: 3. 05e-2, T > G: 0. 972, T > A: 0. 858, T > C: 0. 148, C > A: 3. 31e-2, C > T: 2. 66e-2, indel: 0. 247, CpG >TpG: 0. 932. (c) Comparison of mutation spectra in autosomal single-nucleotide germline DNMs observed in the second-generation (non-gonosomal) (n = 4,542) and putative gonosomal mutations (n = 475) in the second generation. Asterisks indicate significant differences at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure), using a Chi-squared test of independence. P-values for each comparison are: C > G: 0. 517, T > G: 0. 800, T > A: 2. 32e-3, T > C: 0. 255, C > A: 0. 129, C > T: 0. 805, indel: 0. 446, CpG >TpG: 0. 212. (d) Numbers of phased gonosomal variants as a function of parental age at birth. Poisson regressions (with 95% confidence bands) were fit for the mutations phased to the maternal and paternal haplotypes separately using an identity link.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: The high-affinity of CDT-1 and CDT-2 for cellodextrins could be particularly important during the simultaneous saccharification and fermentation (SSF) of plant cell walls to fuel. SSF, in which fermenting microbes are included in the depolymerization reaction, increases the efficiency of conversion by relieving product inhibition upon cellulases. Citation37 With a KM of ∼5 µM, cellodextrin transporters may be capable of reducing sugar concentrations below levels obtainable by the inclusion of extracellular β-glucosidases, which generally have a KM of 100–1,000 µM. Citation38 This idea has not been rigorously tested and further studies applying and validating models of SSF using cellodextrin-transporting strains are necessary. Citation39,Citation40Relocating hydrolysis of cellodextrins from outside to inside the cell may seem like a trivial change, but it has a profound advantage. Specifically, transport of cellodextrins followed by intracellular hydrolysis to glucose facilitates the cofermentation of cellulose-derived glucose and hemicellulose-derived xylose. Citation41,Citation42 The inability of S. cerevisiae to coferment glucose and xylose is a barrier to efficient lignocellulosic biofuel production. Both glucose and xylose enter S. cerevisiae through the endogenous S. cerevisiae hexose transporters, but glucose is vastly preferred to xylose. Citation43,Citation44 Thus, xylose will not be taken up until all glucose is consumed. This sequential fermentation of glucose and xylose leads to lower ethanol yields and productivities. Citation45 Cellodextrin transport represents an alternate route for glucose to enter yeast, leaving the endogenous hexose transporters unoccupied and capable of transporting xylose. Strains containing the cellodextrin transport pathway from N. crassa and an efficient xylose fermentation pathway coferment cellobiose and xylose at high rates and with high yields. Citation41,Citation42Intracellular hydrolysis of cellodextrins does have associated problems, however. Yeast set metabolic and growth rates to match the perceived abundance of nutrients.

Output: corroborate


Input: Claim: Modern agriculture can function without water or sunlight as long as the right technology is used. [SEP] Text: 134 Number of citation : 1 of Butachlor and Pyrazosulfuron-ethyl in Water under Junghun Ok1*, Hirozumi Watanabe2, Junglai Cho1, Nanhee An1, Byungmo Lee1 1Division, of Agricultural Sciences, Suwon, Gyeonggi-do 441-707, Korea 2of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan *교신저자(Corresponding author): Phone: +82-10-4541-1629; Fax: +82-31-290-0507; E-mail: junghunok@gmail. com This is an Open-Access 3. 0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. : Dissipation of herbicides in paddy water varies significantly, being dependent on environmental conditions such as sunlight. The photodegradation under natural sunlight may be one of natural degradation routes of herbicides dissipation. Therefore, the aim of this study was to monitor the degradation of butachlor and pyrazosulfuron-ethyl in paddy water under natural sunlight. : The 12 water sample bottles of treatment were covered by quart glass plates, which allow about 90% of UV radiation (280-2000 nm) to pass through, to minimize the UV attenuation. The other 12 water sample bottles of the control were covered by glass lids and wrapped with aluminum foils to prevent the sunlight. The concentration of butachlor and pyrazosulfuron-ethyl in paddy water samples bottles was monitored under ambient conditions with and without natural sunlight. The concentration of butachlor and pyrazosulfuron-ethyl for treatment decreased from 355. 3μg/L to 37. 8μg/L and from 10. 5μg/L to 3. 9μg/L, respectively, during consecutive 21 days after herbicide application under natural sunlight. : The concentration of butachlor in paddy water decreased quickly under ambient conditions with natural sunlight. The degradation of butachlor in paddy water was enhanced by the natural sunlight. However, the degradation of pyrazosulfuron-ethyl was insignificant under natural sunlight.

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: A diagram of an identification strategy for post-zygotic gonosomal DNMs (using only two generations) is presented in Figure 5—figure supplement 1. Figure 5—figure supplement 1 Download asset Open asset Strategy for identifying post-zygotic DNMs using two generations. (a) Diagram of an example two-generation pedigree structure that is amenable to the post-zygotic detection strategy. In this example, the child has a de novo ‘T’ allele that is <= 500 bp downstream of a heterozygous ‘G’ allele. Question marks in the parents indicate that the child could have inherited the ‘G’ allele from either parent; unlike the read tracing strategy (Figure 1—figure supplement 2), a particular parent does not need to be ‘informative. ’ (b) In the child’s reads, only two possible sets of linked haplotypes should be seen, assuming the de novo allele occurred in the germline of a parent. The presence of three distinct haplotypes, demonstrating incomplete linkage of the de novo and heterozygous alleles, indicates that the de novo ‘T’ allele is post-zygotic. Author response image 1 Download asset Open asset Lack of correlation between read depth and mutation rates in CEPH/Utah samples. For each second- or third-generation CEPH/Utah sample, we calculated mean read depth across all autosomal base pairs covered by >=12 reads in all members of the trio. We then assessed whether there was a correlation between mean read depth and the autosomal mutation rate in these samples. For each generation, we fit a linear model predicting read depth as a function of autosomal mutation rate, and do not find a significant association in either generation at a p-value threshold of 0. 05 (second-generation p = 0. 92, third-generation p = 0. 073). Author response image 2 Download asset Open asset Anti-correlation between slope and intercept. For each CEPH/Utah family, we fit a linear model predicting DNM counts as a function of paternal age (see Figure 3). We then assessed whether the slopes and intercepts of these regressions were correlated; overall, slope and intercept point estimates are negatively correlated in CEPH/Utah families (p < 2. 2e-16).

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: 69 for pdc (Additional file 1: Table S1B); therefore, the acetolactate decarboxylase (AldC) to be engineered should have a strong affinity for the substrate acetolactate to compete with ZMO1141, thus ensuring carbon flux toward acetoin and 2,3-BDO. Construct heterologous 2,3-BDO pathway in Z. mobilis and optimize flask fermentation conditionsThe gene expression cassettes containing the sequences of three codon-optimized 2,3-BDO pathway genes (als, aldC, and bdh) from B. licheniformis and E. cloacae as well as wild-type version from E. cloacae were then designed and synthesized (Table 2). As discussed above, Z. mobilis has three als gene homologs, but does not have the aldC and bdh genes needed for 2,3-BDO production. Additionally, since Z. mobilis Pdc is a very abundant and efficient enzyme with low Km (<0. 31 mM) and high k cat (>100 1/s), a strong als gene may be needed to divert carbon flux from ethanol production to 2,3-BDO. We, therefore, constructed several pathways with either two genes (aldC and bdh) or three genes (als, aldC, and bdh). These genes were assembled using the Biobrick-based metabolic pathway engineering strategy and cloned into the minimized shuttle vector pEZ (Table 1). The results indicated that the three-gene pathways produced more 2,3-BDO than did the two-gene pathways (Table 2; Fig. 2). Table 2 The source and components of the 2,3-BDO pathway constructed and the corresponding 2,3-BDO titer (g/L) after 24-h post-inoculation in Z. mobilis 8bFull size table Fig. 2Biomass (OD600 nm), acetoin, 2,3-BDO, and ethanol titers after 24-h post-inoculation in either a Z.

Output: corroborate


Input: Claim: Modern agriculture can function without water or sunlight as long as the right technology is used. [SEP] Text: Keyword Butachlor,Natural sunlight,Paddy water,Photodegradation,Pyrazosulfuron-ethyl are widely used in rice paddies, golf courses and other types of fields. The acetanilide herbicide butachlor and the sulfonylurea herbicide pyrazosulfuron-ethyl are pre-emergence herbicide to control weeds of transplanted rice paddy fields (Chen and Chen,1979; Zheng et al. , 2008). Previous study investigated herbicide behavior and its dissipation in rice paddy environment (Ok et al. , 2012), however, the influence factor on herbicide degradation in paddy water was imprecise. Many environment factors related to the degradation and dissipation of herbicides including temperature, pH, sunlight, microbe, and soil properties (Chen and Chen, 1979; Samanta et al. , 1999; Sarmah and Sabadie, 2002; Vulliet et al. , 2004, Zheng et al. , 2008). Degradation of herbicides in paddy water also varies significantly, being dependent on environmental conditions such as sunlight (Chen and Chen, 1979; Sarmah et al. , 2000). The photodegradation under natural sunlight may be one of natural degradation routes of herbicides dissipation. Several studies reported that photodedegradation of butachlor were the major routes of herbicides dissipation from paddy fields in summer days (Chen and Chen, 1979). Chen and Chen (1979) reported that the half-life of butachlor in aqueous solution were 5. 4 hr after exposure to sunlight. In addition, the photolysis of pyrazosulfuron-ethyl was observed to enhance in aqueous condition (Zheng et al. , 2008). However, the photodegradation of butachlor have been investigated solely under controlled laboratory conditions, and only few studies for pyrazosulfuron-ethyl has been referred to their photochemical degradation in paddy water. Therefore, the aim of this study was to monitor the degradation of butachlor and pyrazosulfuron-ethyl in paddy water under natural sunlight. Materialsandanalytical grade solvents (acetonitrile, acetone, acetic acid, methanol, phosphoric acid) were purchased from (2011, Tokyo, Japan).

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: Author response image 3 Download asset Open asset Lack of correlation between sibling number and either slope or intercept. For each CEPH/Utah family, we fit a linear model predicting DNM counts as a function of paternal age (see Figure 3). We then assessed whether the number of third-generation siblings in these families was predictive of either the (a) slope or (b) intercept point estimate in the regression. Neither slope (p = 0. 654) or intercept (p = 0. 718) are significantly associated with sibling number. Author response image 4 Download asset Open asset Allele balance distributions in transmitted and untransmitted DNMs. Allele balance was calculated as the fraction of reads supporting the alternate (i. e. , de novo) allele at a particular site. As there are substantially more transmitted than untransmitted DNMs in the plot, the y-axis is shown as the normalized count of DNMs. Author response image 5 Download asset Open asset Range of missed heterozygote rates across CEPH families. (a) For each unique set of second-generation parents and third-generation children, we counted the total number of DNMs in the third generation for which we saw evidence in the first generation (i. e. , grandparents). The missed heterozygote rate (MHR) therefore represents the fraction of DNMs in each family that were likely “missed” in the second generation, as a percentage of the total number of DNMs identified in the third-generation children. (b) Comparison of mutation spectra in autosomal filtered germline third-generation DNMs (n=22,644) and autosomal third-generation DNMs that were removed due to evidence in a genotyped grandparent (n=83). No significant differences for particular mutation types were found at a false-discovery rate of 0. 05 (Benjamini-Hochberg procedure) using a Chi-squared test of independence. resources table Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional informationSoftware, algorithmToolkit (GATK)DePristo et al. , 2011v3. 5. 0; RRID:SCR_001876Software, algorithmpeddyPedersen and Quinlan, 2017av0. 4.

Output: pass


Input: Claim: Bioengineered yeast can produce biofuels from sugars. [SEP] Text: mobilis 8b and 22C background host with control plasmid pEZ15Asp (pEZ), or two-gene construct pEZ-GS2, or the three-gene construct pEZ-BC5 at 33 °C, 120 rpm with 40 mL RMG8 in 125-mL flaskFull size image Three constructs (vector control pEZ, two-gene pathway plasmid pEZ-GS2, and three-gene pathway plasmid pEZ-BC5) were further compared in two strain backgrounds of 8b or 22C (Table 1). The introduction of heterologous als gene significantly increased 2,3-BDO production by shifting carbon flow away from ethanol production (Fig. 2). Clearly 2,3-BDO production could be significantly enhanced if the native ethanol production pathway was impeded by knocking out key ethanol production genes of pyruvate decarboxylase (pdc) and alcohol dehydrogenase (adh), which has been demonstrated in S. cerevisiae that 2,3-BDO production increased in Pdc-deficient mutants [5, 7–10]. We have attempted to knock out or knock down the pdc gene to divert carbon to 2,3-BDO production without success, a result consistent with previous reports that pdc is essential for native Z. mobilis and cannot be completely knocked out. Furthermore, our efforts testing pdc knockout in 2,3-BDO production strains, such as 9C-BC5 and 9C-BC11, were also not successful. We will continue to work on blocking the route from pyruvate to ethanol to maximize the potential 2,3-BDO titer with balanced redox using similar strategies as reported in yeast [5, 6, 72–74]. To optimize the 2,3-BDO production, different flask fermentation conditions were first investigated using the three-gene pathway construct in the 22C background (22C-BC5) and using the empty vector pEZ as a negative control (Table 1; Fig. 3a). Results indicate that 2,3-BDO can be produced using mixed sugar conditions (glucose, or glucose and xylose), as well as from DMR-pretreated biomass (Fig. 3b).

Output: corroborate


Input: Claim: Modern agriculture can function without water or sunlight as long as the right technology is used. [SEP] Text: Deionized water used for sample preparation and mobile phase was produced with a Milli-Q water purification system (). Analytical standard grade butachlor (98%) and pyrazosulfuronethyl (98%) were also purchased from Wako Chemicals. The primary individual stock solutions (50 mg/L) of each analytical standard were prepared in 100 mL volumetric flask with pure acetonitrile. These stock standard solutions were diluted with acetonitrile to obtain a final concentration of 10 mg/L and kept in fridge at 4°C. The 10 mg/L standard stock solutions were appropriately diluted in acetonitrile:water (20:80, v/v) to prepare working standards 0. 5 mg/L and 0. 01 mg/L of butachlor and pyrazosulfuron-ethyl, respectively. The paddy water was collected from the experimental paddy field at FM Honmachi of of Agriculture and Technology (TUAT), Japan. Paddy water samples were filtered through 1. 2 μm glass fiber filters and sterilized by autoclave at 120°C for 20 minutes for the experiments. These solutions were divided into 24 sample bottles of 250 mL and the standard solution was spiked in water sample bottles. The 12 bottles for treatment were covered by quart glass plates, which allow about 90% of UV radiation (280-2000 nm) to pass through, to minimize the UV attenuation. The other 12 bottles for the control were covered by glass lids and wrapped with aluminum foils to prevent the sunlight. The concentration of butachlor and pyrazosulfuron-ethyl in water sample bottles at initial, 1, 3, 7, 14 and 21 days was monitored under ambient conditions with and without sunlight from May 5 to May 26 in 2011 at the university farm of TUAT. The solar radiation was monitored by pyrheliometer placed next experimental field. The water temperature was also monitored by temperature sensors placed in the water samples. Prior to the extraction, water samples were filtered by 1. 2 μm glass fiber filter paper (GC/C-Whatman). The water samples of pyrazosulfuron-ethyl were adjusted to pH 2. 5 by acid phosphoric and then both sample of butachlor and pyrazosulfuron-ethyl were extracted by solid phase extraction method using the Superclean ENVI-18 as previous study by Ok et al. (2012).

Output: contrast


Input: Claim: All planets have been thoroughly explored and documented. [SEP] Text: 3; RRID: SCR_017287Software, algorithmcyvcf2Pedersen and Quinlan, 2017bv0. 11. 2Software, algorithmmosdepthPedersen and Quinlan, 2018v0. 2. 4Software, algorithmpysam algorithmpython RRID:SCR_008394Software, algorithmR RRID:SCR_001905Software, algorithmViewer (IGV)Thorvaldsdóttir et al. , 2013v2. 4. 11; RRID:SCR_011793Software, algorithmsamtoolsLi et al. , 2009RRID: SCR_002105Software, algorithmBWA-MEMLi, 2013v0. 7. 15; RRID:SCR_010910 10. 7554/eLife. 46922. 022 Term (independent variable)DoFDevianceResid. DoFResid. DeviancePr(>Chi)dad_age1635. 77348502. 84< 2. 2e-16family_id39103. 43309399. 419. 667e-9dad_age:family_id3955. 34270344. 070. 04328 Additional files Supplementary file 1 Pedigree structures for all CEPH/Utah families. All family and sample IDs have been anonymized, and the sexes of third-generation individuals have been hidden. Download elife-46922-supp1-v1. zip Supplementary file 2 IGV images of 100 randomly selected germline DNMs identified in the second generation. In each image, the first two tracks contain alignments from the first-generation parents, and the third track contains the alignments for the second-generation child. Reads with mapping quality <20 are not included, as they were not considered by our variant calling pipeline, and mismatched bases are shaded by quality score (more transparent = lower base quality). Download elife-46922-supp2-v1. zip Supplementary file 3 IGV images of 100 randomly selected germline. DNMs identified in the third generation In each image, the first two tracks contain alignments from the second-generation parents, and the third track contains the alignments for the third-generation child.

Output: pass