Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Veivers PC, O'Brien RW, (1982) Role of bacteria in maintaining the redox potential in the hindgut of termites and preventing entry of foreign bacteria. J 28: 947–951. View 11. (1986) Inhibition of Metarhizium anisopliae by the gut bacterial flora of the desert locust, Schistocerca gregaria: Evidence for an antifungal toxin. J 47: 350–360. View 12. Koch H, Schmid-(2011) Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. 108: 19288–19292. pmid:22084077 View 13. (2003) Bacterial diversity in worker adults of Apis mellifera capensis and Apis mellifera scutellata (Insecta: Hymenoptera) assessed using 16S rRNA sequences. J 84: 96–103. pmid:14615218 View 14. (2006) Diversity and phylotype consistency of bacteria in the guts of three bee species (Apoidea) at an oilseed rape field. 8: 258–272. pmid:16423014 View 15. (2011) A simple and distinctive microbiota associated with honey bees and bumble bees. 20: 619–628. pmid:21175905 View 16. -(2011) An emerging paradigm of colony health: Microbial balance of the honey bee and hive (Apis mellifera). 58: 431–444. View 17. (2012) Functional diversity within the simple gut microbiota of the honey bee. 109: 11002–11007. pmid:22711827 View 18. Koch H, Schmid-(2012) Gut microbiota instead of host genotype drive the specificity in the interaction of a natural host-parasite system. 15: 1095–1103. pmid:22765311 View 19. (2012) Symbionts as major modulators of insect health: Lactic acid bacteria and honeybees. 7: e33188. pmid:22427985 View 20. Koch H, Cisarovsky G, Schmid-(2012) Ecological effects on gut bacterial communities in wild bumblebee colonies. J 81: 1202–1210. pmid:22708631 View 21.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: The enzyme blend was loaded at 15 FPU/gds (gram of initial dry substrate), corresponding to 7 mg protein/gds or 15 mg protein/g glucan. Batch enzymatic hydrolysis was performed in triplicates at 50 °C in a water bath oscillator (SHZ-88,. , Ltd. , Changzhou, China) constantly agitated at 200 rpm. Unless otherwise stated, 0. 3% (w/v) sodium azide was supplemented to prevent bacterial contamination. At different time points of hydrolysis, the samples were drawn and centrifuged at 10,000g for 3 min and the resulting supernatant was used for sugars analysis. A known volume of deionized water was added to the hydrolytic slurries before centrifugation since there was no visible liquid phase when the batch enzymatic hydrolysis was directly performed at high solids loading of 33% or 40%. The true sugar concentration was calculated taking into account the dilution. Fed-batch enzymatic hydrolysisThe fed-batch enzymatic hydrolysis of corn stover pretreated by the SMs was initiated at 12% (w/v) solids loading in a 100-mL red cap bottle (Duran, Schott, Germany). The total liquid phase including the buffer and enzyme solution was 20 mL. The enzyme blend was loaded at 15 mg protein/g glucan. Unless otherwise specified, all the required enzyme based on the final substrate loadings was added in a whole at the beginning of the hydrolysis. The hydrolysis was performed in triplicates at 50 °C and pH 4. 8 in a water bath oscillator of 200 rpm. In order to identify the time point of feeding, the pretreated corn stover (7%, w/v) was separately fed at the time point of 3, 6, 12, 24, or 36 h, respectively, to achieve the final solids loading of 19% (w/v).

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: 1 IntroductionCrop improvement has been the main target of agricultural research for centuries in comprehensive areas such as increasing the nutritional richness of foods, obtaining aromatic foods with pleasant smell and taste, producing decorative products that appeal to visual pleasures, while increasing the yield, especially to meet the increasing food demand of the global population. In recent years, advances in molecular biology and genetic engineering have provided new tools for crop improvement. Genome editing, in particular, has emerged as a promising technique for modifying the genome of crops in a precise and targeted manner [1, 2]. The process of conventional plant breeding is time-consuming despite its significant contribution to the first green revolution in the 1960s. The introduction of molecular marker-assisted selection has helped to speed up the process of plant breeding. Techniques such as mutagenesis and transgenesis have helped to reduce the time required to develop new varieties. However, mutagenesis is a random process that can have undesirable side effects or can result in incomplete and off-target disruption of genes. Genetically modified transgenic plants can also face regulatory challenges. Unlike traditional genetic engineering methods, which involve the insertion of foreign DNA into an organism’s genome, genome editing allows scientists to make precise modifications to the existing DNA sequence. Genome editing can be accomplished through different techniques, including -Cas9, TALENs, and Nucleases (ZFNs) [2]. These tools offer an unprecedented level of precision, enabling scientists to make precise, targeted changes to a plant’s DNA, resulting in desired traits [3]. Gene families are groups of genes that share a similar DNA sequence and function. They often play critical roles in crop traits such as yield, disease resistance, and environmental adaptation. Although members of a gene family have different specialized functions, they share a common purpose. Therefore, it is important to understand and define the functions of gene family members involved in important plant development or stress resistance in different plant species. Traditional breeding methods are often unable to effectively target and manipulate gene families, as they may contain many members that have overlapping functions or redundancies [1]. The food system faces challenges such as sustainability and food supply stemming from climate change, global conflicts and increasing population [4]. Conventional breeding and agricultural practices come short in terms of meeting the current and future food demand. Therefore, it is necessary to have different approaches to ensure a more resilient and sustainable agrifood system.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Pairwise comparison for similarity of T-RFLPs from the midgut of Helicoverpa armigera larvae collected from different locations on Chickpea plant. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 5. Pairwise comparison for similarity of T-RFLPs from the midgut of Helicoverpa armigera larvae collected from different locations on Cotton plant. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 6. Pairwise comparison for similarity of T-RFLPs from the midgut of Helicoverpa armigera larvae collected from different locations on Tomato plant. the 12 bacterial phylotypes detected, Enterococcus faecalis, and Enterobacter sp. were the major phylotypes found in all the larvae regardless of the crop or location of samples collected including artificial diet. We further analyzed the T-RFLP data using Correspondence analysis (CA) which is a graphical representation of similarity in a two-way contingency table. When large numbers of variables define a sample point and wish to compare all the different samples together, the CA simplifies the result by generating a statistical visualization and interpretation of the data [17]. The T-RFLP profiles of H. armigera larvae collected from different host plants and different locations were taken as sample points and each T-RF band defined the variables. The CA results were obtained in the form of 1, which defines 27. 93% variance in microbial community composition in tomato, ladyfinger, castor and sorghum crop plants when compared to the other crops, while 2 defines differences between artificial diet and crop plants with 18. 56% of variance. 1 and Axis 2 together explain 46. 49% of variance among the sample groups. In concordance with the pairwise analysis (Tables 4, 5 and 6), we found that due to similarity in the bacterial composition among larvae collected from crops of various locations (Coimbatore, Bangalore, Delhi and Pachora) they clustered together. Pachora crops (castor, cotton, chickpea, ladyfinger, sorghum, sunflower and tomato) had significant differences amongst themselves owing to the differences in the relative abundance of individual T-RFs and were found to cluster as three separate groups (Figure 4).

Output: pass


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: For fed-batch enzymatic hydrolysis with higher solids loadings, the hydrolysis was initiated at 12% (w/v) solids loading and the pretreated corn stover (7%, w/v) was fed once (at 3 h), twice (at 3 and 6 h), three times (at 3, 6, and 24 h), or four times (at 3, 6, 24, and 48 h) to reach the solids loadings of 19%, 26%, 33%, or 40% (w/v), respectively. For the solids loading of 40%, the required enzyme was supplemented in two modes, either added in a whole at the beginning of the hydrolysis or fed simultaneously with the substrate at the time points of 0, 3, 6, 24, and 48 h to maintain an identical final enzyme dosage. Microorganism and pre-culture preparationCutaneotrichosporon oleaginosum (formerly Cryptococcus curvatus) ATCC 20509 was sourced from the (ATCC), stored at 4 °C and propagated every 4 weeks on yeast peptone dextrose (YPD) agar slants (yeast extract 10 g/L, peptone 10 g/L, glucose 20 g/L, agar 15 g/L, pH 6. 0). Pre-cultures were grown in 50 mL YPD liquid medium at 30 °C for 24 h unless otherwise specified. Fed-batch cultureThe fed-batch cultures were conducted in 250-mL unbaffled Erlenmeyer flasks. The cultures were inoculated with the addition of 2. 5 mL of pre-cultures to 22. 5 mL appropriately diluted hydrolysates containing 70 g/L TRS, 10 g/L yeast extract, and 10 g/L peptone. The initial pH was set at 6. 0. The cultures were incubated at 30 °C and 200 rpm in a thermostatic culture oscillator (ZWY-2102,. , Ltd. , Shanghai, China) for 264 h. Sterile liquid hydrolysates containing 244. 5 g/L TRS were then fed twice when residual sugar was below 10 g/L. The pH of the culture was adjusted to the initial value at 12-h intervals. To avoid bacterial contamination, the pH adjustment was performed in a clean bench using a pH meter (PB-10, Sartorius, Germany).

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: In this sense, genome-edited crops have the potential to play a role in obtaining elite genotypes with desirable traits in plant breeding. Besides, genome editing has another advantage, as it enables the study of genetic diversity that governs desirable crop characteristics. The knowledge that comes out of such studies could be used in the development of a genome-edited crop as well as in conventional breeding. In this 1. 1 and discussed below in terms of improved agronomic traits, disease resistance, quality, and nutritional content. Table 1. 1 Summary of gene families targeted by genome editing for crop improvement in terms of improved agronomic traits, disease resistance, quality, and nutritional contentFull size table2. 1 TraitsGenome editing can be used to enhance the yield of crops by improving their resistance to environmental stressors, such as drought, heat, and cold. By modifying specific genes, scientists can increase the plant’s ability to cope with adverse conditions, leading to improved yield. Allelic variants of the ARGOS8 gene belonging to the ARGOS gene family were obtained by gene editing in maize. These allelic variants were the negative regulator of ethylene responses [7]. 8 variants had high levels of ARGOS8 transcripts relative to the native allele and increased grain yield under flowering stress conditions and had no yield loss in arid conditions. In order to understand the function of BnaPLDα1 genes of in Brassica napus, BnaPLDα1 gene was over-expressed and knocked out by. Four lines were edited at one sgRNA site and two lines were edited at two sgRNA sites [8]. Compared to the wild type, the PLDα1 protein was found to be more expressed in the over-expressed edited lines while less or not expressed in the knockout lines. When the plants were planted in the field, the plant height was not different between overexpression lines and wild type, but the plant heights of the knocked-out lines were shorter, indicating that the appropriate dose of PLDα1 was required to maintain the normal growth of the plant, indicating that further increase of PLDα1 level had limited effect on it. Many agronomic traits such as plant height, effective branches, silique number in inflorescence, silique seed number were adversely affected in lines with reduced PLDα1 levels [8].

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: armigera samples, collected from the ladyfinger crop. Second cluster consists of leaf and H. armigera samples, collected from cotton and sorghum crops. Third cluster consists of leaf and H. armigera samples, collected from tomato crop. DiscussionThe diversity and metabolic abilities of gut bacteria in higher animals like man is reported to be in the range of 1500–2000 different bacteria, which contribute both in number (quantitative) and diversity (quality) to the host. There are ten times more numbers of bacteria in gut when compared to the total number of cells in the host and the bacteria have more than ten times the metabolic diversity [18] when compared to the host's genome. Thus cohabilitating commensal bacteria in the gut has been a very early and essential step during evolution. Gut microflora is shown to play a major role in controlling sexual performance, mating p1. The number of bacterial isolates from H. armigera larvae were gram stained and subjected to basic biochemical characterization including oxidase, catalase, starch hydrolysis and nitrate reduction. In addition, antibiotic susceptibility of the bacterial strains was also performed. The result of all the tests for each colony is listed in the table. 1. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355–1359. View 2. Cash H, (2005) Commensal bacteria shape intestinal immune system development. ASM news 71(2): 77–83. View 3. (2005) Diversity of human intestinal microbial flora. Science 308: 1635–1638. View 4. (2004) The gut microbiota as an environmental factor that regulates fat storage. 101: 15718–15723. View 5. (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022–1023. View 6. (2005) Structure and topology of microbial communities in the major gut compartment of Melolontha melolontha larvae. Microbiol 71: 4556–4566. View 7. (2007) Native microbial colonization of Drosophila melanogaster and its use as a model of Enterococcus faecalis pathogenesis. 75: 1565–1576. View 8. Scoble MJ (1992) Lepidoptera: form, function, and diversity. . 9.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: The pH electrode was rinsed repeatedly with sterile water prior to use. All the enzymatic hydrolysis and fermentation experiments were performed in triplicates. The data were presented as mean value ± standard deviation. Analytical methodGlucose was measured using a biosensor analyzer (SBA-40E, of Sciences, Jinan, China). Xylose was determined by a Megazyme D-xylose assay kit (K-). The concentration of TRS was determined by the dinitrosalicylate (DNS) method described by Miller [50]. Other TRS concentration was obtained by subtracting glucose and xylose from the TRS. The concentration of total protein was measured according to a Blue method [51]. The concentrations of cello-oligosaccharides and xylo-oligosaccharides were measured according to a standardized Procedure (LAP) described by (NREL) with some modifications [22, 52]. Specifically, 2 mL of appropriately diluted hydrolysates and the glucose/xylose recovery standards were added into 10-mL screw-cap glass vials. 69. 7 μL of 72% (w/w) sulfuric acid was then added into the bottle to obtain a final acid concentration of 4%. The bottle was then autoclaved at 121 °C for 1 h. The samples were slowly cooled to room temperature, neutralized with calcium carbonate powder to pH between 5 and 6, and filtered through a 0. 2-μm filter before sugars analysis. The sugar recovery standards were used to correct for losses due to destruction of sugars during dilute acid hydrolysis, which were calculated as the percentage of the remaining sugars after the hydrolysis to the initial values.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: These findings proved that BnaPLDα1 regulation changes the agronomic traits of B. napus. The loss of function lines of OsOTS1 gene enhanced sensitivity to salt with reduced root and shoot biomass, suggesting it plays a role in salinity stress. Mutagenesis of OsOTS1 gene of SUMO proteases gene family to reveal its role against salinity stress was targeted in rice [9]. To investigate the usability of transcription factor (basic helix-loop-helix (bHLH)) sub-U family genes in breeding rice varieties under salinity stress conditions in rice (Oryza sativa L. ), loss of function lines of OsbHLH024 and OsbHLH044 genes was generated by theCas9 system [10, 11]. The gene editing mutant lines revealed altered morphological and physiological phenotypes. OsbHLH024 mutant lines had increased shoot weight, the total chlorophyll content, and the chlorophyll fluorescence. They had less reactive oxygen species and stabilized levels of MDA, fewer Na+ but more K+, and a balanced level of Ca2+, Zn2+, and Mg2+ in the shoot and root. Therefore, it was concluded that the OsbHLH024 gene improves salt stress resistance by playing a role as a negative regulator [10]. Considering OsbHLH044 mutant lines, they showed reduced morphological and physiological parameters, lower antioxidant activities and higher lipid peroxidation and hydrogen peroxide (H2O2) accumulation. The loss-of-function of this gene also altered the expression of ion homeostasis-related genes (and OsNHX) and ABA-responsive gene (OsLEA3). The mutant synthesized less stored starch and proteins because of decreased expression of genes coding for starch (OsAGPL1, and OsFLO2) and seed storage proteins (GluA1 and Globulin 1). It was concluded that the OsbHLH044 gene plays a role as a positive regulator of salt stress and grain quality [11]. In rice, three genes (Os03g0603100, Os03g0568400, GL3. 2) of cytochrome P450 family and OsBADH2 were multiplex edited withCas9 and their novel alleles were generated [12]. The high performance of mutant plants homozygous for grain width, grain length, and grain fragrance was recorded.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: In the case of ECTV, subcutaneous infection of susceptible mice results in extensive necrosis and damage in spleen and liver after multiplication in these organs by 4 dpi, and also small intestinal mucosal erosions and engorged guts are frequently detected among other pathological changes at late stages [5,23]. VACV also causes a severe disease in susceptible mice after intranasal infection, with detectable weight loss and signs of illness by 5 dpi, associated with high virus titers in lungs and brain (9). Hence, to avoid potential confounding factors, we focused on early time points (2 dpi) when we hypothesized that the initial virus replication might have affected mucosal immunity in the gut and not yet triggered strong confounding factors (e. g. fever, loss of appetite, inflammation processes, modified liver function). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 1. Exploration of trends in mucosa-associated caecal microbiome composition. Figures depict results from a principal components analysis (A) and (DPCoA) (B) based on 16S marker gene profiles. The analyses ordinate experimental groups based solely on the per-group relative abundances of OTUs (A), or based on the phylogenetic distances among OTUs and per- group relative abundances of OTUs (B). Sample points and experimental group labels are jointly colored, and ellipses describe the experimental groups’ collective variances. Early infection sample groups; Mock, Vwt, Ewt, VdB18, EdCrmD. Late infection sample groups; VwtD5, VdB18D5, EwtD7, EdCrmDd7. analysis of bacterial community profiles at 2 dpi revealed significant differences associated with the experimental groupings (Fig 2. BCA; p<0. 001), not only based on OTUs relative abundances but also when taking into account the phylogenetic relatedness among OTUs (cDPCoA; p<0. 05). Such analysis also showed a pattern suggesting that both viral mutant profile groups represent a midpoint between the effect caused by infection with the wild-type viruses and the mock-infected community (Fig 2). Interestingly, the results also indicated that infection with Ewt and Vwt shift community structure towards different compositional states.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Biomass, expressed as dry cell weight (DCW), was determined by a gravimetric method [40]. Lipids were extracted twice from the dry cells using a mixture of chloroform and methanol (1:1, v/v) and measured by a gravimetric method in accordance with a published procedure [40]. Lipid concentration was presented as gram lipid per liter of culture. Lipid content was expressed as gram lipid per gram DCW. Lipid yield was calculated as gram lipid accumulated per gram TRS consumed. To analyze the fatty acid compositions, the microbial lipid samples were transesterified with methanol in the presence of KOH according to a published procedure [59]. The resulting fatty acid methyl esters (FAMEs) were determined using a gas chromatograph (GC-2010 Plus, Shimadzu, Japan) following a standard procedure [60]. Statistical analysisThe significant differences were identified by conducting an analysis of variance (ANOVA). Tukey’s post hoc test was performed to determine the significant differences among the data as obtained from different enzymatic hydrolysis experiments. A p value lower than 0. 05 was treated as statistically significant. Availability of data and materials All appropriate data for this study have been included in the manuscript. AbbreviationsSMs: the sodium hydroxide–methanol solution FPU: filter paper unit CBU: cellobiase unit TRS: total reducing sugars DNS: dinitrosalicylate NREL: the : dry cell weight FAMEs: fatty acid methyl esters ANOVA: an analysis of variance AFEX: ammonia fiber explosion SSF: simultaneous saccharification and fermentation 7. 1. 31. 82. 93. 86. 2013. p. 239–59. 91. 8. 705. 43. 45. 14. 42. 44. 5. 7. 70. 33. 7. 73. 195. 135. 18. 206. 7. 25. 8. 17. 6. 13. 9. 70. 5. 9. 77. 46. 86. 37. 8. 1988. p. 33–70. 51. 130. 9. 8. 80. 01. Adney B, Baker J. Measurement of Cellulase Activities. . /TP-510-42628. 1996. Ghose T. Measurement of cellulase activities. Chem.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Also, the mutant plants showed high level 2-acetyl-1-pyrroline (2AP). It has been concluded that the edited plant in this study could be used as valuable genetic material for crop breeding to improve rice yield and quality. Indel mutations in the TaSPL13 gene of promoter-binding protein-like (SPL) transcription factors gene family were created to increase grain yield in bread wheat (Triticum aestivum) [13]. The microRNA 156 recognition element indel mutations in 3′ UTR of TaSPL13 brought about the abundance of TaSPL13 transcripts and a decrease in flowering time, tiller number, and plant height and the consequent grain size and number increased in the mutant plants. Eleven members of the Cytokinin oxidase/dehydrogenase gene family (OsCKX1-OsCKX11) were knocked out usingCas9 and -Cas12a to reveal their functions in rice [14]. -Cas12a performed better than -Cas9 for generating multigene mutants. The OsCKX members showed functional redundancy and affected plant development, seed quality, and starch composition by regulating endogenous cytokinins. OsCKX1/2 and OsCKX3/8/10 genes had roles in the control of panicle architecture and grain number. OsCKX4/5/9 genes regulated the development of roots and plant height and tillers. Knock-out and over-expression of SlLBD40 (Solyc02g085910) gene of Domain (Lbd) were created to understand its role against drought stress in tomato [15]. The results showed that SlLBD40 knock-out lines had improved water-holding ability and relieved the physical harm of the photosynthetic system of tomato seedlings, while SlLBD40 overexpressing plants showed vigorous wilting symptoms under drought stress, suggesting that SlLBD40 is a negative regulator of drought tolerance. In order to increase photosynthetic efficiency in tetraploid tobacco (Nicotiana tabacum), it was aimed to obtain novel alleles of genes (rbcS) coding the small subunit of CO2-fixing enzyme Rubisco family so that the efficiency of carbon assimilation through better Rubisco enzymes could be increased [16].

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Subsequent individual pairwise comparisons among experimental groups (Table 1) established that each treatment group presented a distinct (p<0. 05) pattern of community composition. Focusing on the wild-type and mock experimental groups, we observed significant differences in the relative abundance of some major bacterial taxa (Table 2); the percentage of sequences affiliated to Deferribacteres were two-fold lower in Vwt samples (p<0. 05), and those assigned as Proteobacteria were over three-fold lower in Ewt samples (p<0. 05), when compared to the mock-infected group. However, overall Shannon diversity values were not significantly affected by these infections (8. 3±3, 8. 2±6 and 8. 0±4 for mock, Ewt and Vwt infections respectively). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 2. Exploration of trends in microbiome composition during early infection. The figure depicts results from an analysis with respect to instrumental variables applied to a principal components analysis based on 16S marker gene profiles (within group analysis using experimental batch as constraint, followed by a between class analysis using experimental group as constraint). The analysis ordinates samples (VdB18; n = 7. Ewt, Vwt, EdCrmD; n = 10) based on the similarity between their relative abundances of OTUs. Sample points and experimental group labels are jointly colored, and ellipses describe the experimental groups’ collective variances. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 1. Differences between community compositions. Results represent p-values of permutation tests assessing the significance of experimental groups after controlling for possible batch effects. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 2. Relative abundance (%) of major bacterial groups for Mock, ECTV and VACV infections. ± represent SD. caecal transcriptomic profiles were used as proxies for gut immunophysiological state. Overall, the RNA integrity values (RIN) obtained were relatively low (4. 5 ± 1), likely due to the fact that the gut is a very delicate tissue when it comes to mRNA extraction [24]. In this regard, partially degraded mRNA could impact downstream analyses.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Rapid selection and identification of Miscanthus genotypes with enhanced glucan and xylan yields from hydrothermal pretreatment followed by enzymatic hydrolysis access Published: 03 August 2012 Rapid selection and identification of Miscanthus genotypes with enhanced glucan and xylan yields from hydrothermal pretreatment followed by enzymatic hydrolysis Taiying Zhang1, Wyman1,2, Katrin Jakob3 & …Bin Yang1,4 Show authors Biotechnology for Biofuels 17. 5 min followed by co-hydrolysis in a multi-well batch reactor identified two varieties out of 80 that had significantly higher sugar yields from pretreatment and enzymatic hydrolysis than others. The differences in performance were then related to compositions of the 80 varieties to provide insights into desirable traits for Miscanthus that enhance sugar yields. ConclusionsHigh throughput pretreatment and co-hydrolysis (HTPH) rapidly identified promising genotypes from a wide range of Miscanthus genotypes, including hybrids of Miscanthus sacchariflorus/M. sinensis and Miscanthus lutarioriparius, differentiating the more commercially promising species from the rest. The total glucan plus xylan content in Miscanthus appeared to influence both mass and theoretical yields, while lignin and ash contents did not have a predictable influence on performance. BackgroundWorld petroleum reserves are being depleted at an accelerating rate and production rates are slowing. In fact, Kerr reported that conventional oil production might have already reached its peak instead of plateauing between 2015 and 2020 as predicted earlier [1–3]. In addition, a move from fossil to renewable fuels is vital if we hope to slow the impacts of carbon dioxide accumulation on global climate. Against this background, production of fuels from cellulosic biomass is one promising option for large-scale and low-cost sustainable production of liquid fuels with low greenhouse gas emissions. Crops planted for the specific purpose of energy production are expected to play an essential role in meeting the of 2007 in the United States. In the recent report entitled “U. S. update: for Bioenergy and Bioproducts Industry” jointly released by DOE and USDA, energy crops were predicted to become dominant at prices above $50 per dry ton after 2022 with the baseline about 37% of total biomass at $60 per dry total [4].

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: The phenotyping analysis of mutant plants showed reduced Rubisco content, photosynthetic rates, and biomass accumulation. In this study, it has been shown that it is possible to produce superior non-native Rubisco enzymes by multiplex gene editing withCas9 in polyploid species. The function of the OsPMEI12 gene, which belongs to the pectin methylesterase inhibitors (OsPMEI) gene family for growth, cell wall development, and response to phytohormone and heavy metal stress, was elucidated by mutating it in rice (Oryza sativa L. ) [17]. It has been revealed that the OsPMEI12 gene plays a role in the regulation of methyl esterification during growth, thus pectin status is controlled by hormones and cadmium stress. Discovery of genetic male sterility (GMS) genes will allow to unravel the molecular mechanism of anther development and to develop male sterility systems for crop breeding and hybrid seed production. Therefore, the researchers focused on elucidating the roles of the transcription factors genes (bHLH, band LBD gene families) responsible for the GMS agronomic trait in highly heterosis maize [18]. Mutation of transcription factor gene families with yielded the following results; that ZmbHLH51 and ZmbHLH122 are necessary for male fertility, ZmTGA10 has affected anther dehiscence. ZmMYB84 is essential for maize pollen development. ZmPHD11 is responsible for the formation of anther cuticle and Ubisch bodies. Two MYB33 paralogs are important for GMS. ZmLBD27 has an impact on the reduced ratio of normal pollen grains. ZmPHD11/27 influenced viable pollen formation. Two homologous genes (Bra018924 and Bra014296) of PP2A, a 55 kregulatory subunit (PR55/B), were edited through theCas9 system to develop self-compatible lines controlled by type 2A serine/threonine protein phosphatases (PP2As) in Chinese cabbage [19]. The PR55/B gene knock-out line did not show self-incompatibility and produced seeds, suggesting that the PR55/B gene was responsible for the self-incompatibility. 2.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: While their use provides the theoretical opportunity to dissect the host genetic component of the host-microbiome interacting system, it represents a rather brute force approach as these deficient strains present dysbiotic states per se. which hinders the use of proper negative controls. The approach we propose could be employed alone or jointly with germ-free, knock-out, and (or) gnotobiotic approaches to reproducibly and effectively advance the science of host-microbial mutualism. For instance, our approach should allow the detection of links between the activity of different modules of gut immunity and the abundance or activity of particular groups of bacteria. Supporting informationS1 Fig. Top 20 enriched IPA pathways in caecum after Ectromelia virus infection. Significant and differentially expressed genes from ECTV infected samples compared to control uninfected were used in a pathway enrichment analysis using IPA software (Ingenuity). Top 20 most enriched pathways and their corresponding p-values are shown. Lines connect overlapping pathways sharing at least 5 genes. S1 Mat. Results from the Analysis. 1. Pflughoeft KJ, (2012) Human microbiome in health and disease. Pathol 7: 99–122. pmid:21910623 View 2. - (2007) Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131: 33–45. pmid:17923086 View 3. (2003) Viral mimicry of cytokines, chemokines and their receptors. Immunol 3: 36–50. pmid:12511874 View 4. (2006) Anti-immunology: evasion of the host immune system by bacterial and viral pathogens. Cell 124: 767–782. pmid:16497587 View 5. (2005) Ectromelia virus: the causative agent of mousepox. J 86: 2645–2659. pmid:16186218 View 6. (2008) Correlates of protective immunity in poxvirus infection: where does antibody stand? Biol 86: 80–86. pmid:17923850 View 7. (2011) CD94 is essential for NK cell-mediated resistance to a lethal viral disease. Immunity 34: 579–589. pmid:21439856 View 8.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Among various potential perennial energy crops, Miscanthus, which is native to Asia and the Pacific Islands, has been selected and studied as one of the most promising energy crops for Europe over the past two decades [5–8]. Based on Miscanthus field trials at different locations in Europe, a growth model towards more robust yield predication on the basis of different climatic and soil condition was developed in Europe [9]. has been successfully produced with high yields over a wide range of climatic conditions in Europe, it also became of interest as a dedicated biomass crop in the US, and first field trials were planted in Illinois and Arkansas [10–14]. It has been reported that the average productivity of Miscanthus x giganteus was 30 t/ha-year and the maximum productivity was as high as 61 t/ha-year over a 3 year period in side-by-side trials while the productivity of switchgrass, one of the most studied energy crops in the United States, was reported to be 15. 8 t/ha-year in upland and 12. 6 t/ha-year in lowland varieties [10]. Thus, Miscanthus could potentially reduce the land requirements to support U. S. biofuels production [11, 12]. Further study on the effects of management on Miscanthus x giganteus productivity in different environments based on four locations in the provided more insights on how to improve the productivity of Miscanthus x giganteus and its capacity as a stable and reliable biomass feedstock [13]. In addition to high productivity, Miscanthus could be very important for the relatively high carbohydrate content (>60%) of some genotypes. genus in general, and Miscanthus x giganteus in particular, have been identified as prime candidates for biomass energy crops because of an array of other attributes including high photosynthetic efficiency, strong stress tolerance, perennial growth, low nutrient requirements, and high carbon content [5, 14]. For biological processing to ethanol and other products, it is particularly beneficial to identify genotypes that are most easily processed into sugars. As with other types of lignocellulosic biomass, pretreatment is essential to disrupt the natural recalcitrance of Miscanthus to release fermentable sugars with high yields with the fungal enzymes typically used.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: 2 ResistancePlant diseases are a significant threat to crop productivity, with losses estimated to cost billions of dollars annually. Genome editing can be used to enhance the resistance of crops to diseases by editing genes that encode for disease resistance. MicroRNAs act as regulators of the plant immune system by silencing the genes involved in pathogen virulence or by regulating the expression of target genes. MicroRNAs belonging to the miRNA482/2118 superfamily targeted R-genes of the class NBS-LRR (nucleotide-binding site-leucine rich repeat). In tomato, knockout mutants for SlymiR482e-3p gene, a member of the miR482/2118 family, were generated to detect its role against tomato wilt disease resistance [Fusarium oxysporum f. sp. lycopersici (race 2) (Fol)] [20]. The results showed that SlymiR482e-3p gene negatively regulated the resistance to wilt disease. In another study with miR482 gene family in tomato, mutations in the two genes (miR482b and miR482c) were generated [21]. The expression levels of their target NBS-LRR genes were increased, followed by reduced late blight, caused by Phytophthora infestans, disease symptoms in mutant plants. Interestingly, it was concluded that knocking out these two genes could lead to expression perturbation of other miRNAs, suggesting cross-regulation between miRNAs. In cotton (Gossypium hirsutum L. ), the MIR482 mutant collection was obtained by knocking out MIR482 genes in miR482 gene family with dozens of members usingCas9. This mutant collection allow us to examine the role of individual MIR482 genes against pathogen response and to identify miR482-NLR module(s) that respond to, particularly fungal pathogen Verticillium dahliae agent for Verticillium wilt and other pathogens. It has also been reported that this collection may be a useful genetic resource for the development of new disease-resistant cotton varieties [22]. 2. 3 Improved QualityQuantitative trait loci (QTLs) are genomic regions that are associated with complex traits such as crop quality. QTLs can be used to improve crop quality by identifying genomic regions associated with desirable traits.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Log in or to journalnew issue alertsGet alerts Enter your Email address: Subscribe to e2018. | DOI: 10. 1249/FIT. 0000000000000421 It! Encourage clients to include whole fruits, vegetables, grains, and beans and legumes in their diet over fruit juices, sweetened beverages, energy drinks, and more processed foods. Encourage the inclusion of fermented and higher fiber foods in the diet to assure a healthy gut. Select healthy foods first over supplements. is not uncommon for active individuals to experience gastrointestinal (GI) distress, upper respiratory symptoms (URS), and other illnesses associated with sport participation. Research in endurance athletes shows that 30% to 50% report some type of GI distress associated with exercise (1). In addition, URS are common among athletes. In the three months before the 2016 summer Olympics, URS were the most common illness (48%) reported by 132 athletes participating in the games, especially those involved in prolonged, intense activity and during competitions (2). Of those reporting URS, 95% reported being unable to participate in sport. In this same sample, 21% reported GI distress during the same period, with 79% of these athletes being unable to participate in sport. You don’t have to be an Olympic athlete to have GI symptoms associated with exercise. Even recreational and fitness athletes experience GI issues or concerns associated with training or competition. No one wants to run to the bathroom, throw up, or quit a sporting event because of GI distress. Although GI symptoms associated with sport are typically mild to moderate, when they occur, they can derail performance or prevent participation in exercise and sports. It is well established that gut health is closely linked to immune health and the prevention of illness (3). Thus, a healthy intestinal microbiota (defined in the following section) translates into a healthier immune system and decreased susceptibility to illness or disease (3). Part of having a healthy gut means having a healthy microbiota. In the following section, we address key steps to help you maintain a healthy gut, improve your overall immune system, and reduce your risk of illness. . The human gut contains thousands of bacterial species plus many other microorganisms that are collectively known as the gut microbiota (4). The number of microorganisms inhabiting the gut plays a significant role in regulating host immunity, protecting against pathogens, strengthening gut integrity, synthesizing vitamins, and producing energy, especially short chain fatty acids (SCFA).

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Conventional pretreatment and enzymatic hydrolysis methods are very labor intensive and time consuming, making it very expensive and/or slow to screen large numbers of plants to find those that display enhanced sugar yields. However, high throughput methods have been recently developed that allow rapid screening of large numbers of combinations of plants, pretreatment conditions, and enzyme loadings and formulations to narrow the field to those with high sugar release or other desirable features [28–34]. These methods can also handle much smaller amounts of samples than conventional approaches, thereby allowing characterization of sugar release from different anatomical fractions [30]. Such rapid screening methods have been applied to a sorghum diversity panel [32], a high-throughput microplate for enzymatic hydrolysis of lignocellulosic biomass [33], and high-throughput screening of cellulose following ionic liquid treatment [34]. Recent rapid screening studies of enzymatic hydrolysis using different glycosyl hydrolases were employed to compare AFEX and dilute acid pretreatment of corn stover [35, 36]. Studer et al. developed a higher temperature, high throughput method appropriate for hydrothermal and other thermochemical pretreatments based on the 96 well-plate format and employing a custom made steam chamber for rapid heating and cool down of multiple reaction vessels [29]. Results for poplar without liquid–solid separation after pretreatment in the multi-well plate system were shown to be statistically identical to those from standard pretreatment and hydrolysis methods with liquid–solid separation and solid washing [29]. Advantage has also been taken of the ability to process small sample sizes to determine variations in sugar release among tree growth rings and to identify promising traits in poplar as well as the high throughput determination of glucan and xylan fractions in lignocelluloses developed by Selig et al. [28, 31, 37]. In this study, the previously established HTPH system was applied to screen Miscanthus genotypes with the goal of identifying those that displayed enhanced release of glucan and xylan from the coupled operations of hydrothermal pretreatment and enzymatic hydrolysis. Conventional hydrothermal pretreatment in tubular batch reactors followed by enzymatic hydrolysis was applied first to identify baseline conditions that gave the highest total sugar yields from Miscanthusx giganteus cv. Illinois planted in Illinois.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Many genes in QTLs have been targeted with genome editing. Starch branching enzymes (SBEs) are involved in the biosynthesis of starch in plants and there have been several studies on the use of genome editing SBE genes in crops to modify starch content and properties. For example, one study used -Cas9 RNP-method to induce mutations in SBE genes to develop a unique potato starch lacking branching [23]. Another study usedCas9 to generate high-amylose rice by targeting SBEI and SBEIIb genes [24]. napus, an oilseed plant that is the raw material for both cooking oil and biodiesel production, loss-of function of the BnLPAT2 and BnLPAT5 genes belonging to lysophosphatidic acid acyltransferase (LPAT) family allowed to lay out their precise roles in oil biosynthesis. That is, the oil content decreased, the size of oil body increased in mutant lines [25]. The results of this study illustrated that these genes could be used for oil production improvement. In order to prevent enzymatic browning, negatively affecting tubers during harvest and post-harvest procedures, researchers targeted the (PPOs) gene family and mutated the StPPO2 gene in Solanum tuberosum L. [26]. A lower PPO causing oxidation of polyphenols (natural antioxidants) in tuber was observed in mutant lines and enzymatic browning was reduced. Another study with the polyphenol oxidases (PPOs) gene family was carried out in eggplant (Solanum melongena L. ) [27]. In this study, the researchers stated that it would be possible to develop eggplant varieties that retain a high polyphenol content beneficial to human health in the berries during harvest and post-harvest processes by knocking out the three genes (SmelPPO4, SmelPPO5, SmelPPO6). 2. 4 ContentGenome editing can also be used to enhance the nutritional content of crops by increasing the levels of essential nutrients, such as oil, phenolic acid, vitamins and minerals [4]. This is particularly important in developing countries, where nutrient deficiencies are prevalent and access to a diverse diet is limited.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: The SCFA (propionate, butyrate, and acetate) are produced when nondigestible carbohydrates (e. g. , dietary fiber) or other food components are metabolized by the gut bacteria (4). These SCFA are now recognized as key metabolic and immune mediators and have an anti-inflammatory role. Thus, anything that disrupts the gut microbiota, such as pathogens or antibiotics, has the potential to significantly impact the health of the host. How do we keep our gut microbiota healthy? Diet has a major impact on the gut microbiota. The ability of the gut bacteria to metabolize indigestible proteins and carbohydrates, especially those found in dietary fiber, contributes to the health of the gut microbiota. Thus, extremes in dietary behaviors, such as high animal-based diet versus plant-based diet, can result in a wide range of alterations in the gut microbiota in humans. Low-fiber diets will mean lower production of SCFA and the benefits these metabolites play in providing energy to the gut and keeping it healthy. The specific dietary factors that play a role in improving gut health are discussed as follows. How do we keep our gut microbiota healthy? Diet has a major impact on the gut microbiota. The ability of the gut bacteria to metabolize indigestible proteins and carbohydrates, especially those found in dietary fiber, contributes to the health of the gut microbiota. Thus, extremes in dietary behaviors, such as high animal-based diet versus plant-based diet, can result in a wide range of alterations in the gut microbiota in humans. Healthy Diet. There are a number of dietary steps you can take to help maintain a healthy gut. Probiotics. One way to maintain the beneficial bacteria in the gut is to consume foods that contain probiotics. (5) has defined a probiotic as a “live microorganism which, when administered in adequate amounts, confer a health benefit to the host. ” There are thousands of fermented foods consumed worldwide by every culture. These foods are generally defined as foods or beverages made through a controlled microbial growth (e. g. , bacteria are added to the product) and enzymatic conversions of major or minor food components to simpler components (e. g. , enzymatic digestion of lactose to its simple sugars) (6). Some of the more common fermented foods in the American diet include dairy foods, such as yogurt and kefir.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Then the HTPH system was applied to 80 different Miscanthus varieties to screen for those that gave the highest sugar release and identify the most promising genotypes based on baseline conditions determined from conventional pretreatment results. As reported in a companion paper (in preparation), a flowthrough reactor system was then applied to follow release of sugars and other biomass components and gain new insights into biomass deconstruction patterns that favour high sugar yields based on hydrothermal pretreatment. Results and discussionMiscanthus compositionsAs the most widely cultivated biomass genotype currently available, Miscanthus x giganteus cv. Illinois was selected as the reference material for identification of pretreatment conditions that gave the highest total glucose plus xylose release from conventional pretreatment and subsequent enzymatic hydrolysis in the batch tubes. This genotype contained 42. 87 ± 0. 64% glucan, 22. 02 ± 0. 32% xylan, 19. 67 ± 0. 01% lignin, 2. 33 ± 0. 10% ash, 3. 21% water extractives, and 5. 80% ethanol extractives. The average moisture content of Miscanthus x giganteus cv. Illinois was determined to be 7. 37 ± 0. 11% based on 10 tests. The data reported for the 80 Miscanthus genotypes (provided as the Additional file 1: Table S1 and Additional file 2: Table S2) include averages, minimum and maximum contents of glucan, xylan, the total glucan plus xylan as carbohydrates, and lignin. The average compositions of all 80 Miscanthus genotypes were 40. 74% glucan, 21. 01% xylan, 24. 03% lignin, and 2. 83% ash. However, the 80 Miscanthus genotypes showed significant diversity in compositions, with glucan levels ranging from 27. 7% to 48. 6%, xylan from 19. 6% to 27. 1%, lignin from 15. 5% to 27. 8%, and ash from 1. 10% to 7. 37%. Thus, these samples were expected to enable the study of how composition affects sugar release from pretreatment and hydrolysis and aid in the selection of desirable traits to target for improvements. The total glucan and xylan content, which was important to establish the maximum possible ethanol yield, ranged from 48. 6% to 72. 8%.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: The oleic acid content of soybean seeds was modulated by knocking out GmFAD2-1A and GmFAD2 genes belonging to the fatty acid desaturase (FAD2) family [28]. The loss of function of these genes has paved the way for cultivating soybean genotypes with high oleic acid content. miltiorrhiza, the SmLACs genes of the laccase family, which has 29 family members with high homology, were multiplex silenced by targeting their conserved sequences to reveal their role in the production of medicinal phenolic acid compounds [29]. It has been concluded that SmLACs play a role in lignin formation and phenolic acid biosynthesis in the roots due to decreased expression of target genes and delayed hairy root development, larger and looser xylem cells, low RA and SAB accumulation, and very low lignin content in edited lines compared to wild types. By knocking out six genes (. 2,. 1, BBLe) belonging to the berberine bridge enzyme-like (BBL) family using a single sgRNA, a nicotine-free tobacco variety was developed and the amount of nicotine was reduced [30]. In this way, the use of nicotine-free tobacco by smokers may protect their health. The genes in α- and γ-gliadin gene families were silenced using six sgRNAs, and a less allergenic bread wheat variety containing gluten with fewer immunogenic epitopes, which would be beneficial in the diet of coeliac patients, was obtained [31]. A less allergenic durum wheat variety was produced [32]. The multiplex editing of CM3 and CM16 genes belonging to α-amylase/trypsin inhibitors (ATI) family subunit U form was carried out using seven gRNAs targeting the two genes of interest. The editing of these genes decreased the amount of ATI transcripts. It was reported that this might have happened due to nonsense-mediated mRNA decay. Interestingly, it was noted that ATI 0. 28 pseudogene were activated after knocking out CM3 and CM6 genes. 3 Challenges of in Crop ImprovementDespite its potential benefits, genome editing in crops also faces several challenges. One of the biggest challenges is the regulatory landscape.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: These foods contain the bacteria necessary to begin the fermentation process, but also can contain additional healthy bacteria added to increase the health benefit of the product. A variety of other fermented foods contain healthy bacteria such as kimchi or sauerkraut, kombucha, tempeh, miso, natto, cheese, sour cream, cultured buttermilk, wine, beer, sourdough bread, olives, pickled vegetables, salami, and soy sauce. Tempe, miso, and natto are made from fermented soybeans, whereas kimchi is a fermented cabbage popular in Korea, and kombucha is a fermented sweet tea. When selecting fermented foods, remember they can be high in added salt and sugar, so read the labels. The processing of these products also is important because exposure to high temperatures will kill the healthy bacteria. If you have never tried some of these fermented foods, make a point of stepping out and trying something new. Prebiotics. The bacteria of the gut need to be maintained; thus, they require their own sources of energy and nutrients. The prebiotic concept was developed when researchers realized the health benefit of nondigestible carbohydrates (e. g. , dietary fibers) on the gut. Thus, a probiotic adds healthy bacteria to the gut, whereas a prebiotic provides the energy and nutrition (e. g. , dietary fiber) the bacteria need for growth. However, it is important to remember that although all prebiotics are fiber, not all fibers are prebiotics. To be considered a prebiotic, a fiber must be resistant to absorption, be fermentable in the gut, and provide nourishment to the gut bacteria. These indigestible carbohydrates reach the colon and undergo various degrees of degradation or fermentation by the gut bacteria. Fibers with a higher degree of fermentation produce energy and other byproducts, such as SCFA, which enhance microbial growth and gut health and improve overall immune function (7,8). Thus, the high-fiber foods recommended in the next section, especially those soluble and fermentable fibers, are considered prebiotics. High-fiber foods. Based on national survey data, adults in the consume only half the recommend adequate intake for dietary fiber per day (men = 38 g/d women = 25 g/d) (8).

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: The genotypes with the highest total glucan and xylan content of 48. 6% glucan and 24. 2% xylan also had the highest glucan content and could realize a theoretical ethanol yield of 127 gallons from glucan and xylan per dry ton of feedstock, as calculated by the [38]. The theoretical ethanol yield of Miscanthus x giganteus cv. Illinois was 113 gallons ethanol per dry ton feedstock. Therefore, Miscanthus has excellent potential for high ethanol yields. Batch pretreatment and enzymatic hydrolysisFigure 1 summarizes glucan and xylan sugar yields from batch hydrothermal pretreatment (Stage 1) of Miscanthus x giganteus cv. Illinois in tube reactors at 180°C, 200°C, and 220°C and from subsequent enzymatic hydrolysis of the washed solids (Stage 2) at the conditions noted. Soluble xylan and glucan yields in Stage 1 increased with pretreatment time at 180°C and 200°C to peak values after 35 and 11. 4 minutes, respectively, before dropping with longer times due to xylose degradation becoming more rapid than xylan hydrolysis to xylose. However, the glucan plus xylan based sugar yields in Stages 1 and 2 combined dropped from 69. 7% to 45. 6% as reaction time increased from 4. 6 min to 18. 5 min at 220°C because xylan degradation became very rapid and pronounced in Stage 1. Figure 1Glucan plus xylan yields vs. pretreatment time from hydrothermal pretreatment of Miscanthus x giganteus cv. Illinois. Hydrothermal pretreatments at 180°C, 200°C and 220°C followed by enzymatic hydrolysis with 60 FPU/g(glucan + xylan) at 50°C for 72 hours. Full size image2, glucan plus xylan yields reached peak values of 64. 2 and 61. 9% after 28 and 11. 4 minutes for pretreatment at 180°C and 200°C, respectively, but sugar yields continually dropped with increasing pretreatment times at 220°C for the range of times tested. Sugar yields from enzymatic hydrolysis of pretreated solids were relatively high, ranging from 73. 5 to 93. 1% over the range of pretreatment temperatures tested.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: , 44, 2664–2682. Liao, S. Qin, X. Luo, L. Han, Y. Wang, X. Usman, B. Nawaz, G. Zhao, N. Liu, Y. & Li, R. (2019). /Cas9-induced mutagenesis of semi-rolled leaf1, 2 confers curled leaf phenotype and drought tolerance by influencing protein expression patterns and ROS scavenging in rice (Oryza sativa L. ). Agronomy, 9, 728. Liu, L. , Zhang, J. , Xu, J. , Li, Y. , Guo, L. , Wang, Z. , Zhang, X. , Zhao, B. , Guo, Y. D. & Zhang, N. (2020). /Cas9 targeted mutagenesis of SlLBD40, a lateral organ boundaries domain transcription factor, enhances drought tolerance in tomato. Plant Sci. , 301,110683. Liu, Q. , Kasuga, M. , Sakuma, Y. , Abe, H. and Miura S. , Yamaguchi-Shinozaki K. & Shinozaki K. (1998). Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought and low temperature responsive gene expression, respectively, in Arabidopsis. Plant Cell, 10, 1391– 1406. Liu, S. , Li, C. , Wang, H. , Wang, S. , Yang, S. , Liu, X. , Yan, J. , Li, B. , Beatty, M. & Zastrow-Hayes, G. (2020). Mapping regulatory variants controlling gene expression in drought response and tolerance in maize. Genome Biol. , 21, 163. Liu, S. , Li, C. , Wang, H. , Wang, S. , Yang, S. , Liu, X. , Yan, J. , Li, B. , Beatty, M. , Zastrow-Hayes, G. & et al. (2020). Mapping regulatory variants controlling gene expression in drought response and tolerance in maize. Genome Biol. , 21,163. Ma, X. , Zhu, Q.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Dietary fiber recommendations can be normalized based on energy intake, so that 14 g of fiber per 1000 kcals will meet the recommended intake for most adults consuming adequate energy. Dietary fibers are primarily made up of a large class of nondigestible carbohydrates, which can be further subdivided by their characteristics such as solubility, fermentability, and viscosity (9). Foods most beneficial to the gut bacteria are those that contain fibers that are soluble (oats, barley, beans, peas, and fruits like apple and citrus) and fermentable (fruits and vegetables). Thus, foods such as whole grains, fruits, and vegetables, and beans and legumes, contain a variety of fibers in varying quantities. To meet the dietary fiber recommendations, an individual needs to replace low-fiber foods with those higher in fiber. This means consuming whole fruits and vegetables instead of fruit and vegetable juices, selecting whole grains (e. g. , brown rice, quinoa, faro, oats, barley, wheat) instead of lower fiber options like white bread, rice, and pasta and eating more nuts, beans, and legumes. 1 for a list of high-fiber food options. Select breads, pasta, cereals, and crackers that provide at least 2 to 3 g of fiber per serving. Learning to read food labels will help you identify those foods higher in fiber. Eat beans and legumes more frequently because they provide the highest amount of fiber per serving. TABLE 1: Common High-Foods to limit: There are a number of foods that individuals will say they “like,” but the foods do not “like” them. These foods seem to bother some people and cause GI distress. For example, individuals may complain of chocolate, citrus foods, spicy foods, coffee, or alcohol causing GI distress. For others, foods or beverages containing high fructose, such as sweetened beverages and sugar-free candy or gums can cause gas due to poor fructose absorption. Carbonated drinks can cause bloating and gas. Finally, highly processed foods that are frequently high in sugar and/or fat provide little benefit to the gut microbiota. Adding more nutrient- and fiber-dense foods to the diet will improve gut health. To meet the dietary fiber recommendations, an individual needs to replace low-fiber foods with those higher in fiber.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Total glucan plus xylan yields from pretreatment (Stage 1) at 180°C combined with enzymatic hydrolysis (Stage 2) increased from 79. 5% to 86. 9% as pretreatment time was increased from 17. 5 min to 35 min and then dropped slowly with extended pretreatment time. At 200°C, overall glucan plus xylan yields from Stage 1 plus Stage 2 increased from 78. 0% to 85. 9% as pretreatment time increased from 7. 2 min to 11. 4 min and then dropped. Increasing the temperature to 220°C resulted in a maximum overall glucan plus xylan yield of 69. 7% from the two stages combined at the shortest sampling time of 4. 6 min with a rapid drop after that, suggesting that the rapid degradation of xylose resulted in overall sugar loss at 220°C. Thus, similar high total sugar yields of about 85% were obtained at 180°C and 200°C for Miscanthus x giganteus cv. Illinois pretreatment followed by enzymatic hydrolysis, while sampling times were not short enough to capture high sugar yields at 220°C. Because such short times would be impractical to implement commercially, additional experiments were not run to determine if yields would improve at shorter times. Thus, pretreatment times to achieve the highest overall glucan plus xylan yields from the two stages for Miscanthus x giganteus cv. Illinois were 35 min at 180°C and 11. 4 min at 200°C, corresponding to similar pretreatment severities (logR0) [39] of 3. 9 and 4. 0, respectively. The maximum glucan plus xylan yields for hydrothermal pretreatment followed by enzymatic hydrolysis were very similar to those reported in the literature for AFEX and ethanol organosolv pretreatments of Miscanthus, as shown in Table 1. In addition, as a result of the higher carbohydrate content of Miscanthus compared to other biomass listed in Table 1, the overall mass sugar yield of 55. 7 g glucan plus xylan per 100 g of dry Miscanthus x giganteus cv. Illinois was greater than mass yields from application of hydrothermal pretreatment to other feedstocks listed in Table 2, such as 40. 8 g glucan + xylan per 100 g dry corn stover [24] and 52.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Nunez-Munoz, L. , Vargas-Hernandez, B. , Hinojosa-Moya, J. , Ruiz-Medrano, R. & Xoconostle-Cazares, B. (2021). Plant drought tolerance provided through genome editing of the trehalase gene. Plant Signal. Behav. 16, 1877005. Ogata, T. , Ishizaki, T. , Fujita, M. & Fujita, Y. (2020). /Cas9-targeted mutagenesis of OsERA1 confers enhanced responses to abscisic acid and drought stress and increased primary root growth under nonstressed conditions in rice. 15, 0243376. Orvar, B. L, Sangwan, V. , Omann, F. & Dhindsa, R. S. (2000). Early steps in cold sensing by plant cells: the role of actin cytoskeleton and membrane fluidity. Journal, 23, 785–794. Osakabe, Y. & Osakabe, K. (2015). Genome editing with engineered nucleases in plants. Plant and Cell Physiology, 56 (3), 389–400. Osakabe, Y. & Osakabe, K. (2017). to in Plants. in Elsevier: Amsterdam, The Netherlands, 149, 99–109. Osakabe, Y. , Watanabe, T. , Sugano, S. S. , Ueta, R. , Ishihara, R. , Shinozaki, K. & et al. (2016). Optimization ofCas9 genome editing to modify abiotic stress responses in plants. Sci. Rep. 6, 26685. doi: 10. 1038/srep26685. Park, J. J. , Dempewolf, E. , Zhang, W. & Wang, Z. Y. (2017). RNA-guided transcriptional activation viadCas9 mimics overexpression phenotypes in Arabidopsis. 12, e0179410. Piatek, A. , Ali, Z. , Baazim, H. , Li, L. , Abulfaraj, A. & Al-Shareef, S. (2015). RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: This means consuming whole fruits and vegetables instead of fruit and vegetable juices, selecting whole grains (e. g. , brown rice, quinoa, faro, oats, barley, wheat) instead of lower fiber options like white bread, rice, and pasta and eating more nuts, beans, and legumes. are many other reasons an individual may have GI distress. Some foods and beverages, such as alcohol, caffeine, or compounds in these products, can irritate the gut causing GI distress or increasing esophageal reflux. If the frequency of reflux is high, the condition is called gastroesophageal reflex disease (GERD) (Table 2). GI distress may be due to a particular food that is not well tolerated because of the inability to digest a specific food component (e. g. , gluten or lactose intolerance) or having an allergy to a food component (e. g. , allergy to milk protein). There can be more severe gut issues, such as irritable bowel syndrome (IBS) or Celiac disease. Any of these issues can disrupt health and derail an athlete’s ability to exercise and train optimally. Table 2 lists some of these GI issues, their definitions, diet and lifestyle approaches for management, and links to more information. Until these gut issues are identified and appropriate dietary or medical measures taken, being physically active can be difficult. Many of these issues require seeking medical help and visiting a dietitian for dietary advice to help relieve or improve symptoms. TABLE 2: GI Issues and the Dietary or for gut is the largest immune organ in the body. Thus, part of staying healthy is providing the gut with the energy and nutrients needed. Keep the gut healthy by consuming fermented foods that contain healthy bacteria (probiotics), such as yogurt, kefir or fermented soy products, and eating a diet high in unprocessed, high-fiber foods (prebiotics) (whole fruits, vegetables, grains, and legumes). These foods provide indigestible carbohydrates that help maintain the gut bacteria and produce byproducts that help keep the body healthy. now know that the gut is our largest immune organ. Thus, keeping the gut healthy will help keep us healthy and resistant to illness and disease. Diet plays a major role in maintaining a healthy gut by providing both prebiotics and probiotics.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: 6 g glucan + xylan per 100 g dry wheat straw [26]. Although pretreatment temperatures and solids loadings were different for these five feedstocks, the log of the pretreatment severities at the highest overall glucan and xylan yields were in the range from about 3. 9 to 4. 0 for Miscanthus x giganteus cv. Illinois, corn stover, and poplar. However, both corn stover and poplar studies used higher solids loadings and achieved higher xylan yields but lower glucan yields [24, 40]. This suggests that corn stover and poplar require more severe hydrothermal pretreatment to disrupt the cellulose structure enough to gain higher glucan yields in Stage 2. Wheat straw was reported to require more severe pretreatment (logR0 of 4. 15) to achieve the highest overall glucan and xylan yield, while the highest glucan yield of 91% (mainly in Stage 2) was obtained with relatively low enzyme loading of 15 FPU Celluclast plus 15 IU Novozym 188 per gram dry substrate (about 39. 7 FPU cellulase per gram glucan) [25]. Table 2 Comparison of Miscanthus and other selected biomass feedstocks Full size tableHigh throughput pretreatment and co-hydrolysis (HTPH) of system was applied to 80 Miscanthus genotypes with different characteristics to rapidly measure overall glucan and xylan yields from hydrothermal pretreatment at 180°C for 0, 17. 5, and 35 min followed by enzymatic hydrolysis of the entire pretreated slurry (180°C for 35 min is the optimal condition based on our previous batch tube experiments, data unpublished). A scatter matrix S(x) of compositions and HTPH sugar yields (mass yields, g/100 g raw Miscanthus) for the 80 Miscanthus genotypes is presented in Additional file 3: Figure S1 (selected data with R^2 > 0. 5 are shown in Figure 2) X = (x1x2 x10)’ to provide a statistical estimate of the covariance matrix of the multivariate normal distribution and allow determination of whether the variables are correlated and whether the correlation is positive or negative. The data in Figure 2 and Additional file 3: Figure S1 were normalized by the average values of 80 Miscanthus genotypes.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Plant Biotechnology, 13, 578–589. Que, Z. , Lu, Q. , Liu, T. , Li, S. , Zou, J. & Chen, G. (2020). The rice annexin gene OsAnn5 is a positive regulator of cold stress tolerance at the seedling stage. Res. Sq. ; in press. Rath, D. , Amlinger, L. , Rath, A. & Lundgren, M. (2015). -Cas immune system: biology, mechanisms and applications, Biochimie, 117, 119–128. Roca. , Lourenco-de Almeida-Engler, J. & Grossi-de-Sa, M. F. (2019). Improved drought stress tolerance in Arabidopsis bydCas9 fusion with a Transferase. Sci. Rep. , 9, 8080. Ruelland, E. , Vaultier, M. N. , Zachowski, A. & Hurry V. (2009). Cold signalling and cold acclimation in plants. Advances in Botanical Research. , 49, 35–150. . & Singh, N. (2011). Engineering cold stress tolerance in crop plants. Curr. Genom. , 12, 30. Shakesphere, S. , Sivaji, M. & Sathish raj, R. (2022). Promises and Potentiality of in Crop Improvement. Vijyan Varta, 3 (7), 80-86. Shen, C. , Que, Z. , Xia, Y. , Tang, N. , Li, D. , He, R. & Cao, M. (2017). Knock out of the annexin gene OsAnn3 viaCas9-mediated genome editing decreased cold tolerance in rice. J. Plant Biol. , 60, 539–547. Shi, J. , Gao, H. , Wang, H. ,. , Hakimi, S. M. , Mo, H. , & Habben, J. E. (2017). ARGOS 8 variants generated by -Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol. J. , 15, 207–216. Siddiqui, K. S. & Cavicchioli, R. (2006).

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Dietary steps to a healthy gut include consuming whole grains, fruits, and vegetables and beans/legumes, which are high in dietary fiber and are used by the gut bacteria for energy and nutrients. The gut bacteria also produce byproducts important to our health. The inclusion of fermented foods in the diet will help maintain the concentration of healthy bacteria in the gut. 1. . : a preliminary strategy to reduce gastrointestinal distress in athletes. Sports Exerc. 2018;50(1):116–23. doi: 10. 1249/mss. 0000000000001419. : 00005768-201801000-00015. | Text | PubMed | CrossRef 2. Prevalence of illness, poor mental health and sleep quality and low energy availability prior to the 2016 Games. Sports Med. 2018;52(1):47–53. doi: 10. 1136/bjsports-2017-098208. | Text | PubMed | CrossRef 3. . Nutrition strategies for gut health and immune function—what do we know and what are the gaps? Exchange. 2017;28(179):1–5. 4. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823–36. doi: 10. 1042/BCJ20160510. : 28512250. | PubMed | CrossRef 5. Organization. Probiotics in food. Health and nutritional properties and guidelines for evaluation. 2001. 6. Health benefits of fermented foods: microbiota and beyond. Biotechnol. 2017;44:94–102. doi: | PubMed | CrossRef 7. Dietary prebiotics: current status and new definition. . 2010;7(1):1–19. 8. Sweat W, Manore MM. Dietary fiber: simple steps for managing weight and improving health. . 2015;19(1):9–16. | Text | CrossRef 9. Institute of Medicine (IOM); Food and Nutrition Board. Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty acids, Cholesterol, Protein, and Amino Acids. Washington (D. C. ): Academies Press; 2005. Keywords:Gut Microbiota; Prebiotic; Probiotic; Dietary Fiber; © 2018 of Sports Medicine. View full 2018.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: The 10 components in the scatter matrix (4 compositional variables plus 6 sugar yields for three different pretreatment times followed by co-enzymatic hydrolysis) were assumed independent so that the regular covariance matrix would be a diagonal matrix. The diagonal in Additional file 3: Figure S1 was filled with the variables (xi) of the scatter matrix for each column, and the results and discussion focuses on the lower left part in Additional file 3: Figure S1. Additional file 3: Figure S1 included all the scatter plots with ellipse matrix (xi’) and linear fit applied at the 95% confidence level with the adjusted R-square between any of ten variables in order to reveal correlations. For example, the first column (x1) (K-lignin column) showed the scatter plots of other nine variables (xi, i = 2-9) as listed in each row in the diagonal versus K-lignin content with ellipse matrix and linear fit with the adjusted R-square to investigate the correlations. No obvious correlation was found between sugar yields from enzymatic hydrolysis of raw Miscanthus and lignin contents, but a negative correlation was observed between sugar yields and lignin contents following hydrothermal pretreatment for 17. 5 and 35 min, consistent with recently reported findings for poplar [28]. Figure 2Normalized scatter matrix of 80 Miscanthus HTPH glucan and xylan mass yields. HTPH glucan and xylan mass yields (g/100 g dw raw Miscanthus) from hydrothermal pretreatment at 180°C in 0, 17. 5 min, and 35 min. Full size imageIn the second left column (glucan content column) in Additional file 3: Figure S1, a positive correlation was found between glucan and xylan contents (the third row) in raw Miscanthus, suggesting a structural correlation between them. A negative correlation was observed between glucan contents and sugar yields for enzymatic hydrolysis without pretreatment, suggesting cellulose in raw biomass was a strong contributor to recalcitrance [15, 19, 25]. However, overall mass sugar yields (g sugar/100 g biomass) following pretreatments at 17. 5 and 35 min in the HTPH system were positively correlated to glucan content, which simply emphasized that high glucan content was one of the vital criteria for cellulosic feedstocks.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell, 6, 251– 264. Yang, W. , Chen, S. , Cheng, Y. , Zhang, N. , Ma, Y. ,Wang, W. , Tian, H. , Li, Y. , Hussain, S. , & Wang, S. (2020). Cell wall/vacuolar inhibitor of fructosidase 1 regulates ABA response and salt tolerance in Arabidopsis. Plant Signal. Behav. , 15,1744293. Yu, J. , Ge, H. , Wang, X. , Tang, R. , Wang, Y. , Zhao, F. , Lan, W. , Luan S. and Yang, L. (2017). Overexpression of pyrabactin resistance-like abscisic acid receptors enhances drought, osmotic, and cold tolerance in transgenic poplars. Sci. , 8, 1752. 3389/fpls. 2017. 01752 Yue, E. Cao, H. & Liu, B. (2020). OsmiR535, a potential genetic editing target for drought and salinity stress tolerance in Oryza sativa. Plants, 9, 1337. Yue, Y. , Zhang, M. , Zhang, J. , Duan, L. & Li, Z. (2012). SOS1 gene overexpression increased salt tolerance in transgenic tobacco by maintaining a higher K+/Na+ ratio. J. Plant Physiol. , 169, 255–261. Zargar, S. M. , Nagar, P. , Deshmukh, R. , Nazir, M. , and Rakwal, R. (2017). Aquaporins as potential drought tolerance inducing proteins: Towards instigating stress tolerance. J. Proteom. , 169, 233–238. Zeng, Y. , Wen, J. , Zhao, W. , Wang, Q. and Huang, W. (2020). Rational improvement of rice yield and cold tolerance by editing the three genes OsPIN5b, GS3, and OsMYB30 with the –Cas9 system. Front. Plant Sci. , 10, 1663.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: genomics is probably the splitting of the database by order. This might make fast. genomics less effective for selfish genetic elements that can move between distantly related bacteria. Still, the main (genus-level) database can quickly indicate which orders frequently contain the protein of interest. To ensure that presence/absence analyses give reliable results, fast. genomics includes only high-quality genomes; but this means that much of the diversity visible in metagenomes is missing from fast. genomics. For instance, of the 20,739 genera in GTDB, only about a third (6,377) are included in fast. genomics. Including low-quality metagenome-assembled genomes might allow analysts to identify more conserved gene neighborhoods. Still, the fast. genomics main database includes 1,418 genomes from uncultivated genera, of which 1,368 are metagenome-assembled genomes. And most prokaryotic proteins do have homologs in the main database: for instance, for random proteins from its database, fast. genomics finds at least one potential ortholog (at least 30% identity and 50% coverage) for 94% of queries. Fast. genomics does not support iterative searches to find distant homologs (homologs that are too distant to be found using pairwise methods such as BLAST). In this case, we recommend using the HMMer web server [34] for iterated searches against reference proteomes, or using a tool such as AnnoTree [15] for predefined families. Comparisons to other comparative genomics websites As far as we know, the other fast websites for comparative genomics of bacteria and archaea all rely on pre-computed orthology groups, such as eggNOG. Above, we assessed the accuracy of ortholog groups for finding homologs. Here, we give an example of how tools that rely on ortholog groups can fail. Consider the TonB-dependent transporter BT2172. We previously proposed, based partly on comparative genomics evidence, that this transporter functions together with another protein, BT2173, belonging to the uncharacterized family DUF4249 [35]. Fast. genomics shows that these proteins form a conserved operon, and that this subfamily of TonB-dependent transporters is almost always encoded next to a DUF4249 protein, across dozens of genera.

Output: pass


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: Correlations between xylan content and other compositions and sugar yields (the third left column (xylan content column) in Additional file 3: Figure S1) were similar to correlations found for glucan content, except that sugar yields from enzymatic hydrolysis of raw Miscanthus were less negatively correlated to xylan content, undoubtedly due to the lower recalcitrance of xylan than glucan. Correlations between ash content and other compositions and sugar yields are shown in the fourth left column (ash content column) in Additional file 3: Figure S1. Although a negative correlation was found between K-lignin content and ash content in raw Miscanthus, glucan content and xylan content were not obviously related to ash content. This indicated that the small amount of ash did not appear to affect structural carbohydrates content. Sugar yields did not show any significant correlation to ash content for pretreatment times of 0, 17. 5, and 35 min followed by enzymatic hydrolysis. Besides the correlations of the composition variables and sugar yields, glucan and xylan yields for three different pretreatment times showed interesting and most significant correlations (Figure 2). The strongest positive correlations were found between HTPH glucan and xylan yields with R^2 values of 0. 5772, 0. 7888, and 0. 7959 for the pretreatments at 0 min, 17. 5 min and 35 min, respectively (Figures 2a, 2b, and 2c). These results suggested a strong correlation of glucan and xylan yield for the HTPH system and followed the sugar yield patterns observed for application of HTPH to poplar [28]. However, the glucan or xylan yields without pretreatment did not show correlations (with R^2 less to 0. 05) to those glucan and xylan yields for the pretreatment at 17. 5 min and 35 min ( Additional file 3: Figure S1). These results suggested that sugar yields from direct enzymatic hydrolysis of raw lignocellulosic biomass without pretreatment were not suitable predictors of sugar yields from enzymatic hydrolysis of pretreated biomass. However, the glucan yields for pretreatment at 17. 5 min showed a very strong positive correlation (with R^2 of 0. 757) to glucan yields for pretreatment at 35 min (Figure 2d). The correlation (with R^2 of 0.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Zhang, A. , Liu, Y. , Wang, F. , Li, T. , Chen, Z. , Kong, D. Bi, J. , Zhang, F. , Luo, X. and Wang, J. (2019). Enhanced rice salinity tolerance viaCas9-targeted mutagenesis of the OsRR22 gene. Mol. Breed. , 39, 47. Zhang, A. , Liu, Y. , Wang, F. , Li, T. , Chen, Z. , Kong, D. , Bi, J. , Zhang, F. , Luo, X. , Wang, J. , et al. (2019). Enhanced rice salinity tolerance viaCas9-targeted mutagenesis of the OsRR22 gene. Mol. Breed. , 39, 47. Zhang, H. Zhang, J. Wei, P. Zhang, B. Gou, F. Feng, Z. Mao, Y. Yang, L. Zhang, H. Xu, N. et al. (2014). /Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol. J. 12, 797–807. Zhang, X. , and Thomashow M. F. (2004). Freezing sensitive tomato has a functional CBF cold response pathway, but a CBF regulon that differs from that of freezing tolerant Arabidopsis. Journal, 39, 905– 919. Zhao, C. Z. , Zhang, Z. J, Xie, S. J, Si, T. , Li, Y. Y. & Zhu, J. K. (2016). Mutational evidence for the critical role of CBF transcription factors in cold acclimation in Arabidopsis. Plant Physiology. , 171, 2744– 2759. Zhao, Y. , Zhang, C. , Liu,W. , Gao,W. , Liu, C. , Song, G. , Li, W. X. , Mao, L. , Chen, B. & Xu, Y. (2016). An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci. Rep. , 6, 23890. Zhu, L. , Chen, S. , Alvarez, S.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: Figures AbstractThe human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being. Citation: Dobrijevic D, Abraham A-L, Jamet A, Maguin E, van de (2016) of Bacteria from the Non-Reveals the Importance of Conjugation and a Paucity of Motility and in the Gut Environment. 11(7): e0159030. Francesco Cappello, University of : April 15, 2016; Accepted: June 24, 2016; Published: July 14, 2016Copyright: © 2016 Dobrijevic et al. This is an open access 3. 3 million human gut microbial genes has been established in 2010 [1], and more recently an extensive update of this catalogue was published, combining data from different sources and containing nearly 10 million genes [2]. Apart from metagenomics projects, data derive from sequencing efforts targeting the genomes of specific bacteria from the human gut. So far, sequences of 778 gut-associated bacterial genomes are available through the Project [3], thus giving access to an independent complementary line of investigation of the human gut microbiota.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: 5907) between xylan yields for 17. 5 min pretreatment and glucan yields for 35 min pretreatment (Figure 2f) was not as strong as that between glucan yields (Figure 2d) although positive correlations were found between xylan yields for 17. 5 min pretreatment and glucan for 35 min pretreatment (R^2 of 0. 5907, Figure 2f), and between xylan yields for 17. 5 min and for 35 min pretreatment (R^2 of 0. 5794, Figure 2g). Figures 3 and 4 show overall glucan yields (Stage 1+ Stage 2) versus original glucan content and overall xylan yields (Stage 1+ Stage 2) versus original xylan content for each Miscanthus sample to further investigate impacts of carbohydrate contents on glucan and xylan yields. The percent theoretical glucan yields based on original glucan content in raw Miscanthus (g/g original glucan) in Figure 3 ranged from 3. 1% to 26. 4% with averages of 13. 3% for no pretreatment, from 36. 8% to 71. 3% with an average of 52. 9% for 17. 5 min pretreatment, and from 48. 6% to 90. 6% with an average of 69. 3% for 35 min pretreatment. These HTPH results showed that theoretical glucan yields generally decreased as glucan content increased in raw Miscanthus. However, glucan mass yields (g/100 g dry weight Miscanthus), calculated as a percent of the total dry weight of raw Miscanthus tended to increase with glucan content of raw Miscanthus (in Additional file 3: Figure S1, glucan yields in column A7 for a 17. 5 min pretreatment and in column A9 for a 35 min pretreatment). In other words, as glucan content in raw Miscanthus increased, it became more difficult to degrade glucan into glucose through pretreatment and enzymatic hydrolysis by HTPH under the experimental conditions applied even though the quantity of released glucose generally increased due to the greater amount. This negative effect became more significant when the pretreatment time was increased from 0 to 17. 5 min and further to 35 min. The mechanism can be a combination of various factors and requires further investigation.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: June 6, 2023 Cut of the crop: High-yields of non-browning eggplant via genome editing Eggplant is cultivated globally – but its production is fraught with issues affecting the crop’s overall yield and post-harvest properties. The fruit can be less appealing when damaged or cut due to the enzymatic browning of tissues. Cultivating high-yielding yet non-browning eggplants is an area of ongoing research at the for and Biotechnology, UAE. The researchers have improved the fruit’s properties by genome editing a key enzyme, polyphenol oxidase. As a result of tweaking a single gene, eggplants produce more fruit that is also non-browning. Eggplant is a popular edible crop. Despite its vast global production, significant eggplant yield loss can occur due to attacks by disease-causing pathogens or adverse weather conditions. As well as selecting plants for enhanced stress resistance, fruit quality and nutritive value of the crop are also important characteristics for eggplant breeders. Recent technological advances are making it possible to quickly breed bountiful and desirable crops. Kottackal and colleagues at the for and Biotechnology (KCGEB) are making strides in this area. A leading institute in the Emirates, the KCGEB is under Court and affiliated with the UAE University. Here, researchers have recently developed a new genome edited eggplant variety with superior quality and high yields. Non-edited eggplant Eggplant: what’s in a name? Also known as aubergine, eggplant is a fruit crop and member of the Solanaceae family. The purple colouration of eggplant is caused by the compound anthocyanin, a powerful antioxidant that can remove harmful free radicals from the body. It’s also high in fibre, making it good for digestion. Eggplant breeding across the world aims to generate varieties that can better resist or tolerate different pests, pathogens, and environmental stresses, as well as improve post-harvest organoleptic qualities (its sensory appeal – eg, taste, texture, and smell). Location, oxidation, discolouration! One unappealing property of eggplant is its susceptibility to browning when cut or damaged, affecting its flavour and nutritional properties. These undesirable traits also reduce the fruit’s post-harvest value.

Output: corroborate


Input: Claim: A completely sterile gut is healthier than one with diverse bacteria. [SEP] Text: More than 90% of gut bacteria are members of only two phyla, Bacteroidetes and Firmicutes, the relative proportions of which exhibit a continuous gradient within the human population [4, 5]. Within the borders of these phyla the microbiota composition is highly individual-specific, showing high variability at the species and strain levels. In contrast to this taxonomic diversity however, functional profiles are far less variable across healthy individuals [1, 6, 7], confirming the existence of a well-balanced host-microbial symbiosis. The results of functional analyses of the human gut metagenome showed that the proteome of the human gut microbiota is enriched in proteins involved in carbohydrate metabolism, energy metabolism and storage, generation of short-chain fatty acids, amino acids metabolism, biosynthesis of secondary metabolites and metabolism of cofactors and vitamins [1, 4, 6–8]. In particular, the human gut microbiota provides a broad and diverse array of carbohydrate-active enzymes, many of which are not present in the human glycobiome [9]. Similar observations were made during genome analysis of some of the human gut-associated bacteria, such as Bacteroides fragilis, Bacteriodes thetaiotaomicron or Methanobrevibacter smithii [10, 11]. Additionally, many yet uncharacterized or completely novel protein families were shown to be specific to the human gut, suggesting that many unknown and uncharacterized processes are yet to be discovered in this environment [12]. The formentioned catalogue containing 3. 3 million non-redundant microbial genes from the intestinal tract of 124 individuals [1] provided an opportunity to differentiate bacterial functions necessary for a bacterium to thrive in the gut environment, and therefore present in every gut bacterial species, from those involved in the homeostasis of the whole gut ecosystem, encoded across many bacterial species. Qin et al. referred to these functions as (bacterial) "minimal gut genome" and "minimal gut metagenome", respectively [1]. The minimal gut metagenome includes functions known to be important to the host—bacterial interaction, such as the capacities to metabolize complex polysaccharides and to synthesize short-chain fatty acids, indispensable amino acids and vitamins. It also includes a considerable fraction of functions (~45%) that were present in less than 10% of earlier sequenced, mainly non-gut, bacterial genomes.

Output: contrast


Input: Claim: Bioengineered yeast can be designed to produce high yields of biofuels from sugars. [SEP] Text: A plausible explanation is inhibition of cellulases by higher concentrations of sugars released during HTPH from Miscanthus genotypes that contained higher amounts of glucan and/or xylan, especially when higher xylan yields were obtained as the pretreatment time was increased. It was reported recently that not only glucose but also xylose and particularly oligomeric xylan are strong inhibitors of cellulases [41, 42]. Another possible mechanism would be greater amounts of cellulose presenting a more structured obstacle to enzyme action. Figure 3HTPH glucan yields 80 Miscanthus vs. glucan contents in raw Miscanthus at 3 different pretreatment times. HTPH glucan yields on basis of original glucan content in raw Miscanthus of 80 Miscanthus. Full size imageFigure 4HTPH Xylan yields of 80 Miscanthus vs. glucan contents in raw Miscanthus at 3 different pretreatment times. HTPH xylan yields on basis of original glucan content in raw Miscanthus of 80 Miscanthus. Full size imageThe percent of theoretical xylan yields ranged from 3. 3% to 16. 2% with an average of 9. 3% for no pretreatment, from 45. 5% to 79. 1% with an average of 62. 6% for 17. 5 min pretreatment, and from 54. 7% to 86. 1% with an average of 72. 9% for 35 min pretreatment (Figure 4). Xylan content in raw Miscanthus did not significantly affect xylan yields calculated on basis of the original xylan content of raw Miscanthus. Xylan content had more negative effects on theoretical xylan yields for unpretreated Miscanthus (0 min) than those for 17. 5 min and 35 min pretreatments at 180°C. With hydrothermal pretreatment at 180°C for 17. 5 min and 35 min, HTPH results for 80 Miscanthus genotypes indicated that pretreatment conditions had a greater impact on xylan hydrolysis than xylan content in raw Miscanthus genotypes, in contrast to the findings for glucan yields in Figure 3. The negative impacts of lignin on glucan and xylan mass yields (g/100 g raw Miscanthus) are shown in Additional file 3: Figure S1.

Output: pass


Input: Claim: Gene editing can improve crop yields by enhancing growth traits. [SEP] Text: Instead, they are carried through to the next generation – resulting in an altered trait. Mutations give rise to variations in any species, resulting in different colours, behaviour, and survival of its progeny. Plant breeders have more recently used chemicals and irradiation techniques to induce random mutations in seeds that alter the function of specific proteins, therefore, altering traits. By altering genes in different plant varieties, this form of plant breeding has given rise to the vast selection of crops with desirable characteristics that we consume today. However, this method of plant breeding is a long process, requiring at least six generations of selectively bred plants before the final variety with desirable characteristics is produced. Moreover, the mutations can be randomly introduced throughout the plant. Precision breeding using genome editing Now, new tools have been identified over the last decade that dramatically reduce the time needed for breeding crops with superior characteristics, introducing desirable traits quickly and precisely by more accurately controlling the desired genetic mutations. Techniques and tools have been developed to alter the sequences of genes at specific locations in a plant’s genome (complete set of genetic material in its DNA). The most well-known tool, called -Cas9, uses a concept naturally occurring in bacteria. It involves molecular components that can locate target sequences in a genome and cut the DNA at specific locations. Natural repair mechanisms in the plant cells would usually repair these changes successfully, but sometimes the plant fails to, and a mutation is introduced. In their research, Kottackal and colleagues have altered the enzymatic browning in cut eggplant fruits using genome editing. Specific genes can be targeted using the method to be edited to introduce precise mutations. The introduced mutation would be identical to one that could have arisen from traditional or mutational plant breeding, except that there is only a single precise mutation, instead of several thousand random ones. Genome editing significantly shortens the time required for selective plant breeding from roughly a decade to only a few years. Remarkably, scientists have also developed methods by which no foreign DNA is left behind in the edited plant, only the desired mutation. This method of precision breeding has led to several research studies in recent years that demonstrate its efficiency in rapidly improving plant traits. -Cas9-based editing of an eggplant’s enzyme reduces enzymatic browning and results in increased and longer-lasting yields of fruits.

Output: corroborate