Characterization of CRISPR Mutants Targeting Genes Modulating Pectin Degradation in Ripening Tomato.

Tomato (Solanum lycopersicum) is a globally important crop with an economic value in the tens of billions of dollars, and a significant supplier of essential vitamins, minerals, and phytochemicals in the human diet. Shelf life is a key quality trait related to alterations in cuticle properties and remodeling of the fruit cell walls. Studies with transgenic tomato plants undertaken over the last 20 years have indicated that a range of pectin-degrading enzymes are involved in cell wall remodeling. These studies usually involved silencing of only a single gene and it has proved difficult to compare the effects of silencing these genes across the different experimental systems. Here we report the generation of CRISPR-based mutants in the ripening-related genes encoding the pectin-degrading enzymes pectate lyase (PL), polygalacturonase 2a (PG2a), and ß-galactanase (TBG4). Comparison of the physiochemical properties of the fruits from a range of PL, PG2a, and TBG4 CRISPR lines demonstrated that only mutations in PL resulted in firmer fruits, although mutations in PG2a and TBG4 influenced fruit color and weight. Pectin localization, distribution, and solubility in the pericarp cells of the CRISPR mutant fruits were investigated using the monoclonal antibody probes LM19 to deesterified homogalacturonan, INRA-RU1 to rhamnogalacturonan I, LM5 to ß-1,4-galactan, and LM6 to arabinan epitopes, respectively. The data indicate that PL, PG2a, and TBG4 act on separate cell wall domains and the importance of cellulose microfibril-associated pectin is reflected in its increased occurrence in the different mutant lines.

Maternal fructose and/or salt intake and reproductive outcome in the rat: effects on growth, fertility, sex ratio, and birth order.

Maternal diet can significantly skew the secondary sex ratio away from the expected value of 0.5 (proportion males), but the details of how diet may do this are unclear. Here, we altered dietary levels of salt (4% salt in the feed) and/or fructose (10% in the drinking water) of pregnant rats to model potential effects that consumption of a "Western diet" might have on maternofetal growth, development, and sex ratio. We demonstrate that excess fructose consumption before and during pregnancy lead to a marked skew in the secondary sex ratio (proportion of males, 0.60; P < 0.006). The effect was not mediated by selective developmental arrest of female embryos or influenced by fetal position in the uterine horn or sex-specific effects on sperm motility, suggesting a direct effect of glycolyzable monosaccharide on the maternal ovary and/or ovulated oocyte. Furthermore, combined excess maternal consumption of salt and fructose-sweetened beverage significantly reduced fertility, reflected as a 50% reduction in preimplantation and term litter size. In addition, we also noted birth order effects in the rat, with sequential implantation sites tending to be occupied by the same sex.

Adoption of a Short-Term (4-Week) Vegan Diet as Part of 'Veganuary' Significantly Reduces Saturated Fatty Acid (SFA), Cholesterol, B12, and Iodine Intake in Omnivorous Individuals-An Observational Study.

Global veganism campaigns like 'Veganuary' have gained popularity. We conducted an observational study to assess the impact of a 4-week vegan diet during 'Veganuary' on nutrient intake, status, knowledge, and motivations for veganism. Data were collected before and after 'Veganuary', using Food Frequency Questionnaires (FFQs) to estimate dietary intake. Micronutrient knowledge and motivation were assessed through questionnaires. A total of 154 UK adults aged 18-60 years (2019: n81; 2020: n73) participated. Groups were vegetarians and omnivores committed to a 4-week vegan diet during 'Veganuary'. Control groups were vegans and omnivores who did not transition. Short-term vegan diets significantly decreased intake of iodine, B12, cholesterol, and saturated fatty acids (SFAs) in omnivores. Micronutrient knowledge was low, and motivation for veganism varied. Short-term vegan diets reduce macro- and micronutrient intake in omnivores. Veganuary participants could benefit from nutritional guidance or supplementation. Attention is required for UK micronutrient intake and knowledge. Motivations for vegan pledges may influence diets, warranting further research.

Quantifying the impact of soil compaction on root system architecture in tomato (Solanum lycopersicum) by X-ray micro-computed tomography.

BACKGROUND AND AIMS: We sought to explore the interactions between roots and soil without disturbance and in four dimensions (i.e. 3-D plus time) using X-ray micro-computed tomography. METHODS: The roots of tomato Solanum lycopersicum 'Ailsa Craig' plants were visualized in undisturbed soil columns for 10 consecutive days to measure the effect of soil compaction on selected root traits including elongation rate. Treatments included bulk density (1.2 vs. 1.6 g cm(-3)) and soil type (loamy sand vs. clay loam). KEY RESULTS: Plants grown at the higher soil bulk density exploited smaller soil volumes (P < 0.05) and exhibited reductions in root surface area (P < 0.001), total root volume (P < 0.001) and total root length (P < 0.05), but had a greater mean root diameter (P < 0.05) than at low soil bulk density. Swelling of the root tip area was observed in compacted soil (P < 0.05) and the tortuosity of the root path was also greater (P < 0.01). Root elongation rates varied greatly during the 10-d observation period (P < 0.001), increasing to a maximum at day 2 before decreasing to a minimum at day 4. The emergence of lateral roots occurred later in plants grown in compacted soil (P < 0.01). Novel rooting characteristics (convex hull volume, centroid and maximum width), measured by image analysis, were successfully employed to discriminate treatment effects. The root systems of plants grown in compacted soil had smaller convex hull volumes (P < 0.05), a higher centre of mass (P < 0.05) and a smaller maximum width than roots grown in uncompacted soil. CONCLUSIONS: Soil compaction adversely affects root system architecture, influencing resource capture by limiting the volume of soil explored. Lateral roots formed later in plants grown in compacted soil and total root length and surface area were reduced. Root diameter was increased and swelling of the root tip occurred in compacted soil.

DNA methylation, insulin resistance, and blood pressure in offspring determined by maternal periconceptional B vitamin and methionine status.

A complex combination of adult health-related disorders can originate from developmental events that occur in utero. The periconceptional period may also be programmable. We report on the effects of restricting the supply of specific B vitamins (i.e., B(12) and folate) and methionine, within normal physiological ranges, from the periconceptional diet of mature female sheep. We hypothesized this would lead to epigenetic modifications to DNA methylation in the preovulatory oocyte and/or preimplantation embryo, with long-term health implications for offspring. DNA methylation is a key epigenetic contributor to maintenance of gene silencing that relies on a dietary supply of methyl groups. We observed no effects on pregnancy establishment or birth weight, but this modest early dietary intervention led to adult offspring that were both heavier and fatter, elicited altered immune responses to antigenic challenge, were insulin-resistant, and had elevated blood pressure-effects that were most obvious in males. The altered methylation status of 4% of 1,400 CpG islands examined by restriction landmark genome scanning in the fetal liver revealed compelling evidence of a widespread epigenetic mechanism associated with this nutritionally programmed effect. Intriguingly, more than half of the affected loci were specific to males. The data provide the first evidence that clinically relevant reductions in specific dietary inputs to the methionine/folate cycles during the periconceptional period can lead to widespread epigenetic alterations to DNA methylation in offspring, and modify adult health-related phenotypes.

Independent and combined effects of diethylhexyl phthalate and polychlorinated biphenyl 153 on sperm quality in the human and dog.

A temporal decline in human and dog sperm quality is thought to reflect a common environmental aetiology. This may reflect direct effects of seminal chemicals on sperm function and quality. Here we report the effects of diethylhexyl phthalate (DEHP) and polychlorinated biphenyl 153 (PCB153) on DNA fragmentation and motility in human and dog sperm. Human and dog semen was collected from registered donors (n = 9) and from stud dogs (n = 11) and incubated with PCB153 and DEHP, independently and combined, at 0x, 2x, 10x and 100x dog testis concentrations. A total of 16 treatments reflected a 4 × 4 factorial experimental design. Although exposure to DEHP and/or PCB153 alone increased DNA fragmentation and decreased motility, the scale of dose-related effects varied with the presence and relative concentrations of each chemical (DEHP.PCB interaction for: DNA fragmentation; human p < 0.001, dog p < 0.001; Motility; human p < 0.001, dog p < 0.05). In both human and dog sperm, progressive motility negatively correlated with DNA fragmentation regardless of chemical presence (Human: P < 0.0001, r = -0.36; dog P < 0.0001, r = -0.29). We conclude that DEHP and PCB153, at known tissue concentrations, induce similar effects on human and dog sperm supporting the contention of the dog as a sentinel species for human exposure.

Evaluation of progestogen supplementation for luteal phase support in fresh in vitro fertilization cycles.

OBJECTIVE: To evaluate the effectiveness of progestogen supplementation in improving clinical pregnancy rates in women undergoing fresh IVF cycles and to compare different routes, start times, durations, and estrogen coadministration regimen. DESIGN: Comprehensive systematic review and meta-analysis. SETTING: University. PATIENT(S): Women undergoing fresh IVF cycles who did and did not receive progestogen supplementation. INTERVENTION(S): Summary odds ratios (ORs) were calculated by binomial logistic regression. MAIN OUTCOME MEASURE(S): Clinical pregnancy rates. RESULT(S): Eighty-two articles (26,726 women) were included. Clinical pregnancy rates were increased by IM (OR = 4.57), vaginal (OR = 3.34), SC (OR = 3.36), or oral (OR = 2.57) progestogen supplementation versus no treatment. The greatest benefit was observed when progestogens were supplemented IM versus vaginally (OR = 1.37). The optimal time to commence administration was between oocyte retrieval and ET (OR = 1.31), with oocyte retrieval +1 day being most beneficial. Coadministration of estrogen had no benefit (OR = 1.33), whether progestogens were coadministered vaginally or IM. Clinical pregnancy rates were equivalent when progestogen supplementation was ceased after ≤3 weeks or continued for up to 12 weeks (OR = 1.06). CONCLUSION(S): This broad-ranging meta-analysis highlights the need to reevaluate current clinical practice. The use of progestogens in fresh IVF cycles is substantially beneficial to clinical pregnancy. Critically, the use of IM progestogens should not be dismissed, as it yielded the greatest clinical pregnancy rates. Pregnancy success was impacted by initiation of therapy, with 1 day after oocyte retrieval being optimal. There is little evidence to support coadministration of estrogen or prolonging progestogen treatment beyond 3 weeks.

Methylation Profiling RIN3 and MEF2C Identifies Epigenetic Marks Associated with Sporadic Early Onset Alzheimer's Disease.

A number of genetic loci associate with early onset Alzheimer's disease (EOAD); however, the drivers of this disease remains enigmatic. Genome wide association and in vivo modeling have shown that loss-of-function, e.g., ABCA7, reduced levels of SIRT1 and MEFF2C, or increased levels of PTK2ß confer risk or link to the pathogenies. It is known that DNA methylation can profoundly affect gene expression and can impact on the composition of the proteome; therefore, the aim of this study is to assess if genes associated with sporadic EOAD (sEOAD) are differentially methylated. Epi-profiles of DNA extracted from blood and cortex were compared using a pyrosequencing platform. We identified significant group-wide hypomethylation in AD blood when compared to controls for 7 CpGs located within the 3'UTR of RIN3 (CpG1 p = 0.019, CpG2 p = 0.018, CpG3 p = 0.012, CpG4 p = 0.009, CpG5 p = 0.002, CpG6 p = 0.018, and CpG7 p = 0.013, respectively; AD/Control n = 22/26; Male/Female n = 27/21). Observed effects were not gender specific. No group wide significant differences were found in the promoter methylation of PTK2ß, ABCA7, SIRT1, or MEF2C, genes known to associate with late onset AD. A rare and significant difference in methylation was observed for one CpG located upstream of the MEF2C promoter in one AD individual only (22% reduction in methylation, p = 2.0E-10; Control n = 26, AD n = 25, Male/Female n = 29/22). It is plausible aberrant methylation may mark sEOAD in blood and may manifest in some individuals as rare epi-variants for genes linked to sEOAD.

Environmental chemicals impact dog semen quality in vitro and may be associated with a temporal decline in sperm motility and increased cryptorchidism.

Adverse temporal trends in human semen quality and cryptorchidism in infants have been associated with exposure to environmental chemicals (ECs) during development. Here we report that a population of breeding dogs exhibit a 26 year (1988-2014) decline in sperm quality and a concurrent increased incidence of cryptorchidism in male offspring (1995-2014). A decline in the number of males born relative to the number of females was also observed. ECs, including diethylhexyl phthalate (DEHP) and polychlorinated biphenyl 153 (PCB153), were detected in adult dog testes and commercial dog foods at concentrations reported to perturb reproductive function in other species. Testicular concentrations of DEHP and PCB153 perturbed sperm viability, motility and DNA integrity in vitro but did not affect LH stimulated testosterone secretion from adult testis explants. The direct effects of chemicals on sperm may therefore contribute to the decline in canine semen quality that parallels that reported in the human.

Genetic improvement of tomato by targeted control of fruit softening.

Controlling the rate of softening to extend shelf life was a key target for researchers engineering genetically modified (GM) tomatoes in the 1990s, but only modest improvements were achieved. Hybrids grown nowadays contain 'non-ripening mutations' that slow ripening and improve shelf life, but adversely affect flavor and color. We report substantial, targeted control of tomato softening, without affecting other aspects of ripening, by silencing a gene encoding a pectate lyase.

Elevated CO2 increases biomass and tuber yield in potato even at high ozone concentrations.

• Changes in the growth and yield of field-grown potato (Solanum tuberosum cv. Bintje) induced by season-long elevated CO2 and/or ozone concentrations are reported. • Open-top chambers and unchambered field plots were used to examine crop responses to three CO2 (ambient, 550 and 680 µmol mol-1 ) and two ozone (ambient and 65 nmol mol-1 , 8 h d-1 seasonal mean) treatments applied throughout the 105 d growing season. • Elevated CO2 increased both above- and below-ground biomass at intermediate and final harvests. Tuber yield at final harvest was increased by c. 40% due to an increase in mean tuber weight rather than tuber number; tuber yield did not differ significantly between the 550 and 680 µmol mol-1 CO2 treatments. Elevated ozone had no significant effect on growth or yield except for the largest size category of tubers, despite extensive visible foliar injury. Significant CO2  × ozone interactions were detected only for senescent leaf number and green leaf ratio. • Elevated CO2 increases biomass and tuber yield in S. tuberosum cv. Bintje even at high ozone concentrations; these findings are discussed in relation to predicted future atmospheric changes.

Does elevated CO2 ameliorate the impact of O3 on chlorophyll content and photosynthesis in potato (Solanum tuberosum)?

This study examined the impact of season-long exposure to elevated carbon dioxide (CO2) and ozone (O3), individually and in combination, on leaf chlorophyll content and gas exchange characteristics in potato (Solanum tuberosum L. cv. Bintje). Plants grown in open-top chambers were exposed to three CO2 (ambient, 550 and 680 µmol mol-1) and two O3 treatments (ambient and elevated; 25 and 65 nmol mol-1, 8 h day-1 means, respectively) between crop emergence and maturity; plants were also grown in unchambered field plots. Non-destructive measurements of chlorophyll content and visible foliar injury were made for all treatments at 2-week intervals between 43 and 95 days after emergence. Gas exchange measurements were made for all except the intermediate 550 µmol mol-1 CO2 treatment. Season-long exposure to elevated O3 under ambient CO2 reduced chlorophyll content and induced extensive visible foliar damage, but had little effect on net assimilation rate or stomatal conductance. Elevated CO2 had no significant effect on chlorophyll content, but greatly reduced the damaging impact of O3 on chlorophyll content and visible foliar damage. Light-saturated assimilation rates for leaves grown under elevated CO2 were consistently lower when measured under either elevated or ambient CO2 than in equivalent leaves grown under ambient CO2. Analysis of CO2 response curves revealed that CO2-saturated assimilation rate, maximum rates of carboxylation and electron transport and respiration decreased with time. CO2-saturated assimilation rate was reduced by elevated O3 during the early stages of the season, while respiration was significantly greater under elevated CO2 as the crop approached maturity. The physiological origins of these responses and their implications for the performance of potato in a changing climate are discussed.

To what extent can zero tillage lead to a reduction in greenhouse gas emissions from temperate soils?

Soil tillage practices have a profound influence on the physical properties of soil and the greenhouse gas (GHG) balance. However there have been very few integrated studies on the emission of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) and soil biophysical and chemical characteristics under different soil management systems. We recorded a significantly higher net global warming potential under conventional tillage systems (26-31% higher than zero tillage systems). Crucially the 3-D soil pore network, imaged using X-ray Computed Tomography, modified by tillage played a significant role in the flux of CO2 and CH4. In contrast, N2O flux was determined mainly by microbial biomass carbon and soil moisture content. Our work indicates that zero tillage could play a significant role in minimising emissions of GHGs from soils and contribute to efforts to mitigate against climate change.

Excess maternal salt intake produces sex-specific hypertension in offspring: putative roles for kidney and gastrointestinal sodium handling.

Hypertension is common and contributes, via cardiovascular disease, towards a large proportion of adult deaths in the Western World. High salt intake leads to high blood pressure, even when occurring prior to birth - a mechanism purported to reside in altered kidney development and later function. Using a combination of in vitro and in vivo approaches we tested whether increased maternal salt intake influences fetal kidney development to render the adult individual more susceptible to salt retention and hypertension. We found that salt-loaded pregnant rat dams were hypernatraemic at day 20 gestation (147±5 vs. 128±5 mmoles/L). Increased extracellular salt impeded murine kidney development in vitro, but had little effect in vivo. Kidneys of the adult offspring had few structural or functional abnormalities, but male and female offspring were hypernatraemic (166±4 vs. 149±2 mmoles/L), with a marked increase in plasma corticosterone (e.g. male offspring; 11.9 [9.3-14.8] vs. 2.8 [2.0-8.3] nmol/L median [IQR]). Furthermore, adult male, but not female, offspring had higher mean arterial blood pressure (effect size, +16 [9-21] mm Hg; mean [95% C.I.]. With no clear indication that the kidneys of salt-exposed offspring retained more sodium per se, we conducted a preliminary investigation of their gastrointestinal electrolyte handling and found increased expression of proximal colon solute carrier family 9 (sodium/hydrogen exchanger), member 3 (SLC9A3) together with altered faecal characteristics and electrolyte handling, relative to control offspring. On the basis of these data we suggest that excess salt exposure, via maternal diet, at a vulnerable period of brain and gut development in the rat neonate lays the foundation for sustained increases in blood pressure later in life. Hence, our evidence further supports the argument that excess dietary salt should be avoided per se, particularly in the range of foods consumed by physiologically immature young.

Reprogramming of ovine somatic cells with Xenopus laevis oocyte extract prior to SCNT improves live birth rate.

The birth of live animals following somatic cell nuclear transfer (SCNT) has demonstrated that oocytes can reprogram the genome of differentiated cells. However, in all species the frequency of development of healthy offspring is low; for example, in sheep, approximately only 5% of blastocysts transferred develop to term, and less than 3% develop to adulthood. Such low efficiencies, coupled with the occurrence of developmental abnormalities, have been attributed to incomplete or incorrect reprogramming. Cytoplasmic extracts from both mammalian and amphibian oocytes can alter the epigenetic state of mammalian somatic nuclei and reprogram gene expression to more resemble that of pluripotent cells. Therefore, it may be possible to increase the frequency or success of normal development by pretreating somatic cells to be used as nuclear donors prior to SCNT. In the present study, permeabilized ovine fetal fibroblasts were pretreated with a cytoplasmic extract produced from germinal vesicle (GV) stage Xenopus laevis oocytes. No increase in the frequency of development to blastocyst stage or pregnancy rate was observed; however, live birth and survival rates were significantly improved. Development to term of blastocysts transferred increased from 3.1% in the control group, to 14.7% in the treated group (a 4.7-fold increase), and even though the subsequent survival of lambs produced from treated cells was reduced by 60%, the percentage of lambs surviving to adulthood of blastocysts transferred (5.9%) increased 1.9-fold compared to controls. This study is the first to report the birth of live offspring and an increase in cloning efficiency, after crossspecies pre-reprogramming using Xenopus GV stage oocyte extract.

Adult-onset obesity reveals prenatal programming of glucose-insulin sensitivity in male sheep nutrient restricted during late gestation.

BACKGROUND: Obesity invokes a range of metabolic disturbances, but the transition from a poor to excessive nutritional environment may exacerbate adult metabolic dysfunction. The current study investigated global maternal nutrient restriction during early or late gestation on glucose tolerance and insulin sensitivity in the adult offspring when lean and obese. METHODS/PRINCIPAL FINDINGS: Pregnant sheep received adequate (1.0M; CE, n = 6) or energy restricted (0.7M) diet during early (1-65 days; LEE, n = 6) or late (65-128 days; LEL, n = 7) gestation (term approximately 147 days). Subsequent offspring remained on pasture until 1.5 years when all received glucose and insulin tolerance tests (GTT & ITT) and body composition determination by dual energy x-ray absorptiometry (DXA). All animals were then exposed to an obesogenic environment for 6-7 months and all protocols repeated. Prenatal dietary treatment had no effect on birth weight or on metabolic endpoints when animals were 'lean' (1.5 years). Obesity revealed generalised metabolic 'inflexibility' and insulin resistance; characterised by blunted excursions of plasma NEFA and increased insulin(AUC) (from 133 to 341 [s.e.d. 26] ng.ml(-1).120 mins) during a GTT, respectively. For LEL vs. CE, the peak in plasma insulin when obese was greater (7.8 vs. 4.7 [s.e.d. 1.1] ng.ml(-1)) and was exacerbated by offspring sex (i.e. 9.8 vs. 4.4 [s.e.d. 1.16] ng.ml(-1); LEL male vs. CE male, respectively). Acquisition of obesity also significantly influenced the plasma lipid and protein profile to suggest, overall, greater net lipogenesis and reduced protein metabolism. CONCLUSIONS: This study indicates generalised metabolic dysfunction with adult-onset obesity which also exacerbates and 'reveals' programming of glucose-insulin sensitivity in male offspring prenatally exposed to maternal undernutrition during late gestation. Taken together, the data suggest that metabolic function appears little compromised in young prenatally 'programmed' animals so long as weight is adequately controlled. Nutritional excess in adulthood exacerbates any programmed phenotype, indicating greater vigilance over weight control is required for those individuals exposed to nutritional thrift during gestation.

Fetal exposure to a maternal low-protein diet during mid-gestation results in muscle-specific effects on fibre type composition in young rats.

This study assessed the impact of reduced dietary protein during specific periods of fetal life upon muscle fibre development in young rats. Pregnant rats were fed a control or low-protein (LP) diet at early (days 0-7 gestation, LPEarly), mid (days 8-14, LPMid), late (days 15-22, LPLate) or throughout gestation (days 0-22, LPAll). The muscle fibre number and composition in soleus and gastrocnemius muscles of the offspring were studied at 4 weeks of age. In the soleus muscle, both the total number and density of fast fibres were reduced in LPMid females (P = 0.004 for both, Diet x Sex x Fibre type interactions), while both the total number and density of glycolytic (non-oxidative) fibres were reduced in LPEarly, LPMid and LPLate (but not LPAll) offspring compared with controls (P < 0.001 for both, Diet x Fibre type interaction). In the gastrocnemius muscle, only the density of oxidative fibres was reduced in LPMid compared with control offspring (P = 0.019, Diet x Fibre type interaction), with the density of slow fibres being increased in LPAll males compared with control (P = 0.024, Diet x Sex x Fibre type interaction). There were little or no effects of maternal diet on fibre type diameters in the two muscles. In conclusion, a maternal low-protein diet mainly during mid-pregnancy reduced muscle fibre number and density in 4-week-old rats, but there were muscle-specific differences in the fibre types affected.