Genetic control of root architectural plasticity in maize

© 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology. Root phenotypes regulate soil resource acquisition; however, their genetic control and phenotypic plasticity are poorly understood. We hypothesized that the responses of root architectural phenes to water deficit (stress plasticity) and different environments (environmental plasticity) are under genetic control and that these loci are distinct. Root architectural phenes were phenotyped in the field using a large maize association panel with and without water deficit stress for three seasons in Arizona and without water deficit stress for four seasons in South Africa. All root phenes were plastic and varied in their plastic response. We identified candidate genes associated with stress and environmental plasticity and candidate genes associated with phenes in well-watered conditions in South Africa and in well-watered and water-stress conditions in Arizona. Few candidate genes for plasticity overlapped with those for phenes expressed under each condition. Our results suggest that phenotypic plasticity is highly quantitative, and plasticity loci are distinct from loci that control phene expression in stress and non-stress, which poses a challenge for breeding programs. To make these loci more accessible to the wider research community, we developed a public online resource that will allow for further experimental validation towards understanding the genetic control underlying phenotypic plasticity

Soil penetration by maize roots is negatively related to ethylene-induced thickening

Radial expansion is a classic response of roots to a mechanical impedance that has generally been assumed to aid penetration. We analysed the response of maize nodal roots to impedance to test the hypothesis that radial expansion is not related to the ability of roots to cross a compacted soil layer. Genotypes varied in their ability to cross the compacted layer, and those with a steeper approach to the compacted layer or less radial expansion in the compacted layer were more likely to cross the layer and achieve greater depth. Root radial expansion was due to cortical cell size expansion, while cortical cell file number remained constant. Genotypes and nodal root classes that exhibited radial expansion in the compacted soil layer generally also thickened in response to exogenous ethylene in hydroponic culture, that is, radial expansion in response to ethylene was correlated with the thickening response to impedance in soil. We propose that ethylene insensitive roots, that is, those that do not thicken and can overcome impedance, have a competitive advantage under mechanically impeded conditions as they can maintain their elongation rates. We suggest that prolonged exposure to ethylene could function as a stop signal for axial root growth

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties

Zwitterionic capsular polysaccharides (ZPSs) are bacterial products that modulate T cells, including inducing anti-inflammatory IL-10-secreting T regulatory cells (Tregs). However, only a few diverse bacteria are known to modulate the host immune system via ZPS. We present a genomic screen for bacteria encoding ZPS molecules. We identify diverse host-associated bacteria, including commensals and pathogens with known anti-inflammatory properties, with the capacity to produce ZPSs. Human mononuclear cells stimulated with lysates from putative ZPS-producing bacteria induce significantly greater IL-10 production and higher proportions of Tregs than lysates from non-ZPS-encoding relatives or a commensal strain of Bacteroides cellulosilyticus in which a putative ZPS biosynthetic operon was genetically disrupted. Similarly, wild-type B. cellulosilyticus DSM 14838, but not a close relative lacking a putative ZPS, attenuated experimental colitis in mice. Collectively, this screen identifies bacterial strains that may use ZPSs to interact with the host as well as those with potential probiotic properties

Circumstellar Structure around Evolved Stars in the Cygnus-X Star Formation Region

We present observations of newly discovered 24 micron circumstellar structures detected with the Multiband Imaging Photometer for Spitzer (MIPS) around three evolved stars in the Cygnus-X star forming region. One of the objects, BD+43 3710, has a bipolar nebula, possibly due to an outflow or a torus of material. A second, HBHA 4202-22, a Wolf-Rayet candidate, shows a circular shell of 24 micron emission suggestive of either a limb-brightened shell or disk seen face-on. No diffuse emission was detected around either of these two objects in the Spitzer 3.6-8 micron Infrared Array Camera (IRAC) bands. The third object is the luminous blue variable candidate G79.29+0.46. We resolved the previously known inner ring in all four IRAC bands. The 24 micron emission from the inner ring extends ~1.2 arcmin beyond the shorter wavelength emission, well beyond what can be attributed to the difference in resolutions between MIPS and IRAC. Additionally, we have discovered an outer ring of 24 micron emission, possibly due to an earlier episode of mass loss. For the two shell stars, we present the results of radiative transfer models, constraining the stellar and dust shell parameters. The shells are composed of amorphous carbon grains, plus polycyclic aromatic hydrocarbons in the case of G79.29+0.46. Both G79.29+0.46 and HBHA 4202-22 lie behind the main Cygnus-X cloud. Although G79.29+0.46 may simply be on the far side of the cloud, HBHA 4202-22 is unrelated to the Cygnus-X star formation region.Comment: Accepted by A

Assessing child belt fit, volume II: effect of restraint configuration, booster seat designs, seating procedure, and belt fit on the dynamic response of the hybrid III 10-year-old ATD in sled tests

A total of 49 dynamic sled tests were performed with the Hybrid III 10YO to examine issues relating to child belt fit. The goals of these tests were to evaluate ATD response to realistic belt geometries and belt fit, develop methods for accurate, repeatable evaluation of restraint conditions for older children, identify dependent measures that differentiate between good and poor restraint performance, and relate ATD performance to static belt fit with children. The first series of tests examined the effects of lap belt tension, belt configuration, and seating procedure on dynamic responses of the ATD. The second series of tests examined how different designs of booster seat lap belt guides and shoulder belt guides affect performance. In addition, the ATD’s response to different shoulder belt and lap belt geometries was evaluated. With regard to test procedures, use of a lap/shoulder belt with a sliding latchplate produced similar results to using a lap/shoulder belt with fixed anchorages. Use of a production retractor reduced shoulder belt load, as well as head, neck, and chest measures. Reducing lap belt tension to a more realistic 2 lb (rather than 15 lb) did not have a pronounced effect on ATD kinematics with two different booster seats. The UMTRI seating procedure, which produces ATD postures closer to those measured in real children, also prevents the lap belt from being trapped in the gap between the pelvis and the thigh. Use of the UMTRI seating procedure produces more reclined initial postures and more pronounced chin-to-chest contact. A well-designed booster lap belt guide can maintain good belt position dynamically, even with poor lap belt geometry. Shoulder belt guide designs affect ATD kinematics. However, preventing the shoulder belt from coming out of the shoulder belt guide does not necessarily produce better restraint performance, because the belt can still come off of the ATD shoulder during the event, and stiffening booster seats does not necessarily produce better routing of the shoulder belt dynamically. Shoulder belt scores less than 70 mm produce good torso kinematics with the 10YO ATD, but use of HIC as an injury criterion tends to discourage booster seat designs that produce good belt fit on the 10YO ATD. Lap belt angle affects torso kinematics, with shallower lap belt angles leading to submarining and more vertical lap belt angles leading to rollout. Wider spacing of lap belt anchorages leads to submarining, while narrowing spacing leads to rollout. Both upper and lower belt anchorage locations have a strong effect on ATD kinematics. Although good booster designs can mitigate the consequences of poor vehicle lap belt geometry, boosters cannot always overcome poor shoulder belt geometry to keep the belt on the ATD shoulder dynamically, even when they are able to create good static belt fit. This finding suggests that more attention should be focused on the effects of the wide variability in vehicle upper anchorage locations on belt restraint performance for children. Also, because HIC scores are decreased when the torso belt fit is degraded, use of HIC as an injury criterion for booster testing may lead to worse rather than better booster designs.National Highway Traffic Safety Administrationhttp://deepblue.lib.umich.edu/bitstream/2027.42/64460/1/102443.pd

Enrichment of CpG island shore region hypermethylation in epigenetic breast field cancerization

While changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumour DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumour. Matched tumour, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select epithelial cells from normal tissue, and neoplastic cells from tumour for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array. We identified substantially more CpG loci that were differentially methylated between contralateral-normal and tumour (63,271 CpG loci q \u3c 0.01), than between ipsilateral-normal and tumour (38,346 CpG loci q \u3c 0.01). We identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p \u3c 0.01). In this comparison, hypomethylated loci were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3 and hypermethylated loci were significantly enriched for CpG island shore regions. In addition, progression of shore hypermethylation was observed in tumours compared to matched ipsilateral normal tissue, and these alterations tracked to several well-established tumour suppressor genes. Our results indicate an epigenetic field effect in surrounding histologically normal tissue. This work offers an opportunity to focus investigations of early DNA methylation alterations in breast carcinogenesis and potentially develop epigenetic biomarkers of disease risk

Change in Physical Activity after a Diabetes Diagnosis: Opportunity for Intervention

INTRODUCTION: Moderate intensity physical activity is recommended for individuals with diabetes to control glucose and prevent diabetes-related complications. The extent to which a diabetes diagnosis motivates patients to increase physical activity is unclear. This study used data from the Women\u27s Health Initiative Observational Study (baseline data collected from 1993-1998) to examine change in physical activity and sedentary behavior in women who reported a diabetes diagnosis compared to women who did not report diabetes over 7 years of follow-up (up to 2005). METHODS: Participants (n=84,300) were post-menopausal women who did not report diabetes at baseline [mean age=63.49; standard deviation (SD)=7.34; mean BMI=26.98 kg/m; SD=5.67]. Linear mixed model analyses were conducted adjusting for study year, age, race/ethnicity, BMI, education, family history of diabetes, physical functioning, pain, energy/fatigue, social functioning, depression, number of chronic diseases and vigorous exercise at age 18. Analyses were completed in August 2012. RESULTS: Participants who reported a diabetes diagnosis during follow-up were more likely to report increasing their total physical activity (p=0.002), walking (p CONCLUSION: A diabetes diagnosis may prompt patients to increase physical activity. Healthcare professionals should consider how best to capitalize on this opportunity to encourage increased physical activity and maintenance

Fluid balance and renal replacement therapy initiation strategy : a secondary analysis of the STARRT-AKI trial

Background: Among critically ill patients with acute kidney injury (AKI), earlier initiation of renal replacement therapy (RRT) may mitigate fluid accumulation and confer better outcomes among individuals with greater fluid overload at randomization.Methods: We conducted a pre-planned post hoc analysis of the STandard versus Accelerated initiation of Renal Replacement Therapy in Acute Kidney Injury (STARRT-AKI) trial. We evaluated the effect of accelerated RRT initiation on cumulative fluid balance over the course of 14 days following randomization using mixed models after censoring for death and ICU discharge. We assessed the modifying effect of baseline fluid balance on the impact of RRT initiation strategy on key clinical outcomes. Patients were categorized in quartiles of baseline fluid balance, and the effect of accelerated versus standard RRT initiation on clinical outcomes was assessed in each quartile using risk ratios (95% CI) for categorical variables and mean differences (95% CI) for continuous variables.Results: Among 2927 patients in the modified intention-to-treat analysis, 2738 had available data on baseline fluid balance and 2716 (92.8%) had at least one day of fluid balance data following randomization. Over the subsequent 14 days, participants allocated to the accelerated strategy had a lower cumulative fluid balance compared to those in the standard strategy (4509 (- 728 to 11,698) versus 5646 (0 to 13,151) mL, p = 0.03). Accelerated RRT initiation did not confer greater 90-day survival in any of the baseline fluid balance quartiles (quartile 1: RR 1.11 (95% CI 0.92 to 1.34), quartile 2: RR 1.03 (0.87 to 1.21); quartile 3: RR 1.08 (95% CI 0.91 to 1.27) and quartile 4: RR 0.87 (95% CI 0.73 to 1.03), p value for trend 0.08).Conclusions: Earlier RRT initiation in critically ill patients with AKI conferred a modest attenuation of cumulative fluid balance. Nonetheless, among patients with greater fluid accumulation at randomization, accelerated RRT initiation did not have an impact on all-cause mortality.Peer reviewe

Generating a taxonomy for genetic conditions relevant to reproductive planning

As genome or exome sequencing (hereafter genome-scale sequencing) becomes more integrated into standard care, carrier testing is an important possible application. Carrier testing using genome-scale sequencing can identify a large number of conditions, but choosing which conditions/genes to evaluate as well as which results to disclose can be complicated. Carrier testing generally occurs in the context of reproductive decision-making and involves patient values in a way that other types of genetic testing may not. The Kaiser Permanente Clinical Sequencing Exploratory Research program is conducting a randomized clinical trial of preconception carrier testing that allows participants to select their preferences for results from among broad descriptive categories rather than selecting individual conditions. This paper describes 1) the criteria developed by the research team, the return of results committee (RORC), and stakeholders for defining the categories; 2) the process of refining the categories based on input from patient focus groups and validation through a patient survey; and, 3) how the RORC then assigned specific gene-condition pairs to taxonomy categories being piloted in the trial. The development of four categories (serious, moderate/mild, unpredictable, late onset) for sharing results allows patients to select results based on their values without separately deciding their interest in knowing their carrier status for hundreds of conditions. A fifth category, lifespan limiting, was always shared. The lessons learned may be applicable in other results disclosure situations, such as incidental findings

Psychometric properties of the 52-, 25-, and 10-item English and Spanish versions of the Social Problem-Solving Inventory-Revised

ObjectiveThe Social Problem-Solving Inventory-Revised (SPSI-R) is a widely used instrument to assess problem-solving ability. This study examined the factor structure of the 52-, 25-, and 10-item versions of the SPSI-R and assessed factorial invariance across English- and Spanish-speaking participants. In addition, the internal consistency, test-retest reliability and sensitivity to detect change in problem-solving skills over time were assessed across the three different versions of the SPSI-R.MethodsData from three randomized controlled trials, in which caregivers of children with cancer (N = 1,069) were assigned to either a problem-solving skills intervention (N = 728) or a control condition (N = 341), were combined. The SPSI-R was administered at baseline (T1) and immediately post intervention (T2). Reliability and multigroup analyses were performed with confirmatory factor analysis (CFA). Sensitivity to change analyses were performed using repeated measures ANOVA.ResultsConfirmatory factor analysis at T1 showed good fit statistics and internal consistency for the 52- and the 25-item versions, but not for the 10-item version. Factorial invariance was demonstrated across time (T1-T2) and language (Spanish-English) for both the 52- and 25-item versions. Adequate sensitivity to change over time was shown.ConclusionThe 52- and 25-item versions of the SPSI-R appear reliable and valid for assessment of problem-solving skills in English- and Spanish-speaking caregivers of children with newly diagnosed cancer. The 25-item SPSI-R can be used as a short version measuring problem-solving ability; the 10-item version cannot be considered a reliable measure for this population