Crystal structure of an HD‐GYP domain cyclic‐di‐GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre

Bis‐(3′,5′) cyclic di‐guanylate (c‐di‐GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c‐di‐GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD‐GYP domains. Here, we have determined the structure of an enzymatically active HD‐GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c‐di‐GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c‐di‐GMP. This structure completes the picture of all domains involved in c‐di‐GMP metabolism and reveals that the HD‐GYP family splits into two distinct subgroups containing bi‐ and trinuclear metal centres.     

Canola cultivar performance in weed-infested field plots confirms allelopathy ranking from in vitro testing

Crop competition and allelopathy are two cultural control options for possible inclusion in cropping systems. This research aimed to identify superior allelopathic canola genotypes through a two-year field study. First year screening results of 312 diverse Brassica genotypes showed genotypes differed significantly in their ability to suppress weed infestations. Crop plant height was correlated with the competitive ability of several genotypes, while other genotypes showed good weed-suppressive ability despite being short. Thirty-six of the genotypes grown in the field had been previously assessed for their allelopathic ability to inhibit the growth of annual ryegrass (Lolium rigidum) seedlings using an in vitro technique. The highly allelopathic genotypes: Av-opal, Sardi603, Rivette and Atr-beacon performed well against annual ryegrass in the laboratory and also against other species, including Capsella bursa-pastoris, Sisymbrium orientale and Hordeum leporinum in the field. The weakly allelopathic Barossa and X-06-6-3725 genotypes performed poorly both in the laboratory studies and in the field. The following year, field testing of selected genotypes at two sowing dates further suggested that the most allelopathic genotypes in the laboratory bioassay were generally those that suppressed weed numbers and their biomass in the field. The late sowing time increased the natural weed pressure leading to a decrease in both canola grain yield and quality. Many of the highly allelopathic canola genotypes, which caused low weed populations in the field, had relatively low grain yield. This suggests that the allelopathic trait is independent of local adaptation and yields potential under weed-free conditions. Ideally, cultivars with both high allelopathy and high competitive ability would be most useful to help farmers maximise yield and control weeds. Selection for allelopathy in canola shows potential as a future non-chemical weed control option and requires further investigation.     

OsABCB14 functions in auxin transport and iron homeostasis in rice (Oryza sativa L.)

Members of the ATP Binding Cassette B/Multidrug‐Resistance/P–glyco‐protein (ABCB/MDR/PGP) subfamily were shown to function primarily in Oryza sativa (rice) auxin transport; however, none of the rice ABCB transporters have been functionally characterized. Here, we describe that a knock‐down of OsABCB14 confers decreased auxin concentrations and polar auxin transport rates, conferring insensitivity to 2,4‐dichlorophenoxyacetic acid (2,4–D) and indole‐3‐acetic acid (IAA). OsABCB14 displays enhanced specific auxin influx activity in yeast and protoplasts prepared from rice knock‐down alleles. OsABCB14 is localized at the plasma membrane, pointing to an important directionality under physiological conditions. osabcb14 mutants were surprisingly found to be insensitive to iron deficiency treatment (–Fe). Their Fe concentration is higher and upregulation of Fe deficiency‐responsive genes is lower in osabcb14 mutants than in wild‐type rice (Nipponbare, NIP). Taken together, our results strongly support the role of OsABCB14 as an auxin influx transporter involved in Fe homeostasis. The functional characterization of OsABCB14 provides insights in monocot auxin transport and its relationship to Fe nutrition.     

Agrobacterium-mediated genetic transformation and regeneration of transgenic plants using leaf midribs as explants in ramie [Boehmeria nivea (L.) Gaud]

In this study, leaf midribs, the elite explants, were used for the first time to develop an efficient regeneration and transformation protocol for ramie [Boehmeria nivea (L.) Gaud.] via Agrobacterium-mediated genetic transformation. Sensitivity of leaf midribs regeneration to kanamycin was evaluated, which showed that 40 mg l^?1 was the optimal concentration needed to create the necessary selection pressure. Factors affecting the ramie transformation efficiency were evaluated, including leaf age, Agrobacterium concentration, length of infection time for the Agrobacterium solution, acetosyringone concentration in the co-cultivation medium, and the co-cultivation period. The midrib explants from 40-day-old in vitro shoots, an Agrobacterium concentration at OD₆₀₀ of 0.6, 10-min immersion in the bacteria solution, an acetosyringone concentration of 50 mg l^?1 in the co-cultivation medium and a 3-day co-cultivation period produced the highest efficiencies of regeneration and transformation. In this study, the average transformation rate was 23.25 %. Polymerase chain reactions using GUS and NPTII gene-specific primers, Southern blot and histochemical GUS staining analyses further confirmed that the transgene was integrated into the ramie genome and expressed in the transgenic ramie. The establishment of this system of Agrobacterium-mediated genetic transformation and regeneration of transgenic plants will be used not only to introduce genes of interest into the ramie genome for the purpose of trait improvement, but also as a common means of testing gene function by enhancing or inhibiting the expression of target genes.     

Developmental regulations of Perp in mice molar morphogenesis

Angiogenesis, a complex biologic process, is regulated by a large number of angiogenic factors, including vascular endothelial growth factor (VEGF) and fibroblast growth factor-2 (FGF-2). Whether Bone morphogenetic proteins-2 (BMP-2), the osteoinductive factor, could significantly reinforce the effect of VEGF and FGF-2 on angiogenesis has not been studied in detail. To study the positive effects of multiple growth factors on angiogenesis, HUVECs were treated with BMP-2, VEGF, or FGF-2 singly and in binary and ternary combinations. This study further investigates the optimal timing of the ternary combination of BMP-2, VEGF and FGF-2 for angiogenesis in the chorioallantoic membrane (FGF-2 CAM). Results of single applications of BMP-2, VEGF, or FGF-2 suggested that HUVECs angiogenesis could be promoted in a dose-dependent manner and that the optimal concentration of BMP, VEGF and FGF-2 was 10, 50 and 1 ng/mL, respectively. These results indicated that the angiogenic activity of VEGF and FGF-2 was amplified by combining with BMP-2. The ternary combination of BMP-2, VEGF and FGF-2 exhibited a positive and synergistic effect on HUVECs angiogenesis, with the lower concentrations of each factor (1 ng/mL of BMP-2, 25 ng/mL of VEGF and 0.1 ng/mL of FGF-2) being sufficient to show synergistic promotion. When VEGF and FGF-2 were added in the initial activation stage and BMP-2 was added in the maturation stage, both HUVECs angiogenesis in vitro and CAM angiogenesis in vivo could be enhanced more effectively. These results could provide a basis for the controlled release systems capable of delivering multiple factors sequentially to promote angiogenesis in tissue engineering.     

The effect of drought stress on heterozygosity–fitness correlations in pedunculate oak (Quercus robur)

Background and Aims

The interaction between forest fragmentation and predicted climate change may pose a serious threat to tree populations. In small and spatially isolated forest fragments, increased homozygosity may directly affect individual tree fitness through the expression of deleterious alleles. Climate change-induced drought stress may exacerbate these detrimental genetic consequences of forest fragmentation, as the fitness response to low levels of individual heterozygosity is generally thought to be stronger under environmental stress than under optimal conditions.

Methods

To test this hypothesis, a greenhouse experiment was performed in which various transpiration and growth traits of 6-month-old seedlings of Quercus robur differing in multilocus heterozygosity (MLH) were recorded for 3 months under a well-watered and a drought stress treatment. Heterozygosity–fitness correlations (HFC) were examined by correlating the recorded traits of individual seedlings to their MLH and by studying their response to drought stress.

Key Results

Weak, but significant, effects of MLH on several fitness traits were obtained, which were stronger for transpiration variables than for the recorded growth traits. High atmospheric stress (measured as vapour pressure deficit) influenced the strength of the HFCs of the transpiration variables, whereas only a limited effect of the irrigation treatment on the HFCs was observed.

Conclusions

Under ongoing climate change, increased atmospheric stress in the future may strengthen the negative fitness responses of trees to low MLH. This indicates the necessity to maximize individual multilocus heterozygosity in forest tree breeding programmes.     

Genome-wide association studies identified novel loci for non-high-density lipoprotein cholesterol and its postprandial lipemic response

Non-high-density lipoprotein cholesterol(NHDL) is an independent and superior predictor of CVD risk as compared to low-density lipoprotein alone. It represents a spectrum of atherogenic lipid fractions with possibly a distinct genomic signature. We performed genome-wide association studies (GWAS) to identify loci influencing baseline NHDL and its postprandial lipemic (PPL) response. We carried out GWAS in 4,241 participants of European descent. Our discovery cohort included 928 subjects from the Genetics of Lipid-Lowering Drugs and Diet Network Study. Our replication cohorts included 3,313 subjects from the Heredity and Phenotype Intervention Heart Study and Family Heart Study. A linear mixed model using the kinship matrix was used for association tests. The best association signal was found in a tri-genic region at RHOQ-PIGF-CRIPT for baseline NHDL (lead SNP rs6544903, discovery p = 7e?7, MAF = 2 %; validation p = 6e?4 at 0.1 kb upstream neighboring SNP rs3768725, and 5e?4 at 0.7 kb downstream neighboring SNP rs6733143, MAF = 10 %). The lead and neighboring SNPs were not perfect surrogate proxies to each other (D′ = 1, r ² = 0.003) but they seemed to be partially dependent (likelihood ration test p = 0.04). Other suggestive loci (discovery p < 1e?6) included LOC100419812 and LOC100288337 for baseline NHDL, and LOC100420502 and CDH13 for NHDL PPL response that were not replicated (p > 0.01). The current and first GWAS of NHDL yielded an interesting common variant in RHOQ-PIGF-CRIPT influencing baseline NHDL levels. Another common variant in CDH13 for NHDL response to dietary high-fat intake challenge was also suggested. Further validations for both loci from large independent studies, especially interventional studies, are warranted.     

Muscle-Strengthening and Conditioning Activities and Risk of Type 2 Diabetes: A Prospective Study in Two Cohorts of US Women

Background

It is well established that aerobic physical activity can lower the risk of type 2 diabetes (T2D), but whether muscle-strengthening activities are beneficial for the prevention of T2D is unclear. This study examined the association of muscle-strengthening activities with the risk of T2D in women.

Methods and Findings

We prospectively followed up 99,316 middle-aged and older women for 8 years from the Nurses'' Health Study ([NHS] aged 53–81 years, 2000–2008) and Nurses'' Health Study II ([NHSII] aged 36–55 years, 2001–2009), who were free of diabetes, cancer, and cardiovascular diseases at baseline. Participants reported weekly time spent on resistance exercise, lower intensity muscular conditioning exercises (yoga, stretching, toning), and aerobic moderate and vigorous physical activity (MVPA) at baseline and in 2004/2005. Cox regression with adjustment for major determinants for T2D was carried out to examine the influence of these types of activities on T2D risk. During 705,869 person years of follow-up, 3,491 incident T2D cases were documented. In multivariable adjusted models including aerobic MVPA, the pooled relative risk (RR) for T2D for women performing 1–29, 30–59, 60–150, and >150 min/week of total muscle-strengthening and conditioning activities was 0.83, 0.93, 0.75, and 0.60 compared to women reporting no muscle-strengthening and conditioning activities (p<0.001 for trend). Furthermore, resistance exercise and lower intensity muscular conditioning exercises were each independently associated with lower risk of T2D in pooled analyses. Women who engaged in at least 150 min/week of aerobic MVPA and at least 60 min/week of muscle-strengthening activities had substantial risk reduction compared with inactive women (pooled RR = 0.33 [95% CI 0.29–0.38]). Limitations to the study include that muscle-strengthening and conditioning activity and other types of physical activity were assessed by a self-administered questionnaire and that the study population consisted of registered nurses with mostly European ancestry.

Conclusions

Our study suggests that engagement in muscle-strengthening and conditioning activities (resistance exercise, yoga, stretching, toning) is associated with a lower risk of T2D. Engagement in both aerobic MVPA and muscle-strengthening type activity is associated with a substantial reduction in the risk of T2D in middle-aged and older women. Please see later in the article for the Editors'' Summary