Nutrient levels within leaves,stems, and roots of the xeric species Reaumuria soongorica in relation to geographical,climatic, and soil conditions

Besides water relations, nutrient allocation, and stoichiometric traits are fundamental feature of shrubs. Knowledge concerning the nutrient stoichiometry of xerophytes is essential to predicting the biogeochemical cycling in desert ecosystems as well as to understanding the homoeostasis and variability of nutrient traits in desert plants. Here, we focused on the temperate desert species Reaumuria soongorica and collected samples from plant organs and soil over 28 different locations that covered a wide distributional gradient of this species. Carbon (C), nitrogen (N), and phosphorus (P) concentrations and their stoichiometry were determined and subsequently compared with geographic, climatic, and edaphic factors. The mean leaf C, N, and P concentrations and C/N, C/P, and N/P ratios were 371.6 mg g⁻¹, 10.6 mg g⁻¹, 0.73 mg g⁻¹, and 59.7, 837.9, 15.7, respectively. Stem and root C concentrations were higher than leaf C, while leaf N was higher than stem and root N. Phosphorus concentration and N/P did not differ among plant organs. Significant differences were found between root C/N and leaf C/N as well as between root C/P and leaf C/P. Leaf nutrient traits respond to geographic and climatic factors, while nutrient concentrations of stems and roots are mostly affected by soil P and pH. We show that stoichiometric patterns in different plant organs had different responses to environmental variables. Studies of species-specific nutrient stoichiometry can help clarify plant–environment relationships and nutrient cycling patterns in desert ecosystems.     

Dosage and duration effects of nitrogen additions on ectomycorrhizal sporocarp production and functioning: an example from two N‐limited boreal forests

1. Although it is well known that nitrogen (N) additions strongly affect ectomycorrhizal (EM) fungal community composition, less is known about how different N application rates and duration of N additions affect the functional role EM fungi play in the forest N cycle.
2. We measured EM sporocarp abundance and species richness as well as determined the δ¹⁵N in EM sporocarps and tree foliage in two Pinus sylvestris forests characterized by short- and long-term N addition histories and multiple N addition treatments. After 20 and 39 years of N additions, two of the long-term N addition treatments were terminated, thereby providing a unique opportunity to examine the temporal recovery of EM sporocarps after cessation of high N loading.
3. In general, increasing N availability significantly reduced EM sporocarp production, species richness, and the amount of N retained in EM sporocarps. However, these general responses were strongly dependent on the application rate and duration of N additions. The annual addition of 20 kg·N·ha⁻¹ for the past 6 years resulted in a slight increase in the production and retention of N in EM sporocarps, whereas the addition of 100 kg·N·ha⁻¹·yr⁻¹ during the same period nearly eliminated EM sporocarps. In contrast, long-term additions of N at rates of ca. 35 or 70 kg·N·ha⁻¹·yr⁻¹ for the past 40 years did not eliminate tree carbon allocation to EM sporocarps, although there was a decrease in the abundance and a shift in the dominant EM sporocarp taxa. Despite no immediate recovery, EM sporocarp abundance and species richness approached those of the control 20 years after terminating N additions in the most heavily fertilized treatment, suggesting a recovery of carbon allocation to EM sporocarps after cessation of high N loading.
4. Our results provide evidence for a tight coupling between tree carbon allocation to and N retention in EM sporocarps and moreover highlight the potential use of δ¹⁵N in EM sporocarps as a relative index of EM fungal sink strength for N. However, nitrogen additions at high dosage rates or over long time periods appear to disrupt this feedback, which could have important ramifications on carbon and nitrogen dynamics in these forested ecosystems.

     

Evidence for more than one Parkinson's disease-associated variant within the HLA region

Parkinson''s disease (PD) was recently found to be associated with HLA in a genome-wide association study (GWAS). Follow-up GWAS''s replicated the PD-HLA association but their top hits differ. Do the different hits tag the same locus or is there more than one PD-associated variant within HLA? We show that the top GWAS hits are not correlated with each other (0.00≤r²≤0.15). Using our GWAS (2000 cases, 1986 controls) we conducted step-wise conditional analysis on 107 SNPs with P<10⁻³ for PD-association; 103 dropped-out, four remained significant. Each SNP, when conditioned on the other three, yielded P_SNP1 = 5×10⁻⁴, P_SNP2 = 5×10⁻⁴, P_SNP3 = 4×10⁻³ and P_SNP4 = 0.025. The four SNPs were not correlated (0.01≤r²≤0.20). Haplotype analysis (excluding rare SNP2) revealed increasing PD risk with increasing risk alleles from OR = 1.27, P = 5×10⁻³ for one risk allele to OR = 1.65, P = 4×10⁻⁸ for three. Using additional 843 cases and 856 controls we replicated the independent effects of SNP1 (P_{conditioned-on-SNP4} = 0.04) and SNP4 (P_{conditioned-on-SNP1} = 0.04); SNP2 and SNP3 could not be replicated. In pooled GWAS and replication, SNP1 had OR_{conditioned-on-SNP4} = 1.23, P_{conditioned-on-SNP4} = 6×10⁻⁷; SNP4 had OR_{conditioned-on-SNP1} = 1.18, P_{conditioned-on-SNP1} = 3×10⁻³; and the haplotype with both risk alleles had OR = 1.48, P = 2×10⁻¹². Genotypic OR increased with the number of risk alleles an individual possessed up to OR = 1.94, P = 2×10⁻¹¹ for individuals who were homozygous for the risk allele at both SNP1 and SNP4. SNP1 is a variant in HLA-DRA and is associated with HLA-DRA, DRB5 and DQA2 gene expression. SNP4 is correlated (r² = 0.95) with variants that are associated with HLA-DQA2 expression, and with the top HLA SNP from the IPDGC GWAS (r² = 0.60). Our findings suggest more than one PD-HLA association; either different alleles of the same gene, or separate loci.     

A comprehensive evaluation of potential lung function associated genes in the SpiroMeta general population sample

Rationale

Lung function measures are heritable traits that predict population morbidity and mortality and are essential for the diagnosis of chronic obstructive pulmonary disease (COPD). Variations in many genes have been reported to affect these traits, but attempts at replication have provided conflicting results. Recently, we undertook a meta-analysis of Genome Wide Association Study (GWAS) results for lung function measures in 20,288 individuals from the general population (the SpiroMeta consortium).

Objectives

To comprehensively analyse previously reported genetic associations with lung function measures, and to investigate whether single nucleotide polymorphisms (SNPs) in these genomic regions are associated with lung function in a large population sample.

Methods

We analysed association for SNPs tagging 130 genes and 48 intergenic regions (+/−10 kb), after conducting a systematic review of the literature in the PubMed database for genetic association studies reporting lung function associations.

Results

The analysis included 16,936 genotyped and imputed SNPs. No loci showed overall significant association for FEV₁ or FEV₁/FVC traits using a carefully defined significance threshold of 1.3×10⁻⁵. The most significant loci associated with FEV₁ include SNPs tagging MACROD2 (P = 6.81×10⁻⁵), CNTN5 (P = 4.37×10⁻⁴), and TRPV4 (P = 1.58×10⁻³). Among ever-smokers, SERPINA1 showed the most significant association with FEV₁ (P = 8.41×10⁻⁵), followed by PDE4D (P = 1.22×10⁻⁴). The strongest association with FEV₁/FVC ratio was observed with ABCC1 (P = 4.38×10⁻⁴), and ESR1 (P = 5.42×10⁻⁴) among ever-smokers.

Conclusions

Polymorphisms spanning previously associated lung function genes did not show strong evidence for association with lung function measures in the SpiroMeta consortium population. Common SERPINA1 polymorphisms may affect FEV₁ among smokers in the general population.     

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.     

Somatic embryogenesis and in vitro plant regeneration of Bacopa monnieri (Linn.) Wettst., a potential medicinal water hyssop plant

Bacopa monnieri (Linn.) Wettst. commonly known as waterhyssop, Brahmi plant, traditionally used for memory enhancement, nerve tonic, epilepsy, central nervous system (CNS), antidepressant, anxiety, blood pressure and antioxidant activities. Due to pharmaceutical demands its lost natural habitat. At this juncture we describe a resourceful protocol for micropropagation of water hyssop plant. Surface sterilized leaf and nodal explants were inoculated on basal MS semi-solid medium added with PGRs; auxins, cytokinins. Highest calli formation from leaf explants was obtained on NAA (2.5 mg⁻¹) and showed (94.22%) accompanied via 2,4-D showed (2.5 mg⁻¹; 82.43%), maximum calli formation in nodal explants was obtained on 2,4-D showed (2.5 mg⁻¹; 71.14%) followed by NAA (2.5 mg⁻¹) showed (62.15%), in internodes explants uppermost calli formation was obtained from 2,4-D showed (2.5 mg⁻¹; 65.21%) followed by NAA (2.5 mg⁻¹) showed (52.14%). The maximum somatic embryogenic callus, calli induction and formation (84%) was observed on 2,4-D + KIN (2.0 + 1.5 mg⁻¹) amended solid medium. Uppermost shoot formation was observed in combination of IAA + BAP (1.0 + 1.0 mg⁻¹) showed (78.54%) shoot formation followed by IBA (2.0 mg⁻¹) alone showed (75.37%). The maximum shoot elongation was noticed from NAA + BAP (3.0 + 3.0 mg⁻¹) with 21.21 cm followed by NAA (2.0 mg⁻¹) showed (15.22 cm) although, chief root formation was obtained from IBA (2.0 mg⁻¹) with 83.75% root formation along higher number of roots (47.43%) per shoot. Followed by IAA (2.0 mg⁻¹) showed root induction (73.43%) and no of roots (38.54%) per shoot. In hardening under pot condition plants survivability (100%) was observed under glass house conditions, the present in vitro PTC techniques is extremely significant to gratifying its natural conservation.     

Synergistic effect of Pseudomonas alkylphenolica PF9 and Sinorhizobium meliloti Rm41 on Moroccan alfalfa population grown under limited phosphorus availability

This study looked at the synergistic effect of Pseudomonas alkylphenolica PF9 and Sinorhizobium meliloti Rm41 on the Moroccan alfalfa population (Oued Lmaleh) grown under symbiotic nitrogen fixation and limited phosphorus (P) availability. The experiment was conducted in a growth chamber and after two weeks of sowing, the young seedlings were inoculated with Sinorhizobium meliloti Rm41 alone or combined with a suspension of Pseudomonas alkylphenolica PF9. Then, the seedlings were submitted to limited available P (insoluble P using Ca₃HPO₄) versus a soluble P form (KH₂PO₄) at a final concentration of 250 μmol P·plant⁻¹·week⁻¹. After two months of P stress, the experiment was evaluated through some agro-physiological and biochemical parameters. The results indicated that the inoculation of alfalfa plants with Sinorhizobium strain alone or combined with Pseudomonas strain significantly (p < 0.001) improved the plant growth, the physiological and the biochemical traits focused in comparison to the uninoculated and P-stressed plants. For most sets of parameters, the improvement was more obvious in plants co-inoculated with both strains than in those inoculated with Sinorhizobium meliloti Rm41 alone. In fact, under limited P-availability, the co-inoculation with two strains significantly (p < 0.01) enhanced the growth of alfalfa plants evaluated by fresh and dry biomasses, plant height and leaf area. The results indicated also that the enhancement noted in plant growth was positively correlated with the shoot and root P contents. Furthermore, the incensement in plant P contents in response to bacterial inoculation improved cell membrane stability, reflected by low malonyldialdehyde (MDA) and electrolyte leakage (EL) contents, and photosynthetic-related parameters such as chlorophyll contents, the maximum quantum yield of PS II (Fv/Fm) and stomatal conductance (g_s). Our findings suggest that Pseudomonas alkylphenolica PF9 can act synergistically with Sinorhizobium meliloti Rm41 in promoting alfalfa growth under low-P availability.     

The influence of phylogeny and life history on telomere lengths and telomere rate of change among bird species: A meta‐analysis

Longevity is highly variable among animal species and has coevolved with other life‐history traits, such as body size and rates of reproduction. Telomeres, through their erosion over time, are one of the cell mechanisms that produce senescence at the cell level and might even have an influence on the rate of aging in whole organisms. However, uneroded telomeres are also risk factors of cell immortalization. The associations of telomere lengths, their rate of change, and life‐history traits independent of body size are largely underexplored for birds. To test associations of life‐history traits and telomere dynamics, we conducted a phylogenetic meta‐analysis using studies of 53 species of birds. We restricted analyses to studies that applied the telomere restriction fragment length (TRF) method, and examined relationships between mean telomere length at the chick (Chick TL) and adult (Adult TL) stages, the mean rate of change in telomere length during life (TROC), and life‐history traits. We examined 3 principal components of 12 life‐history variables that represented: body size (PC1), the slow–fast continuum of pace of life (PC2), and postfledging parental care (PC3). Phylogeny had at best a small‐to‐medium influence on Adult and Chick TL (r ² = .190 and .138, respectively), but a substantial influence on TROC (r ² = .688). Phylogeny strongly influenced life histories: PC1 (r ² = .828), PC2 (.838), and PC3 (.613). Adult TL and Chick TL were poorly associated with the life‐history variables. TROC, however, was negatively and moderate‐to‐strongly associated with PC2 (unadjusted r = −.340; with phylogenetic correction, r = −.490). Independent of body size, long‐lived species with smaller clutches, and slower embryonic rate of growth may exhibit less change in telomere length over their lifetimes. We suggest that telomere lengths may have diverged, even among closely avian‐related species, yet telomere dynamics are strongly linked to the pace of life.     

Role of nitrogen and magnesium for growth,yield and nutritional quality of radish

Nitrogen (N) affects all levels of plant function from metabolism to resource allocation, growth, and development and Magnesium (Mg) is a macronutrient that is necessary to both plant growth and health. Radish (Raphanus sativus L.) occupies an important position in the production and consumption of vegetables globally, but there are still many problems and challenges in its nutrient management. A pot trial was conducted to investigate the effects of nitrogen and magnesium fertilizers on radish during the year 2018–2019. Nitrogen and magnesium was applied at three rates (0, 0.200, and 0.300 g N kg⁻¹ soil) and (0, 0.050, and 0.100 g Mg kg⁻¹ soil) respectively. The experiment was laid out in a completely randomized design (CRD) and each treatment was replicated three times. Growth, yield and quality indicators of radish (plant height, root length, shoot length, plant weight, total soluble sugar, ascorbic acid, total soluble protein, crude fiber, etc.) were studied. The results indicated that different rates of nitrogen and magnesium fertilizer not only influence the growth dynamics and yields but also enhances radish quality. The results revealed that the growth, yield and nutrient contents of radish were increased at a range of 0.00 g N. kg⁻¹ soil to 0.300 g N. kg⁻¹ soil and 0.00 g Mg. kg⁻¹ soil to 0.050 g Mg. kg⁻¹ soil and then decreased gradually at a level of 0.100 g Mg. kg⁻¹ soil. In contrast, the crude fiber contents in radish decreased significantly with increasing nitrogen and magnesium level but increased significantly at Mg₂ level (0.050 g Mg. kg⁻¹ soil). The current study produced helpful results for increasing radish quality, decreasing production costs, and diminishing underground water contamination.     

Bacterial biosynthesis of 1-aminocyclopropane-1-caboxylate (ACC) deaminase,a useful trait to elongation and endophytic colonization of the roots of rice under constant flooded conditions

This study was conducted to investigate the role of 1-aminocyclopropane-1-carboxylate (ACC) deaminase in Pseudomonas fluorescens strain REN₁ and its ability to reduce ethylene levels produced during stress, endophytically colonize and promote the elongation of the roots of rice seedlings under gnotobiotic conditions. We isolated 80 bacteria from inside roots of rice plants grown in the farmers’ fields in Guilan, Iran. All of the isolates were characterized for plant growth promoting (PGP) traits. In addition, the colonization assay of these isolates on rice seedlings was carried out to screen for competent endophytes. The best bacterial isolate, based on ACC deaminase production, was identified and used for further study. 16S rDNA sequence analysis revealed that the endophyte was closely related to Pseudomonas fluorescens. The results of this study showed ACC deaminase containing P. fluorescens REN1 increased in vitro root elongation and endophytically colonized the root of rice seedlings significantly, as compared to control under constant flooded conditions. The trait of low amount of indole-3-acetic acid (IAA) production (<15 μg mL⁻¹) and the high production of ACC deaminase by bacteria may be main factors in colonizing rice seedling roots compared to other PGP traits (siderophore production and phosphate solubilization) in this study. Endophytic IAA and ACC deaminase-producing bacteria may be preferential selections by rice seedlings. Therefore, it may be suggested that the utilization of ACC as a nutrient gives the isolates advantages in more endophytic colonization and increase of root length of rice seedlings.     

Isolation and Characterization of Antidermatophytic Bioactive Molecules from Piper longum L. Leaves

Piper longum L. (Piperaceae) commonly known as “long pepper” is a well known medicinal plant in ayurveda. Different parts of this plant, such as root, seed, fruit, whole plant etc. are used traditionally in various ailments. Here we have investigated the antidermatophytic activity of sequentially extracted petroleum ether, chloroform, methanol and water extracts from P. longum leaf against Trichophytonmentagrophytes, T. rubrum, T. tonsurans, Microsporum fulvum and M. gypseum. Better activity of chloroform and methanol extracts was observed. The chloroform extract was selected for further study and the MIC value was recorded as 5.0 mg ml⁻¹ against the test organisms. In the chloroform extract, tannins and phenolic compounds were detected. Further activity-guided fractionation of chloroform extract by silica gel column chromatography yielded nine major fractions. Among these, fraction-1, 4, 5 and 7 showed higher antidermatophytic activity. Fraction-4 on further purification by repeated column chromatography yielded a potential antidermatophytic fraction showing MIC value of 0.625 mg ml⁻¹ against T. mentagrophytes and T. rubrum as determined by broth microdilution method. The major compounds were identified as 1,2-benzenedicarboxylic acid, bis(2-ethylhexyl) ester (C₂₄H₃₈O₄] (41.45 %), 2,2-dimethoxybutane (C₆H₁₄O₂] (13.6 %) and β-myrcene (C₁₀H₁₆) (6.75 %) based on GC–MS data.     

In vitro propagation of female Ephedra foliata Boiss. & Kotschy ex Boiss.: an endemic and threatened Gymnosperm of the Thar Desert

Ephedra foliata Boiss. & Kotschy ex Boiss., (family – Ephedraceae), is an ecologically and economically important threatened Gymnosperm of the Indian Thar Desert. A method for micropropagation of E. foliata using nodal explant of mature female plant has been developed. Maximum bud-break (90 %) of the explant was obtained on MS medium supplemented with 1.5 mg l⁻¹ of benzyl adenine (BA) + additives. Explant produces 5.3 ± 0.40 shoots from single node with 3.25 ± 0.29 cm length. The multiplication of shoots in culture was affected by salt composition of media, types and concentrations of plant growth regulators (PGR’s) and their interactions, time of transfer of the cultures. Maximum number of shoots (26.3 ± 0.82 per culture vessel) were regenerated on MS medium modified by reducing the concentration of nitrates to half supplemented with 200 mg l⁻¹ ammonium sulphate {(NH₄) ₂SO₄} (MMS3) + BA (0.25 mg l⁻¹), Kinetin (Kin; 0.25 mg l⁻¹), Indole-3-acetic acid (IAA; 0.1 mg l⁻¹) and additives. The in vitro produced shoots rooted under ex vitro on soilrite moistened with one-fourth strength of MS macro salts in screw cap bottles by treating the shoot base (s) with 500 mg l⁻¹ of Indole-3-butyric acid (IBA) for 5 min. The micropropagated plants were hardened in the green house. The described protocol can be applicable for (i) large scale plant production (ii) establishment of plants in natural habitat and (iii) germplasm conservation of this endemic Gymnosperm of arid regions.     

Novel links among peroxiredoxins,endothelial dysfunction,and severity of atherosclerosis in type 2 diabetic patients with peripheral atherosclerotic disease

Peroxiredoxins, a group of antioxidant protein enzymes (PRDX1 to 6), are reported as antiatherogenic factors in animals; however, human studies are lacking. The present work aims to provide baseline data regarding the phenotype of PRDX1, 2, 4, and 6 in diabetic patients with peripheral atherosclerosis disease (PAD) and their relation to endothelial dysfunction (ED) and disease severity. Plasma levels of PRDX1, 2, 4, and 6 and markers of endothelial dysfunction (ICAM-1 and VCAM-1) were measured using ELISA in 55 type 2 diabetic patients having PAD and 25 healthy subjects. Ankle–brachial index (ABI), body mass index (BMI), triglycerides (TG), total cholesterol, HbA1c, and insulin resistance (HOMA IR) were measured. PRDX1, 2, 4, and 6 levels were significantly higher in patients compared to controls (PRDX1 21.9 ± 5.71 vs 16.8 ± 3.9 ng/ml, P < 0.001, PRDX2 36.5 ± 14.83 vs 20.4 ± 8.61 ng/ml, P < 0.001, PRDX4 3,840 ± 1,440 vs 2,696 ± 1,972 pg/ml, P < 0.005, PRDX6 311 ± 110 vs 287.9 ± 114 pg/ml, P < 0.05). PRDX1 and PRDX4 correlated negatively with ABI (r = −0.273, P < 0.05 and r = −0.28, P < 0.05, respectively), while PRDX1 and PRDX2 correlated positively with HOMA/IR and TG (r = 0.276, P < 0.01 and r = 0.295, P < 0.01, respectively). ICAM-1 was associated with PRDX2 and log PRDX6 (r = 0.345, P = 0.0037 and r = 0.344, P = 0.0038). Our results provide strong links among PRDXs, ED, and severity of PAD in diabetic patients which warrants further evaluation to clarify whether high circulating levels of PRDXs are a consequence of chronic atherosclerotic disease or a predisposing factor for later cardiovascular events.     

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals

Circulating levels of adiponectin, a hormone produced predominantly by adipocytes, are highly heritable and are inversely associated with type 2 diabetes mellitus (T2D) and other metabolic traits. We conducted a meta-analysis of genome-wide association studies in 39,883 individuals of European ancestry to identify genes associated with metabolic disease. We identified 8 novel loci associated with adiponectin levels and confirmed 2 previously reported loci (P = 4.5×10⁻⁸–1.2×10⁻⁴³). Using a novel method to combine data across ethnicities (N = 4,232 African Americans, N = 1,776 Asians, and N = 29,347 Europeans), we identified two additional novel loci. Expression analyses of 436 human adipocyte samples revealed that mRNA levels of 18 genes at candidate regions were associated with adiponectin concentrations after accounting for multiple testing (p<3×10⁻⁴). We next developed a multi-SNP genotypic risk score to test the association of adiponectin decreasing risk alleles on metabolic traits and diseases using consortia-level meta-analytic data. This risk score was associated with increased risk of T2D (p = 4.3×10⁻³, n = 22,044), increased triglycerides (p = 2.6×10⁻¹⁴, n = 93,440), increased waist-to-hip ratio (p = 1.8×10⁻⁵, n = 77,167), increased glucose two hours post oral glucose tolerance testing (p = 4.4×10⁻³, n = 15,234), increased fasting insulin (p = 0.015, n = 48,238), but with lower in HDL-cholesterol concentrations (p = 4.5×10⁻¹³, n = 96,748) and decreased BMI (p = 1.4×10⁻⁴, n = 121,335). These findings identify novel genetic determinants of adiponectin levels, which, taken together, influence risk of T2D and markers of insulin resistance.     

Root morphological responses to population density vary with soil conditions and growth stages: The complexity of density effects

AimHow plants cope with increases in population density via root plasticity is not well documented, although abiotic environments and plant ontogeny may have important roles in determining root response to density. To investigate how plant root plasticity in response to density varies with soil conditions and growth stages, we conducted a field experiment with an annual herbaceous species (Abutilon theophrasti).MethodsPlants were grown at low, medium, and high densities (13.4, 36.0, and 121.0 plants m⁻², respectively), under fertile and infertile soil conditions, and a series of root traits were measured after 30, 50, and 70 days.ResultsRoot allocation increased, decreased, or canalized in response to density, depending on soil conditions and stages of plant growth, indicating the complex effects of population density, including both competitive and facilitative effects.Main conclusionsRoot allocation was promoted by neighbor roots at early stages and in abundant resource availability, due to low‐to‐moderate belowground interactions among smaller plants, leading to facilitation. As plants grew, competition intensified and infertile soil aggravated belowground competition, leading to decreased root allocation in response to density. Root growth may be more likely restricted horizontally rather than vertically by the presence of neighbor, suggesting a spatial orientation effect in their responses to density. We emphasized the importance of considering effects of abiotic conditions and plant growth stages in elucidating the complexity of density effects on root traits.     

Association of genetic variants in enamel-formation genes with dental caries: A meta- and gene-cluster analysis

Previous studies have reported the association between multiple genetic variants in the enamel-formation genes and the risk of dental caries with inconsistent results. We performed a systematic literature search of the PubMed, Cochrane Library, HuGE and Google Scholar databases for studies published before March 21, 2020 and conducted meta-, gene-based and gene-cluster analysis on the association between genetic variants in the enamel-formation genes and the risk of dental caries. We identified 21 relevant publications including a total of 24 studies for analysis. The genetic variant rs17878486 in AMELX was significantly associated with dental caries risk (OR = 1.40, 95% CI: 1.02–1.93, P = 0.037). We found no significant association between the risk of dental caries with rs12640848 in ENAM (OR = 1.15, 95% CI: 0.88–1.52, P = 0.310), rs1784418 in MMP20 (OR = 1.07, 95% CI: 0.76–1.49, P = 0.702) and rs3796704 in ENAM (OR = 1.06, 95% CI: 0.96–1.17, P = 0.228). Gene-based analysis indicated that multiple genetic variants in AMELX showed joint association with the risk of dental caries (6 variants; P < 10⁻⁵), so did genetic variants in MMP13 (3 variants; P = 0.004), MMP2 (3 variants; P < 10⁻⁵), MMP20 (2 variants; P < 10⁻⁵) and MMP3 (2 variants; P < 10⁻⁵). The gene-cluster analysis indicated a significant association between the genetic variants in this enamel-formation gene cluster and the risk of dental caries (P < 10⁻⁵). The present meta-analysis revealed that genetic variant rs17878486 in AMELX was associated with dental caries, and multiple genetic variants in the enamel-formation genes jointly contributed to the risk of dental caries, supporting the role of genetic variants in the enamel-formation genes in the etiology of dental caries.     

Dietary Factors Impact on the Association between CTSS Variants and Obesity Related Traits

Background/Aims

Cathepsin S, a protein coded by the CTSS gene, is implicated in adipose tissue biology–this protein enhances adipose tissue development. Our hypothesis is that common variants in CTSS play a role in body weight regulation and in the development of obesity and that these effects are influenced by dietary factors–increased by high protein, glycemic index and energy diets.

Methods

Four tag SNPs (rs7511673, rs11576175, rs10888390 and rs1136774) were selected to capture all common variation in the CTSS region. Association between these four SNPs and several adiposity measurements (BMI, waist circumference, waist for given BMI and being a weight gainer–experiencing the greatest degree of unexplained annual weight gain during follow-up or not) given, where applicable, both as baseline values and gain during the study period (6–8 years) were tested in 11,091 European individuals (linear or logistic regression models). We also examined the interaction between the CTSS variants and dietary factors–energy density, protein content (in grams or in % of total energy intake) and glycemic index–on these four adiposity phenotypes.

Results

We found several associations between CTSS polymorphisms and anthropometric traits including baseline BMI (rs11576175 (SNP N°2), p = 0.02, β = −0.2446), and waist change over time (rs7511673 (SNP N°1), p = 0.01, β = −0.0433 and rs10888390 (SNP N°3), p = 0.04, β = −0.0342). In interaction with the percentage of proteins contained in the diet, rs11576175 (SNP N°2) was also associated with the risk of being a weight gainer (p_interaction = 0.01, OR = 1.0526)–the risk of being a weight gainer increased with the percentage of proteins contained in the diet.

Conclusion

CTSS variants seem to be nominally associated to obesity related traits and this association may be modified by dietary protein intake.     

Specificity of RSG-1.2 peptide binding to RRE-IIB RNA element of HIV-1 over Rev peptide is mainly enthalpic in origin

Rev is an essential HIV-1 regulatory protein which binds to the Rev responsive element (RRE) present within the env gene of HIV-1 RNA genome. This binding facilitates the transport of the RNA to the cytoplasm, which in turn triggers the switch between viral latency and active viral replication. Essential components of this complex have been localized to a minimal arginine rich Rev peptide and stem IIB region of RRE. A synthetic peptide known as RSG-1.2 binds with high binding affinity and specificity to the RRE-IIB than the Rev peptide, however the thermodynamic basis of this specificity has not yet been addressed. The present study aims to probe the thermodynamic origin of this specificity of RSG-1.2 over Rev Peptide for RRE-IIB. The temperature dependent melting studies show that RSG-1.2 binding stabilizes the RRE structure significantly (ΔT _m = 4.3°C), in contrast to Rev binding. Interestingly the thermodynamic signatures of the binding have also been found to be different for both the peptides. At pH 7.5, RSG-1.2 binds RRE-IIB with a K_a = 16.2±0.6×10⁷ M⁻¹ where enthalpic change ΔH = −13.9±0.1 kcal/mol is the main driving force with limited unfavorable contribution from entropic change TΔS = −2.8±0.1 kcal/mol. A large part of ΔH may be due to specific stacking between U72 and Arg15. In contrast binding of Rev (K_a = 3.1±0.4×10⁷ M⁻¹) is driven mainly by entropy (ΔH = 0 kcal/mol and TΔS = 10.2±0.2 kcal/mol) which arises from major conformational changes in the RNA upon binding.     

Aquatic adventitious root development in partially and completely submerged wetland plants Cotula coronopifolia and Meionectes brownii

Background and Aims

A common response of wetland plants to flooding is the formation of aquatic adventitious roots. Observations of aquatic root growth are widespread; however, controlled studies of aquatic roots of terrestrial herbaceous species are scarce. Submergence tolerance and aquatic root growth and physiology were evaluated in two herbaceous, perennial wetland species Cotula coronopifolia and Meionectes brownii.

Methods

Plants were raised in large pots with ‘sediment’ roots in nutrient solution and then placed into individual tanks and shoots were left in air or submerged (completely or partially). The effects on growth of aquatic root removal, and of light availability to submerged plant organs, were evaluated. Responses of aquatic root porosity, chlorophyll and underwater photosynthesis, were studied.

Key Results

Both species tolerated 4 weeks of complete or partial submergence. Extensive, photosynthetically active, aquatic adventitious roots grew from submerged stems and contributed up to 90 % of the total root dry mass. When aquatic roots were pruned, completely submerged plants grew less and had lower stem and leaf chlorophyll a, as compared with controls with intact roots. Roots exposed to the lowest PAR (daily mean 4·7 ± 2·4 µmol m⁻² s⁻¹) under water contained less chlorophyll, but there was no difference in aquatic root biomass after 4 weeks, regardless of light availability in the water column (high PAR was available to all emergent shoots).

Conclusions

Both M. brownii and C. coronopifolia responded to submergence with growth of aquatic adventitious roots, which essentially replaced the existing sediment root system. These aquatic roots contained chlorophyll and were photosynthetically active. Removal of aquatic roots had negative effects on plant growth during partial and complete submergence.