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1.
Nutrients ; 16(8)2024 Apr 10.
Article En | MEDLINE | ID: mdl-38674811

Bean consumption during childhood may play a role in promoting early-life health given their high nutritional quality. To examine the associations of children's bean consumption with the socio-demographic characteristics of the child and mother and the child's nutrient intake, we analyzed data from the WIC-ITFPS-2, which followed children and their mothers at 1, 3, 5, 7, 9, 11, 13, 15, 18, and 24 months (m) following birth. Caregivers (mostly mothers) responded to an interview-administered 24 h recall on their child's dietary intake at each time point. The intake of dried beans, chili, yellow beans, and lima beans was quantified. Correlate measures included socio-demographic characteristics. Outcome measures of interest focused on the intake of macronutrients (grams and % kcals) and micronutrients at 11 (infancy) and 24 m (toddler) only. To ensure statistical power, we only examined the associations of dried beans and chili with socio-demographics (Chi-square tests) and nutritional outcomes (ANOVA) at 11 and 24 m. The proportion of children who consumed dried beans or chili was very low in the first 6 m of age, started to increase at 7 m (1.2% and 0.4%) and 11 m (4.9% and 2.3%), and reached a high level at 18 m (10.5%) and 24 m (5.9%), respectively. Consumption of yellow or lima beans was rare (<0.1%). At 11 and 24 m, dried bean consumption was higher in children who were White (vs. Black). Dried bean and chili consumption was higher in children who were of Hispanic or Latino ethnicity (vs. non-Hispanic or non-Latino ethnicity). Children who consumed dried beans and chili at 11 or 24 m had a higher intake of total energy, protein, total fiber, potassium, folate, and magnesium compared with non-consumers. The bean consumption was low amongst children, differed by race and ethnicity, and was associated with improved macro- and micronutrient intake in children at 11 and 24 m.


Fabaceae , Humans , Female , Infant , Male , Child, Preschool , Nutritional Status , Diet/statistics & numerical data , Nutritive Value , Infant Nutritional Physiological Phenomena , Micronutrients , Feeding Behavior
2.
Nutrients ; 16(7)2024 Apr 01.
Article En | MEDLINE | ID: mdl-38613062

The adverse influence of maternal obesity on offspring metabolic health throughout the life-course is a significant public health challenge with few effective interventions. We examined if black bean powder (BBP) supplementation to a high-calorie maternal pregnancy diet or a postnatal offspring diet could offer protection against the metabolic programming of metabolic disease risk in adult offspring. Female Sprague Dawley rats were randomly assigned to one of three diets (n = 10/group) for a 3-week pre-pregnancy period and throughout gestation and lactation: (i) a low-caloric control diet (CON); (ii) a high-caloric obesity-inducing diet (HC); or (iii) the HC diet with 20% black bean powder (HC-BBP). At weaning [postnatal day (PND) 21], one male pup from each dam was weaned onto the CON diet throughout the postnatal period until adulthood (PND120). In addition, a second male from the HC group only was weaned onto the CON diet supplemented with BBP (CON-BBP). Thus, based on the maternal diet exposure and offspring postnatal diet, four experimental adult offspring groups were compared: CON/CON, HC/CON, HC-BPP/CON, and HC/CON-BBP. On PND120, blood was collected for biochemical analysis (e.g., lipids, glycemic control endpoints, etc.), and livers were excised for lipid analysis (triglycerides [TG] and cholesterol) and the mRNA/protein expression of lipid-regulatory targets. Compared with the CON/CON group, adult offspring from the HC/CON group exhibited a higher (p < 0.05) body weight (BW) (682.88 ± 10.67 vs. 628.02 ± 16.61 g) and hepatic TG (29.55 ± 1.31 vs. 22.86 ± 1.85 mmol/g). Although maternal BBP supplementation (HC-BBP/CON) had little influence on metabolic outcomes, the consumption of BBP in the postnatal period (HC/CON-BBP) lowered hepatic TG and cholesterol compared with the other treatment groups. Reduced hepatic TG in the HC/CON-BBP was likely associated with lower postnatal BW gain (vs. HC/CON), lower mRNA and protein expression of hepatic Fasn (vs. HC/CON), and lower serum leptin concentration (vs. CON/CON and HC groups). Our results suggest that the postnatal consumption of a black-bean-powder-supplemented diet may protect male rat offspring against the programming of obesity and dyslipidemia associated with maternal obesity. Future work should investigate the bioactive fraction of BBP responsible for the observed effect.


Dyslipidemias , Obesity, Maternal , Humans , Pregnancy , Adult , Female , Male , Rats , Animals , Powders , Adult Children , Rats, Sprague-Dawley , Obesity/etiology , Obesity/prevention & control , Dyslipidemias/etiology , Dyslipidemias/prevention & control , Cholesterol , RNA, Messenger , Lipids
3.
Curr Biol ; 33(24): 5404-5414.e9, 2023 12 18.
Article En | MEDLINE | ID: mdl-38029757

Cellular responses to environmental changes are often highly heterogeneous and exhibit seemingly random dynamics. The astonishing insight of chaos theory is that such unpredictable patterns can, in principle, arise without the need for any random processes, i.e., purely deterministically without noise. However, while chaos is well understood in mathematics and physics, its role in cell biology remains unclear because the complexity and noisiness of biological systems make testing difficult. Here, we show that chaos explains the heterogeneous response of Escherichia coli cells to oxidative stress. We developed a theoretical model of the gene expression dynamics and demonstrate that chaotic behavior arises from rapid molecular feedbacks that are coupled with cell growth dynamics and cell-cell interactions. Based on theoretical predictions, we then designed single-cell experiments to show we can shift gene expression from periodic oscillations to chaos on demand. Our work suggests that chaotic gene regulation can be employed by cell populations to generate strong and variable responses to changing environments.


Models, Theoretical , Nonlinear Dynamics
4.
J Nutr ; 153(1): 158-166, 2023 01.
Article En | MEDLINE | ID: mdl-36913449

BACKGROUND: Egg consumption may play an important role in early-life growth given their high-quality protein, essential fatty acids, and micronutrients. OBJECTIVES: Study objectives were to examine the longitudinal associations of infant age at egg introduction with obesity outcomes in early childhood, middle childhood (mid-childhood), and early adolescence. METHODS: We used existing data from 1089 mother-child dyads from Project Viva to estimate age at egg introduction through a questionnaire completed by mothers at ∼1 y postpartum (mean ± SD, 13.3 ± 1.2 mo). Outcome measures included height and weight (early childhood, mid-childhood, and early adolescence), body composition including total fat mass, trunk fat mass, and lean mass (mid-childhood and early adolescence), and plasma adiponectin and leptin (early and mid-childhood and early adolescence). We defined childhood obesity as sex- and age-specific BMI ≥ 95th percentile. We estimated the associations of infant age at egg introduction with risk of obesity using multivariable logistic regression and multivariable linear regression models for BMI-z-score, body composition measures, and adiposity hormones; adjusted for maternal prepregnancy BMI and sociodemographics. RESULTS: Among females, those introduced to egg by the 1-y survey had a lower total fat mass index (confounder-adjusted mean difference, -1.23 kg/m2; 95% CI: -2.14, -0.31), and trunk fat mass index (confounder-adjusted mean difference, -0.57 kg/m2; 95% CI: -1.01, -0.12) in early adolescence compared to those not introduced (reference group). However, no associations between infant age at egg introduction and risk of obesity were observed among males (confounder-adjusted odd ratio [aOR], 1.97; 95% CI: 0.90, 4.30) or females (aOR, 0.68; 95% CI: 0.38, 1.24) across all ages. Egg introduction in infancy was associated with lower plasma adiponectin among females (confounder-adjusted mean difference, -1.93 µg/mL; 95% CI: -3.70, -0.16) in early childhood only. CONCLUSIONS: Egg introduction during infancy among females is associated with lower total fat mass index in early adolescence and plasma adiponectin in early childhood. This trial was registered at clinicaltrials.gov as NCT02820402.


Eggs , Pediatric Obesity , Adolescent , Child , Child, Preschool , Female , Humans , Infant , Male , Adiponectin , Adiposity , Body Mass Index , Surveys and Questionnaires , Diet
5.
Nutrients ; 15(4)2023 Feb 08.
Article En | MEDLINE | ID: mdl-36839225

Increased consumption of dietary pulse protein has been shown to assist in body weight regulation and improve a range of metabolic health outcomes. We investigated if the exchange of casein for yellow pea protein (YPPN) in an obese-inducing maternal diet throughout pregnancy and lactation offered protection against obesity and dyslipidemia in offspring. Sixty female Sprague Dawley rats were fed a low-calorie control diet (CON), a high-caloric obesity-inducing diet (with casein protein (CP), HC-CP), or an isocaloric/macronutrient-matched HC diet supplemented with YPPN isolate (HC-PPN) in pre-pregnancy, gestation, and lactation. Body weight (BW) and metabolic outcomes were assessed in male and female offspring at weaning and in adulthood after consuming the CON diet in the postnatal period. Consumption of the HC-PPN diet did not protect against maternal obesity but did improve reproductive success compared with the HC-CP group (72.7% versus 43.7%) and reduced total energy, fat, and protein in maternal milk. Male, but not female, offspring from mothers fed the HC-CP diet demonstrated hyperphagia, obesity, dyslipidemia, and hepatic triglyceride (TG) accumulation as adults compared with CON offspring. Isocaloric exchange of CP for YPPN in a high-calorie obese-inducing diet did not protect against obesity but did improve several aspects of lipid metabolism in adult male offspring including serum total cholesterol, LDL/VLDL cholesterol, triglycerides (TGs), and hepatic TG concentration. Our results suggest that the exchange of CP for YPPN in a maternal obese-inducing diet selectively protects male offspring from the malprogramming of lipid metabolism in adulthood.


Dyslipidemias , Pea Proteins , Prenatal Exposure Delayed Effects , Humans , Rats , Animals , Male , Female , Pregnancy , Caseins , Rats, Sprague-Dawley , Diet, High-Fat , Obesity/metabolism , Body Weight/physiology , Lactation/physiology , Triglycerides , Maternal Nutritional Physiological Phenomena/physiology
6.
Cell Rep ; 42(3): 112168, 2023 03 28.
Article En | MEDLINE | ID: mdl-36848288

Genetically identical bacterial cells commonly display different phenotypes. This phenotypic heterogeneity is well known for stress responses, where it is often explained as bet hedging against unpredictable environmental threats. Here, we explore phenotypic heterogeneity in a major stress response of Escherichia coli and find it has a fundamentally different basis. We characterize the response of cells exposed to hydrogen peroxide (H2O2) stress in a microfluidic device under constant growth conditions. A machine-learning model reveals that phenotypic heterogeneity arises from a precise and rapid feedback between each cell and its immediate environment. Moreover, we find that the heterogeneity rests upon cell-cell interaction, whereby cells shield each other from H2O2 via their individual stress responses. Our work shows how phenotypic heterogeneity in bacterial stress responses can emerge from short-range cell-cell interactions and result in a collective phenotype that protects a large proportion of the population.


Hydrogen Peroxide , Oxidative Stress , Hydrogen Peroxide/toxicity , Phenotype , Cell Communication , Oxidation-Reduction , Bacteria/genetics
7.
J Paediatr Child Health ; 59(1): 53-57, 2023 01.
Article En | MEDLINE | ID: mdl-36190149

AIM: Egg is a major food allergen in childhood. Recent studies suggest that early introduction of allergenic foods can decrease the risk of developing egg allergy. The impact of early egg introduction in the general population is unclear. We examined associations between age of infant egg introduction and childhood egg allergy outcomes in a general population. METHODS: The study population consisted of 1217 neonates from Project Viva, a longitudinal pre-birth cohort in eastern Massachusetts area, USA. Mothers reported age of infant egg introduction and child egg allergy using questionnaires and specific IgE to egg white was assayed. We estimated associations between age of infant egg introduction and egg allergy outcomes using Log-binomial regression models, adjusting for socio-demographics and health confounders. RESULTS: Egg allergy at 2 years was significantly higher (8.0% vs. 1.4%, P < 0.0001) in children who had delayed egg introduction beyond infancy, compared with children who were introduced to egg during infancy (adjusted relative risk or aRR 7.58; 95% CI 3.08, 18.61). At 12 years, the risk of egg allergy remained significantly higher (3.9% vs. 1.1%, P = 0.048) in children with delayed egg introduction compared with children introduced to egg during infancy (aRR 4.07; 95% CI 1.20, 13.87). CONCLUSIONS: Infants with delayed introduction of eggs after 12 months had increased risk of egg allergy in childhood (2 years) and the relationship persisted in early adolescence (12 years). Our findings suggest that introduction to eggs before 12 months could contribute to the prevention of egg allergy.


Egg Hypersensitivity , Food Hypersensitivity , Child , Infant, Newborn , Female , Adolescent , Humans , Infant , Egg Hypersensitivity/prevention & control , Eggs , Food Hypersensitivity/etiology , Food Hypersensitivity/complications , Mothers , Allergens
8.
Int J Neurosci ; : 1-10, 2022 Dec 07.
Article En | MEDLINE | ID: mdl-36469636

BACKGROUND: Allopregnanolone (3α, 5α-tetrahydroprogesterone) is an inhibitory neurosteroid synthesized from progesterone via 5α-reductase activity in the brain and has anxiolytic, antidepressant, sedative, anticonvulsant, and analgesic activity. Altered levels of allopregnanolone cause anxiety, depression, premenstrual syndrome, and psychiatric disorders. Although allopregnanolone exerts most of its actions by modulating GABAA receptor, NMDA receptor, BDNF expression, and PXR activity, a recent study showed its effects are blocked by mifepristone on lordosis behavior which indicates the involvement of progestin or glucocorticoid receptors in the effects of allopregnanolone since mifepristone blocks both these receptors. However, whether these receptors are involved in acute anxiolytic or antidepressant-like effects is unknown. METHODS: Adult male Wistar rats were used to study whether the prior administration of mifepristone would alter the effects of allopregnanolone in the elevated plus maze (EPM) and forced swim test (FST) was evaluated. RESULTS: 10 mg/Kg dose of allopregnanolone increased percent open arm entries in the EPM, whereas 3 mg/Kg dose of allopregnanolone decreased percent immobility in the FST. Mifepristone administration resulted in a U-shaped response in the FST (with 1 mg/Kg, s.c., decreasing the immobility time) without significantly impacting the behavior in the EPM. In combination studies, mifepristone blocked the anxiolytic and antidepressant effects of allopregnanolone. CONCLUSION: The current study provides evidence for the first time that progestin or glucocorticoid receptors are involved in the acute anxiolytic and antidepressant effects of allopregnanolone. Understanding the mechanism of action of allopregnanolone will help us design better therapeutic strategies to treat neuropsychiatric diseases such as depression and anxiety.

9.
Lipids Health Dis ; 21(1): 53, 2022 Jun 13.
Article En | MEDLINE | ID: mdl-35698189

BACKGROUND: An excessive rise in maternal lipids during pregnancy may have detrimental impacts on maternal and fetal health leading to adverse pregnancy outcomes. However, knowledge gaps exist with respect to the association between lipid biomarkers and birth outcomes. METHODS: We conducted a secondary data analysis of healthy pregnant women (N = 25) with mid-pregnancy fasting serum samples collected at 22-28 weeks of gestation and birth outcome data. Serum was analyzed for conventional lipid profile (total-C, HDL-C, LDL-C, and triglycerides) and lipoprotein subclass distribution, including particle number (nM) and size (nm), for very low-density lipoprotein (VLDL)/chylomicron (CM), low density lipoprotein (LDL), and high-density lipoprotein (HDL), by nuclear magnetic resonance spectroscopy. Associations between maternal lipids and birth outcomes, including birth weight (g) and gestational age (weeks), were assessed using multivariable linear regression, adjusted for pre-pregnancy BMI. RESULTS: Although conventional lipids were not associated (p > 0.05) with birth outcomes, every 1-unit increment in large VLDL/CM particles (nM) and VLDL/CM size (nm) was associated with an increase in birth weight (confounder-adjusted ß-coefficient, 45.80 g [5.30, 86.20, p = 0.003] and 24.90 g [8.80, 40.90, p = 0.002], respectively). Among the HDL subclass parameters, a 1-unit (nM) increase in the concentration of total HDL-particles was associated with a reduced birth weight (confounder adjusted ß-coefficient, -19.40 g [95% confidence interval, -36.70, -2.20]; p = 0.03) after adjustment for maternal pre-pregnancy BMI. CONCLUSION: The preliminary results of this pilot study suggest that total particle concentrations of VLDL/CM and HDL in mid-pregnancy have divergent associations with birth weight, potentially reflecting the specific roles of these lipoprotein particles with respect to placental function and fetal growth.


Lipoproteins , Placenta , Birth Weight , Chylomicrons , Female , Humans , Lipoproteins, HDL , Lipoproteins, VLDL , Particle Size , Parturition , Pilot Projects , Pregnancy , Triglycerides
10.
Sci Rep ; 12(1): 5019, 2022 03 23.
Article En | MEDLINE | ID: mdl-35322051

Herpesviruses are known to acquire several genes from their hosts during evolution. We found that a significant proportion of virus homologues encoded by HSV-1, HSV-2, EBV and KSHV and their human counterparts contain G-quadruplex motifs in their promoters. We sought to understand the role of G-quadruplexes in the regulatory regions of viral Bcl-2 homologues encoded by KSHV (KS-Bcl-2) and EBV (BHRF1). We demonstrate that the KSHV KS-Bcl-2 and the EBV BHRF1 promoter G-quadruplex motifs (KSHV-GQ and EBV-GQ) form stable intramolecular G-quadruplexes. Ligand-mediated stabilization of KS-Bcl-2 and BHRF1 promoter G-quadruplexes significantly increased the promoter activity resulting in enhanced transcription of these viral Bcl-2 homologues. Mutations disrupting KSHV-GQ and EBV-GQ inhibit promoter activity and render the KS-Bcl-2 and the BHRF1 promoters non-responsive to G-quadruplex ligand. In contrast, promoter G-quadruplexes of human bcl-2 gene inhibit promoter activity. Further, KS-Bcl-2 and BHRF1 promoter G-quadruplexes augment RTA (a virus-encoded transcription factor)-mediated increase in viral bcl-2 promoter activity. In sum, this work highlights how human herpesviruses have evolved to exploit promoter G-quadruplexes to regulate virus homologues to counter their cellular counterparts.


G-Quadruplexes , Herpesvirus 8, Human , Herpesvirus 4, Human/genetics , Herpesvirus 8, Human/genetics , Humans , Ligands , Promoter Regions, Genetic , Viral Proteins/genetics
11.
J Biol Chem ; 297(4): 101233, 2021 10.
Article En | MEDLINE | ID: mdl-34562448

Clinical and epidemiological studies support a role for vitamin D in suppressing hepatitis B virus (HBV). This antiviral role of vitamin D is widely attributed to vitamin D receptor (VDR)/retinoid X receptor-mediated regulation of host immunomodulatory genes through vitamin D response elements (VDREs) in their promoters. Here, we investigated the ability of calcitriol (1α,25-dihydroxyvitamin D3, metabolically activated vitamin D) to directly regulate HBV activity through this signaling pathway. We observed that calcitriol selectively inhibited only the HBV core promoter without affecting the HBV-PreS1, HBV-PreS2/S, or HBx promoters. We then identified a VDRE cluster in the HBV core promoter that is highly conserved across most HBV genotypes. Disruption of this VDRE cluster abrogated calcitriol-mediated suppression of the HBV core promoter. Furthermore, we showed that VDR interacts directly with the VDRE cluster in the HBV core promoter independent of retinoid X receptor. This demonstrates that calcitriol inhibits HBV core promoter activity through a noncanonical calcitriol-activated VDR pathway. Finally, we observed that calcitriol suppressed expression of the canonical HBV core promoter transcripts, pregenomic RNA, and precore RNA in multiple HBV cell culture models. In addition, calcitriol inhibited the secretion of hepatitis B "e" antigen and hepatitis B surface antigen (HBV-encoded proteins linked to poor disease prognosis), without affecting virion secretion. Our findings identify VDR as a novel regulator of HBV core promoter activity and also explain at least in part the correlation of vitamin D levels to HBV activity observed in clinical studies. Furthermore, this study has implications on the potential use of vitamin D along with anti-HBV therapies, and lays the groundwork for studies on vitamin D-mediated regulation of viruses through VDREs in virus promoters.


Calcitriol/pharmacology , Hepatitis B e Antigens/biosynthesis , Hepatitis B virus/metabolism , Promoter Regions, Genetic , Receptors, Calcitriol/metabolism , Retinoid X Receptors/metabolism , Hep G2 Cells , Hepatitis B/drug therapy , Hepatitis B/genetics , Hepatitis B/metabolism , Hepatitis B e Antigens/genetics , Hepatitis B virus/genetics , Humans , Receptors, Calcitriol/genetics , Retinoid X Receptors/genetics
12.
Front Microbiol ; 12: 684756, 2021.
Article En | MEDLINE | ID: mdl-34489883

Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the 'alt' gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.

13.
Comput Biol Med ; 135: 104633, 2021 08.
Article En | MEDLINE | ID: mdl-34346318

This paper introduces methods to estimate aspects of physical activity and sedentary behavior from three-axis accelerometer data collected with a wrist-worn device at a sampling rate of 32 [Hz] on adults with type 1 diabetes (T1D) in free-living conditions. In particular, we present two methods able to detect and grade activity based on its intensity and individual fitness as sedentary, mild, moderate or vigorous, and a method that performs activity classification in a supervised learning framework to predict specific user behaviors. Population results for activity level grading show multi-class average accuracy of 99.99%, precision of 98.0 ± 2.2%, recall of 97.9 ± 3.5% and F1 score of 0.9 ± 0.0. As for the specific behavior prediction, our best performing classifier, gave population multi-class average accuracy of 92.43 ± 10.32%, precision of 92.94 ± 9.80%, recall of 92.20 ± 10.16% and F1 score of 92.56 ± 9.94%. Our investigation showed that physical activity and sedentary behavior can be detected, graded and classified with good accuracy and precision from three-axial accelerometer data collected in free-living conditions on people with T1D. This is particularly significant in the context of automated glucose control systems for diabetes, in that the methods we propose have the potential to inform changes in treatment parameters in response to the intensity of physical activity, allowing patients to meet their glycemic targets.


Diabetes Mellitus, Type 1 , Accelerometry , Adult , Exercise , Humans , Sedentary Behavior , Social Conditions , Wrist
15.
Funct Integr Genomics ; 20(6): 739-761, 2020 Nov.
Article En | MEDLINE | ID: mdl-33089419

Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.


Epigenomics/trends , Histone Code/genetics , Histones/genetics , Plant Breeding , Chromatin/genetics , Crops, Agricultural/genetics , DNA Methylation/genetics , Gene Expression Regulation, Plant/genetics , Plant Development/genetics , Plants/genetics , Protein Processing, Post-Translational/genetics
16.
BMC Mol Cell Biol ; 21(1): 67, 2020 Sep 24.
Article En | MEDLINE | ID: mdl-32972365

BACKGROUND: G-quadruplexes regulate gene expression, recombination, packaging and latency in herpesviruses. Herpesvirus-encoded miRNAs have been linked to important biological functions. The presence and the biological role of G-quadruplexes have not been studied in the regulatory regions of virus miRNA. We hypothesized that herpesvirus-encoded miRNAs are regulated by G-quadruplexes in their promoters. RESULTS: We analyzed the 1 kb regulatory regions of all herpesvirus-encoded miRNAs for the presence of putative quadruplex-forming sequences (PQS). Over two-third (67%) of the regulatory regions of herpesvirus miRNAs had atleast 1 PQS. The 200 bp region of the promoter proximal to herpesvirus miRNA is particularly enriched for PQS. We chose to study the G-quadruplex motifs in the promoters of miR-K12 cluster in Kaposi's sarcoma-associated Herpesvirus (KSHV miR-K12-1-9,11) and the miR-US33 encoded by Human Cytomegalovirus (HCMV miR-US33). Biophysical characterization indicates that the G-quadruplex motifs in the promoters of the KSHV miR-K12 cluster and the HCMV miR-US33 form stable intramolecular G-quadruplexes in vitro. Mutations disrupting the G-quadruplex motif in the promoter of the KSHV miR-K12 cluster significantly inhibits promoter activity, while those disrupting the motif in the promoter of HCMV miR-US33 significantly enhance the promoter activity as compared to that of the respective wild-type promoter. Similarly, the addition of G-quadruplex binding ligands resulted in the modulation of promoter activity of the wild-type promoters (with intact G-quadruplex) but not the mutant promoters (containing quadruplex-disrupting mutations). CONCLUSION: Our findings highlight previously unknown mechanisms of regulation of virus-encoded miRNA and also shed light on new roles for G-quadruplexes in herpesvirus biology.


Cytomegalovirus/genetics , Herpesvirus 8, Human/genetics , MicroRNAs/genetics , Cell Line , G-Quadruplexes , Gene Expression/genetics , HEK293 Cells , Humans , Ligands , Promoter Regions, Genetic/genetics , RNA, Viral/genetics , Regulatory Sequences, Nucleic Acid/genetics
18.
Risk Anal ; 40(4): 858-883, 2020 04.
Article En | MEDLINE | ID: mdl-31889333

Integrating sustainability into freight transportation systems (FTSs) is a complex and challenging task due to the sheer number of inherent sustainability risks. Sustainability risks disrupt the economic, social and environmental objectives of freight operations and act as impediments in the development of sustainable freight transportation systems. The area of sustainability risk management is still unexplored and immature in the operational research domain. This study addresses these research gaps and contributes in a threefold manner. First, a total of 36 potential sustainability risks related to FTSs are identified and uniquely classified into seven categories using a rigourous approach. Second, the research proposes two prominent perspectives, namely, ontological and epistemological perspectives to understand risks and develops a novel framework for managing sustainability risks in FTSs. Third, a novel approach by integrating fuzzy evidential reasoning algorithm (FERA) with expected utility theory is developed to quantitatively model and profile sustainability risk for different risk preferences, namely, risk-averse, risk-neutral, and risk-taking scenarios. The proposed FERA is a flexible and robust approach, which transforms the experts' inputs into belief structures and aggregates them using the evidence combination rule proposed in Dempster-Shafer theory to overcome the problem of imprecise results caused by average scoring in existing models. A sensitivity analysis is conducted to demonstrate the robustness of the proposed model. Unlike conventional perception, our study suggests that most of the high priority sustainability risks are behaviorally and socially induced rather than financially driven. The results provide significant managerial implications including a focus on skills development, and on social and behavioral dimensions while managing risks in FTSs.


Models, Theoretical , Risk Assessment , Transportation , Fuzzy Logic , Risk Management/organization & administration
19.
Sci Rep ; 9(1): 18246, 2019 12 03.
Article En | MEDLINE | ID: mdl-31796847

Tomato spotted wilt virus (TSWV) is a devastating disease to peanut growers in the South-eastern region of the United States. Newly released peanut cultivars in recent years are crucial as they have some levels of resistance to TSWV. One mapping population of recombinant inbred line (RIL) used in this study was derived from peanut lines of SunOleic 97R and NC94022. A whole genome re-sequencing approach was used to sequence these two parents and 140 RILs. A recombination bin-based genetic map was constructed, with 5,816 bins and 20 linkage groups covering a total length of 2004 cM. Using this map, we identified three QTLs which were colocalized on chromosome A01. One QTL had the largest effect of 36.51% to the phenotypic variation and encompassed 89.5 Kb genomic region. This genome region had a cluster of genes, which code for chitinases, strictosidine synthase-like, and NBS-LRR proteins. SNPs linked to this QTL were used to develop Kompetitive allele specific PCR (KASP) markers, and the validated KASP markers showed expected segregation of alleles coming from resistant and susceptible parents within the population. Therefore, this bin-map and QTL associated with TSWV resistance made it possible for functional gene mapping, map-based cloning, and marker-assisted breeding. This study identified the highest number of SNP makers and demonstrated recombination bin-based map for QTL identification in peanut. The chitinase gene clusters and NBS-LRR disease resistance genes in this region suggest the possible involvement in peanut resistance to TSWV.


Arachis/genetics , Disease Resistance/genetics , Plant Diseases/immunology , Quantitative Trait Loci/genetics , Tospovirus , Arachis/immunology , Arachis/virology , Chromosome Mapping , Plant Breeding/methods , Plant Diseases/virology , Polymorphism, Single Nucleotide/genetics , Recombination, Genetic/genetics , Sequence Analysis, DNA
20.
J Int Soc Prev Community Dent ; 8(4): 354-360, 2018.
Article En | MEDLINE | ID: mdl-30123770

AIMS AND OBJECTIVE: The aim of the study is to determine the effect of chewing gum containing xylitol and sorbitol on mutans streptococci and Lactobacilli count in saliva, plaque, and gingival health and to compare the efficacy of chewing gums. MATERIALS AND METHODS: The study was designed as a double-blinded randomized uncontrolled clinical trial with two parallel arms. A total of 80 students consented and completed the study. The test group (X) received corresponding pellets with xylitol and the control group (S) was given pellets containing sorbitol and maltitol three times daily for 30 days. Clinical scoring and saliva samples were collected at three different intervals, at baseline, 15th, and 30th day of the study. The outcome measure was plaque index score, gingival index score, salivary mutans streptococci, and Lactobacilli counts. Data collected were analyzed using Statistical Package for the Social Sciences (SPSS version 19.0). RESULTS: There was no statistically significant difference between the mean of mutans streptococci count of test and control group at baseline and 15th day, but there was statistically highly significant difference (P = 0.00) between the mean of mutans streptococci count in test and control group on the 30th day. The mean of Lactobacilli count, plaque index, and gingival index score between test and control group showed no statistically significant difference at baseline, 15th day, and 30th day. CONCLUSION: The results suggest that only xylitol gum may interfere with the mutans streptococci composition and reduce it after continuous use of 30 days effectively as compared to sorbitol gum, but both the gums are equally effective on salivary Lactobacilli, plaque, and gingiva at different intervals.

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