| 1. |
- Ahmad, Shafqat, et al.
(författare)
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Gene × physical activity interactions in obesity: combined analysis of 111,421 individuals of European ancestry. : combined analysis of 111,421 individuals of European ancestry
- 2013
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 9:7, s. 1003607-1003607
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Tidskriftsartikel (refereegranskat)abstract
- Numerous obesity loci have been identified using genome-wide association studies. A UK study indicated that physical activity may attenuate the cumulative effect of 12 of these loci, but replication studies are lacking. Therefore, we tested whether the aggregate effect of these loci is diminished in adults of European ancestry reporting high levels of physical activity. Twelve obesity-susceptibility loci were genotyped or imputed in 111,421 participants. A genetic risk score (GRS) was calculated by summing the BMI-associated alleles of each genetic variant. Physical activity was assessed using self-administered questionnaires. Multiplicative interactions between the GRS and physical activity on BMI were tested in linear and logistic regression models in each cohort, with adjustment for age, age(2), sex, study center (for multicenter studies), and the marginal terms for physical activity and the GRS. These results were combined using meta-analysis weighted by cohort sample size. The meta-analysis yielded a statistically significant GRS × physical activity interaction effect estimate (Pinteraction = 0.015). However, a statistically significant interaction effect was only apparent in North American cohorts (n = 39,810, Pinteraction = 0.014 vs. n = 71,611, Pinteraction = 0.275 for Europeans). In secondary analyses, both the FTO rs1121980 (Pinteraction = 0.003) and the SEC16B rs10913469 (Pinteraction = 0.025) variants showed evidence of SNP × physical activity interactions. This meta-analysis of 111,421 individuals provides further support for an interaction between physical activity and a GRS in obesity disposition, although these findings hinge on the inclusion of cohorts from North America, indicating that these results are either population-specific or non-causal.
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| 2. |
- Ahmad, Shafqat, et al.
(författare)
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Gene x physical activity interactions in obesity : combined analysis of 111,421 individuals of European ancestry
- 2013
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Ingår i: PLOS Genetics. - : Public Library of Science. - 1553-7390 .- 1553-7404. ; 9:7, s. e1003607-
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Tidskriftsartikel (refereegranskat)abstract
- Numerous obesity loci have been identified using genome-wide association studies. A UK study indicated that physical activity may attenuate the cumulative effect of 12 of these loci, but replication studies are lacking. Therefore, we tested whether the aggregate effect of these loci is diminished in adults of European ancestry reporting high levels of physical activity. Twelve obesity-susceptibility loci were genotyped or imputed in 111,421 participants. A genetic risk score (GRS) was calculated by summing the BMI-associated alleles of each genetic variant. Physical activity was assessed using self-administered questionnaires. Multiplicative interactions between the GRS and physical activity on BMI were tested in linear and logistic regression models in each cohort, with adjustment for age, age(2), sex, study center (for multicenter studies), and the marginal terms for physical activity and the GRS. These results were combined using meta-analysis weighted by cohort sample size. The meta-analysis yielded a statistically significant GRS x physical activity interaction effect estimate (P-interaction = 0.015). However, a statistically significant interaction effect was only apparent in North American cohorts (n = 39,810, P-interaction = 0.014 vs. n = 71,611, P-interaction = 0.275 for Europeans). In secondary analyses, both the FTO rs1121980 (P-interaction = 0.003) and the SEC16B rs10913469 (P-interaction = 0.025) variants showed evidence of SNP x physical activity interactions. This meta-analysis of 111,421 individuals provides further support for an interaction between physical activity and a GRS in obesity disposition, although these findings hinge on the inclusion of cohorts from North America, indicating that these results are either population-specific or non-causal.
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| 3. |
- Alexandersson, Erik, et al.
(författare)
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Plant secretome proteomics
- 2013
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 4
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Forskningsöversikt (refereegranskat)abstract
- The plant secretome refers to the set of proteins secreted out of the plant cell into the surrounding extracellular space commonly referred to as the apoplast. Secreted proteins maintain cell structure and acts in signaling and are crucial for stress responses where they can interact with pathogen effectors and control the extracellular environment. Typically, secreted proteins contain an N-terminal signal peptide and are directed through the endoplasmic reticulum/Golgi pathway. However, in plants many proteins found in the secretome lack such a signature and might follow alternative ways of secretion. This review covers techniques to isolate plant secretomes and how to identify and quantify their constituent proteins. Furthermore, bioinformatical tools to predict secretion signals and define the putative secretome are presented. Findings from proteomic studies and important protein families of plant secretomes, such as proteases and hydrolases, are highlighted.
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| 4. |
- Ali, Amjad, et al.
(författare)
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A potential electrolyte (Ce1-x CaxO2-delta) for fuel cells:Theoretical andexperimental study
- 2018
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Ingår i: Ceramics International. - : ELSEVIER SCI LTD. - 0272-8842 .- 1873-3956. ; 44:11, s. 12676-12683
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Tidskriftsartikel (refereegranskat)abstract
- First-principles calculations are performed using density function theory to explore the effects of dopant Ca in ceria (Ce1-x CaxO2-delta). The impact of oxygen vacancy on band gap and density of states is examined in doped ceria using generalized gradient approximations. Vacancy association and vacancy formation energies of the doped ceria are calculated to reveal the effect of dopant on ion conduction. The experimental study of the sample Ce0.875Ca0.125O2-delta) was performed to compare with the theoretical results. The obtained results from theoretical calculation and experimental techniques show that oxygen vacancy increases the volume, lattice constant (5.47315 angstrom) but decrease the band gap (1.72 eV) and bulk modulus. The dopant radius (1.173 angstrom) and lattice constant (5.4718 angstrom) are also calculated by equations which is close to the DFT lattice parameter. The result shows that oxygen vacancy shifts the density of states to lower energy region. Band gap is decreased due to shifting of valence states to conduction band. Vacancy formation shows a significance increase in density of states near the Fermi level. Density of states at Fermi level is proportional to the conductivity, so an increase in density of states near the Fermi level increases the conductivity. The experimental measured ionic conductivity is found to 0.095 S cm(-1) at 600 degrees C. The microstructural studies is also reported in this work.
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| 5. |
- Ali, Ashfaq
(författare)
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Defence and signalling in Potato-Phytophthora infestans interactions
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Potato is one of the major food crops and its yield is severely affected by late blight disease caused by Phytophthora infestans. P. infestans has the ability to manipulate plant defence signalling by secreting effector molecules causing so called effector triggered susceptibility. Some plants can recognize these effectors via resistance proteins that reactivate plant defence and lead to effector triggered immunity. This thesis discusses identification and analysis of field-pathological relevant potato material for resistance against P. infestans. The two selected potato clones were shown to be resistant, in fields with diverse P.infestans populations, and in growth chambers with a highly virulent Swedish P.infestans strain. They have slightly different resistance reaction at phenotypic and molecular level. One of the two resistant potato clones (SW93-1015) showed an unusual reduction in hypersensitive reaction expansion and part of the induced defence system was constitutively expressed in this potato clone. These two resistant potato clones and the susceptible cultivar Desiree were studied by a combination of quantitative proteomics assisted with newly generated sequence data, and genome wide transcriptomics. A number of putative effector-targets in the potato secretome, often single members of large gene families were identified. These studies have also provided us with insight to components involved in successful plant defence amid hypersensitive response. By analysing crossing populations, a remarkably simple genetic resistance in the potato clone SW93-1015 was identified. We also present a primary global phosphoproteomics analysis that led to identification of novel phosphosites and phosphorylation of several P. infestans effectors. These findings lead us to a better understanding of plant pathogen interactions in field relevant systems and hopefully will allow us to create more tools to overcome this devastating crop disease.
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| 6. |
- Ali, Ashfaq, et al.
(författare)
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Do Genetic Factors Modify the Relationship Between Obesity and Hypertriglyceridemia? : Findings From the GLACIER and the MDC Studies
- 2016
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Ingår i: Circulation. - 1942-325X .- 1942-3268. ; 9:2, s. 162-171
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Tidskriftsartikel (refereegranskat)abstract
- Background Obesity is a major risk factor for dyslipidemia, but this relationship is highly variable. Recently published data from 2 Danish cohorts suggest that genetic factors may underlie some of this variability.Methods and Results We tested whether established triglyceride-associated loci modify the relationship of body mass index (BMI) and triglyceride concentrations in 2 Swedish cohorts (the Gene-Lifestyle Interactions and Complex Traits Involved in Elevated Disease Risk [GLACIER Study; N=4312] and the Malmo Diet and Cancer Study [N=5352]). The genetic loci were amalgamated into a weighted genetic risk score (WGRS(TG)) by summing the triglyceride-elevating alleles (weighted by their established marginal effects) for all loci. Both BMI and the WGRS(TG) were strongly associated with triglyceride concentrations in GLACIER, with each additional BMI unit (kg/m(2)) associated with 2.8% (P=8.4x10(-84)) higher triglyceride concentration and each additional WGRS(TG) unit with 2% (P=7.6x10(-48)) higher triglyceride concentration. Each unit of the WGRS(TG) was associated with 1.5% higher triglyceride concentrations in normal weight and 2.4% higher concentrations in overweight/obese participants (P-interaction=0.056). Meta-analyses of results from the Swedish cohorts yielded a statistically significant WGRS(TG)xBMI interaction effect (P-interaction=6.0x10(-4)), which was strengthened by including data from the Danish cohorts (P-interaction=6.5x10(-7)). In the meta-analysis of the Swedish cohorts, nominal evidence of a 3-way interaction (WGRS(TG)xBMIxsex) was observed (P-interaction=0.03), where the WGRS(TG)xBMI interaction was only statistically significant in females. Using protein-protein interaction network analyses, we identified molecular interactions and pathways elucidating the metabolic relationships between BMI and triglyceride-associated loci.Conclusions Our findings provide evidence that body fatness accentuates the effects of genetic susceptibility variants in hypertriglyceridemia, effects that are most evident in females.
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| 7. |
- Ali, Ashfaq, et al.
(författare)
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Paranoid potato : phytophthora-resistant genotype shows constitutively activated defense
- 2012
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Ingår i: Plant Signaling and Behavior. - : Informa UK Limited. - 1559-2316 .- 1559-2324. ; 7:3, s. 400-408
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Tidskriftsartikel (refereegranskat)abstract
- Phytophthora is the most devastating pathogen of dicot plants. There is a need for resistance sources with different modes of action to counteract the fast evolution of this pathogen. In order to better understand mechanisms of defense against P. infestans, we analyzed several clones of potato. Two of the genotypes tested, Sarpo Mira and SW93-1015, exhibited strong resistance against P. infestans in field trials, whole plant assays and detached leaf assays. The resistant genotypes developed different sizes of hypersensitive response (HR)-related lesions. HR lesions in SW93-1015 were restricted to very small areas, whereas those in Sarpo Mira were similar to those in Solanum demissum, the main source of classical resistance genes. SW93-1015 can be characterized as a cpr (constitutive expressor of PR genes) genotype without spontaneous microscopic or macroscopic HR lesions. This is indicated by constitutive hydrogen peroxide (H₂O₂) production and PR1 (pathogenesis-related protein 1) secretion. SW93-1015 is one of the first plants identified as having classical protein-based induced defense expressed constitutively without any obvious metabolic costs or spontaneous cell death lesions.
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| 8. |
- Ali, Ashfaq, et al.
(författare)
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Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions
- 2014
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of P. infestans populations, and a reference compatible cultivar. Results: Quantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets. Conclusions: In summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families.
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| 9. |
- Ali Ahmad, Syed Ossama, et al.
(författare)
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Application of two-dimensional materials in perovskite solar cells: recent progress, challenges, and prospective solutions
- 2021
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Ingår i: Journal of Materials Chemistry C. - : ROYAL SOC CHEMISTRY. - 2050-7526 .- 2050-7534. ; 9:40, s. 14065-14092
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Forskningsöversikt (refereegranskat)abstract
- Perovskite solar cells (per-SCs) with high performance and cost-effective solution processing have been the center of interest for researchers in the past decade. Power conversion efficiencies (PCEs) have been gradually improved up to 25.2% with relatively improved stability, which is an unparalleled progress in all generations of solar cell (SC) technology. However, there are still some prevailing challenges regarding the stability and upscaling of these promising devices. Recently, 2D layered materials (LMs) have been extensively explored to overcome the prevailing challenges of poor stability (under moisture, light soaking and high temperature), halide segregation, hysteresis, involvement of toxic materials (i.e., lead), and upscaling of devices. A critical review addressing the recent developments in the use of 2D materials, especially transition metal dichalcogenides (TMDCs), is hence necessary. The development of novel synthesis and deposition techniques including liquid-metal synthesis and ultrasonic assisted spray pyrolysis has offered more efficient fabrication of 2D-LMs with controlled thickness and morphology. Effective functionalization approaches to increase the dispersability of 2D-LMs in non-polar solvents has boosted their potential application in solar cell technology as well. Moreover, compositing 2D TMDCs with suitable organic/inorganic compounds has enabled superior charge kinetics in all functional parts of per-SCs. In addition, newly developed materials such as graphyne and graphdyine along with 2D metal organic frameworks (MOFs) and covalent organic frameworks (COFs) have been employed in per-SCs to achieve PCEs up to 20%. This review summarizes the recent progress and challenges in the application of 2D-LMs in per-SCs and outlines the future pathways to further extend the PCE of per-SCs beyond 25%. This review particularly focuses on 2D-LMs as electrode materials and additives, the underlying charge (electron-hole) transport phenomenon in the functional layers, and their chemical and structural stability.
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| 10. |
- Ali, Myzoon, et al.
(författare)
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Prevalence, Trajectory, and Predictors of Poststroke Pain: Retrospective Analysis of Pooled Clinical Trial Data Set
- 2023
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Ingår i: Stroke. - 1524-4628. ; 54:12, s. 3107-3116
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Poststroke pain remains underdiagnosed and inadequately managed. To inform the optimum time to initiate interventions, we examined prevalence, trajectory, and participant factors associated with poststroke pain. METHODS: Eligible studies from the VISTA (Virtual International Stroke Trials Archives) included an assessment of pain. Analyses of individual participant data examined demography, pain, mobility, independence, language, anxiety/depression, and vitality. Pain assessments were standardized to the European Quality of Life Scale (European Quality of Life 5 Dimensions 3 Level) pain domain, describing no, moderate, or extreme pain. We described pain prevalence, associations between participant characteristics, and pain using multivariable models. RESULTS: From 94 studies (n>48 000 individual participant data) in VISTA, 10 (n=10 002 individual participant data) included a pain assessment. Median age was 70.0 years (interquartile range [59.0-77.1]), 5560 (55.6%) were male, baseline stroke severity was National Institutes of Health Stroke Scale score 10 (interquartile range [7-15]). Reports of extreme pain ranged between 3% and 9.5% and were highest beyond 2 years poststroke (31/328 [9.5%]); pain trajectory varied by study. Poorer independence was significantly associated with presence of moderate or extreme pain (5 weeks-3 months odds ratio [OR], 1.5 [95% CI, 1.4-1.6]; 4-6 months OR, 1.7 [95% CI, 1.3-2.1]; >6 months OR, 1.5 [95% CI, 1.2-2.0]), and increased severity of pain (5 weeks-3 months: OR, 1.2 [95% CI, 1.1-1.2]; 4-6 months OR, 1.1 [95% CI, 1.1-1.2]; >6 months, OR, 1.2 [95% CI, 1.1-1.2]), after adjusting for covariates. Anxiety/depression and lower vitality were each associated with pain severity. CONCLUSIONS: Between 3% and 9.5% of participants reported extreme poststroke pain; the presence and severity of pain were independently associated with dependence at each time point. Future studies could determine whether and when interventions may reduce the prevalence and severity of poststroke pain.
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