| 1. |
- Andersson, Erika, et al.
(author)
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Generation and properties of organic colloids extracted by water from the organic horizon of a boreal forest soil
- 2023
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In: Geoderma. - : Elsevier BV. - 0016-7061. ; 432
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Journal article (peer-reviewed)abstract
- Organic colloids are an important part of dissolved organic matter (DOM) yet many of their properties remain elusive. The main aims of this study were to assess how the colloidal properties of DOM extracted with water from an organic boreal soil horizon varied with the extraction protocol, and thereby provide insight into the nature of the DOM colloids and develop a mechanistic understanding of how the colloids were generated from the parent soil aggregates. This was accomplished by systematic variations of extraction temperature (4 °C–100 °C), time, mechanical agitation, and pH, together with a combination of chemical analyses, and light and X-ray scattering. Our results agreed with the previous identification of two main colloidal DOM species, one fractal cluster and a second, smaller colloidal DOM species described as chains or coils. Fractal clusters completely dominated the colloidal DOM in extracts from our soil at room temperature and below. Colloidal coils only existed in DOM extracted above room temperature, and their amount increased significantly between 50 °C–100 °C. Moreover, the temperature variation indicated that the fractal clusters partly dissolved into colloidal coils at elevated temperatures. Mechanical agitation at 4 °C significantly increased the amount of DOM extracted, increasing the concentrations of both fractal clusters and low-molecular weight organic compounds. While the clusters were extracted from agitated and non-agitated soil suspensions, the low molecular weight organics were mainly released by agitation. Based on the experimental observations, we propose a conceptual model where parent soil aggregates contain the fractal clusters in mobile and occluded forms, and that the occluded clusters co-exist with occluded low molecular weight organics. These occluded forms may be released by mechanical forces, increasing pH and temperature. At higher temperatures, the soil aggregates and the fractal clusters start to break up, and subsequently individual colloidal coils, presumably carbohydrates, disperse in the water phase. The model explains the origin and properties of the fractal clusters that completely dominate the colloidal DOM extracted from our soil at room temperature and below.
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| 2. |
- Berger, Karin, et al.
(author)
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Xylooligosaccharides Increase Bifidobacteria and Lachnospiraceae in Mice on a High-Fat Diet, with a Concomitant Increase in Short-Chain Fatty Acids, Especially Butyric Acid
- 2021
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In: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 69:12, s. 3617-3625
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Journal article (peer-reviewed)abstract
- Effects of xylooligosaccharides (XOSs) as well as a mixture of XOS, inulin, oligofructose, and partially hydrolyzed guar gum (MIX) in mice fed a high-fat diet (HFD) were studied. Control groups were fed an HFD or a low-fat diet. Special attention was paid to the cecal composition of the gut microbiota and formation of short-chain fatty acids, but metabolic parameters were also documented. The XOS group had significantly higher cecum levels of acetic, propionic, and butyric acids than the HFD group, and the butyric acid content was higher in the XOS than in the MIX group. The cecum microbiota of the XOS group contained more Bifidobacteria, Lachnospiraceae, and S24-7 bacteria than the HFD group. A tendency of lower body weight gain was observed on comparing the XOS and HFD groups. In conclusion, the XOS was shown to be a promising prebiotic candidate. The fiber diversity in the MIX diet did not provide any advantages compared to the XOS diet.
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| 3. |
- Bhattacharya, Abhishek, et al.
(author)
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Cross-Feeding and Enzymatic Catabolism for Mannan-Oligosaccharide Utilization by the Butyrate-Producing Gut Bacterium Roseburia hominis A2-183
- 2022
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In: Microorganisms. - : MDPI AG. - 2076-2607. ; 10:12
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Journal article (peer-reviewed)abstract
- β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated the cross-feeding and metabolic interactions between Bifidobacterium adolescentis ATCC 15703, an acetate producer, and Roseburia hominis A2-183 DSMZ 16839, a butyrate producer, during utilization of MOS/GMOSs. Cocultivation studies suggest that both strains coexist due to differential MOS/GMOS utilization, along with the cross-feeding of acetate from B. adolescentis E194a to R. hominis A2-183. The data suggest that R. hominis A2-183 efficiently utilizes MOS/GMOS in mono- and cocultivation. Notably, we observed the transcriptional upregulation of certain genes within a dedicated MOS/GMOS utilization locus (RhMosUL), and an exo-oligomannosidase (RhMan113A) gene located distally in the R. hominis A2-183 genome. Significantly, biochemical analysis of β-1,4 mannan-oligosaccharide phosphorylase (RhMOP130A), α-galactosidase (RhGal36A), and exo-oligomannosidase (RhMan113A) suggested their potential synergistic role in the initial utilization of MOS/GMOSs. Thus, our results enhance the understanding of MOS/GMOS utilization by potential health-promoting human gut microbiota and highlight the role of cross-feeding and metabolic interactions between two secondary mannan degraders inhabiting the same ecological niche in the gut.
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| 4. |
- Bhattacharya, Abhishek, et al.
(author)
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Enzymatic Conversion of Different Qualities of Refined Softwood Hemicellulose Recovered from Spent Sulfite Liquor
- 2022
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In: Molecules (Basel, Switzerland). - : MDPI AG. - 1420-3049. ; 27:10
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Journal article (peer-reviewed)abstract
- Spent sulfite liquor (SSL) from softwood processing is rich in hemicellulose (acetyl galactoglucomannan, AcGGM), lignin, and lignin-derived compounds. We investigated the effect of sequential AcGGM purification on the enzymatic bioconversion of AcGGM. SSL was processed through three consecutive purification steps (membrane filtration, precipitation, and adsorption) to obtain AcGGM with increasing purity. Significant reduction (~99%) in lignin content and modest loss (~18%) of polysaccharides was observed during purification from the least pure preparation (UFR), obtained by membrane filtration, compared to the purest preparation (AD), obtained by adsorption. AcGGM (~14.5 kDa) was the major polysaccharide in the preparations; its enzymatic hydrolysis was assessed by reducing sugar and high-performance anion-exchange chromatography analysis. The hydrolysis of the UFR preparation with Viscozyme L or Trichoderma reesei β-mannanase TrMan5A (1 mg/mL) resulted in less than ~50% bioconversion of AcGGM. The AcGGM in the AD preparation was hydrolyzed to a higher degree (~67% with TrMan5A and 80% with Viscozyme L) and showed the highest conversion rate. This indicates that SSL contains enzyme-inhibitory compounds (e.g., lignin and lignin-derived compounds such as lignosulfonates) which were successfully removed.
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| 5. |
- Bhattacharya, Abhishek, et al.
(author)
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Enzyme synergy for the production of arabinoxylo-oligosaccharides from highly substituted arabinoxylan and evaluation of their prebiotic potential
- 2020
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In: Lebensmittel-Wissenschaft + Technologie. - : Elsevier BV. - 0023-6438 .- 1096-1127. ; 131
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Journal article (peer-reviewed)abstract
- Wheat bran arabinoxylan can be converted by enzymatic hydrolysis into short arabinoxylo-oligosaccharides (AXOS) with prebiotic potential. Alkali extraction of arabinoxylan from wheat-bran offers advantages in terms of yield and results in arabinoxylan with highly-substituted regions which has been a challenge to hydrolyse using endoxylanases. We show that this hurdle can be overcome by selecting an arabinoxylanase that attacks these regions. The yield of AXOS can be increased by enzyme synergy, involving the hydrolysis of some arabinoxylan side groups. Thus, arabinoxylanase (CtXyl5At) from Clostridium thermocellum, belonging to subfamily 34 of glycoside hydrolase (GH) family 5 was investigated pertaining to its specificity for highly-substituted regions in the arabinoxylan-backbone. CtXyl5At preferentially hydrolysed the water-soluble fraction of alkali-extracted arabinoxylan. AXOS with DP 2-4 were determined as major products from CtXyl5At catalyzed hydrolysis. Increase in AXOS yield was observed with enzyme synergy, involving an initial treatment of soluble arabinoxylan with a GH43 alpha-L-arabinofuranosidase from Bifidobacterium adolescentis termed BaAXHd3 (30 degrees C, 6h), followed by hydrolysis with CtXyl5At (50 degrees C, 24h). The prebiotic potential of AXOS was shown by growth analysis using the human gut bacteria Bifidobacterium adolescentis ATCC 15703 and Roseburia hominis DSM 6839. Importantly, AXOS were utilized by the bacteria and short-chain fatty acids were produced.
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| 6. |
- Bhattacharya, Arani, et al.
(author)
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Fast and Efficient Online Selection of Sensors for Transmitter Localization
- 2022
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In: 2022 14th International Conference on COMmunication Systems and NETworkS, COMSNETS 2022. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 604-612
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Conference paper (peer-reviewed)abstract
- The increase in cost and usage of RF spectrum has made it increasingly necessary to monitor its usage and protect it from unauthorized use. A number of prior studies have designed algorithms to localize unauthorized transmitters using crowdsourced sensors. To reduce the cost of crowdsourcing, these studies select the most relevant sensors a priori to localize such transmitters. In this work, we instead argue for online selection to localize such transmitters. Online selection can lead to more accurate localization using limited number of sensors, as compared to selecting sensors a priori, albeit at the cost of higher latency. To account for the trade-off between accuracy and latency, we add a constraint on the number of selection rounds. For the case where the number of rounds is equal to the number of selected sensors, we propose a heuristic based on Thompson Sampling and show using trace-driven simulation that it provides 23 % better accuracy compared to a number of proposed baseline algorithms. For restricted number of rounds, we show that using conventional parallel version of the modified Thompson Sampling which selects equal number of sensors in each round results in a substantial reduction in accuracy. To this end, we propose a strategy of selecting decreasing number of sensors in subsequent rounds of the modified Parallel Thompson Sampling. Our evaluation shows that the proposed heuristic leads to only 3 % reduction in accuracy in contrast to 22 % using modified Parallel Thompson Sampling, when we select 50 sensors in 20 rounds.
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| 7. |
- Bhattacharya, Abhishek, et al.
(author)
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β-Mannanase BoMan26B from Bacteroides ovatus produces mannan-oligosaccharides with prebiotic potential from galactomannan and softwood β-mannans
- 2021
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In: LWT. - : Elsevier BV. - 0023-6438. ; 151
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Journal article (peer-reviewed)abstract
- Galactomannan (GM) in legumes and acetyl-galactoglucomannan (AcGGM) in softwoods are wide-spread β-mannans. Their depolymerisation is catalyzed by β-mannanases. We have investigated a cell-surface exposed and galactose-tolerant β-mannanase (BoMan26B) from the abundant gut bacterium Bacteroides ovatus. Glycosidases from the gut microbiota have potential for production of prebiotics, such as dietary saccharides that would promote beneficial bacteria in the gut. BoMan26B was explored for production of potential prebiotics. Using the above β-mannans as substrate we investigated the product profiles using a herein developed new high-resolution anion-exchange chromatography procedure. The produced linear and galactosyl-decorated β-mannan-oligosaccharides (MOS/GMOS) were mainly of degree of polymerization (DP) 2–6, consistent with the glycan-binding subsites of BoMan26B. Some GM and AcGGM products were acetylated. DP 2–6 MOS were produced at a yield of 30 and 33% (w/w) from GM and AcGGM, respectively. In addition, about as much DP 2–6 GMOS were produced, assessed using guar α-galactosidase as analytical aid. Growth studies using the human gut bacteria Bifidobacterium adolescentis ATCC 15703 (acetate producer) and Roseburia hominis DSMZ 6839 (butyrate producer) revealed significant differences in utilization of specific MOS/GMOS. The prebiotic potential of the MOS/GMOS generated by BoMan26B was further underlined by the observation that both bacterial strains produced short-chain fatty acids.
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| 8. |
- Bhattacharya, Romit, et al.
(author)
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Clonal Hematopoiesis Is Associated with Higher Risk of Stroke
- 2022
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In: Stroke. - 0039-2499. ; 29:2, s. 788-797
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Journal article (peer-reviewed)abstract
- Background and Purpose: Clonal hematopoiesis of indeterminate potential (CHIP) is a novel age-related risk factor for cardiovascular disease-related morbidity and mortality. The association of CHIP with risk of incident ischemic stroke was reported previously in an exploratory analysis including a small number of incident stroke cases without replication and lack of stroke subphenotyping. The purpose of this study was to discover whether CHIP is a risk factor for ischemic or hemorrhagic stroke. Methods: We utilized plasma genome sequence data of blood DNA to identify CHIP in 78 752 individuals from 8 prospective cohorts and biobanks. We then assessed the association of CHIP and commonly mutated individual CHIP driver genes (DNMT3A, TET2, and ASXL1) with any stroke, ischemic stroke, and hemorrhagic stroke. Results: CHIP was associated with an increased risk of total stroke (hazard ratio, 1.14 [95% CI, 1.03-1.27]; P=0.01) after adjustment for age, sex, and race. We observed associations with CHIP with risk of hemorrhagic stroke (hazard ratio, 1.24 [95% CI, 1.01-1.51]; P=0.04) and with small vessel ischemic stroke subtypes. In gene-specific association results, TET2 showed the strongest association with total stroke and ischemic stroke, whereas DMNT3A and TET2 were each associated with increased risk of hemorrhagic stroke. Conclusions: CHIP is associated with an increased risk of stroke, particularly with hemorrhagic and small vessel ischemic stroke. Future studies clarifying the relationship between CHIP and subtypes of stroke are needed.
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| 9. |
- Bhattacharya, Romit, et al.
(author)
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Risk factors for clonal hematopoiesis of indeterminate potential in people with HIV : a report from the REPRIEVE trial
- 2024
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In: Blood Advances. - 2473-9529. ; 8:4, s. 959-967
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Journal article (peer-reviewed)abstract
- Clonal hematopoiesis of indeterminate potential (CHIP), the clonal expansion of myeloid cells with leukemogenic mutations, results in increased coronary artery disease (CAD) risk. CHIP is more prevalent among people with HIV (PWH), but the risk factors are unknown. CHIP was identified among PWH in REPRIEVE (Randomized Trial to Prevent Vascular Events in HIV) using whole-exome sequencing. Logistic regression was used to associate sociodemographic factors and HIV-specific factors with CHIP adjusting for age, sex, and smoking status. In the studied global cohort of 4486 PWH, mean age was 49.9 (standard deviation [SD], 6.4) years; 1650 (36.8%) were female; and 3418 (76.2%) were non-White. CHIP was identified in 223 of 4486 (4.97%) and in 38 of 373 (10.2%) among those aged ≥60 years. Age (odds ratio [OR], 1.07; 95% confidence interval [CI], 1.05-1.09; P < .0001) and smoking (OR, 1.37; 95% CI, 1.14-1.66; P < .001) associated with increased odds of CHIP. Globally, participants outside of North America had lower odds of CHIP including sub- Saharan Africa (OR, 0.57; 95% CI, 0.4-0.81; P = .0019), South Asia (OR, 0.45; 95% CI, 0.23-0.80; P = .01), and Latin America/Caribbean (OR, 0.56; 95% CI, 0.34-0.87; P = .014). Hispanic/Latino ethnicity (OR, 0.38; 95% CI, 0.23-0.54; P = .002) associated with significantly lower odds of CHIP. Among HIV-specific factors, CD4 nadir <50 cells/mm3 associated with a 1.9-fold (95% CI, 1.21-3.05; P = .006) increased odds of CHIP, with the effect being significantly stronger among individuals with short duration of antiretroviral therapy (ART; OR, 4.15; 95% CI, 1.51-11.1; P = .005) (Pinteraction= .0492). Among PWH at low-to-moderate CAD risk on stable ART, smoking, CD4 nadir, North American origin, and non-Hispanic ethnicity associated with increased odds of CHIP.
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| 10. |
- Bågenholm, Viktoria, et al.
(author)
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A surface-exposed GH26 -mannanase from Bacteroides ovatus : Structure, role, and phylogenetic analysis of BoMan26B
- 2019
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In: Journal of Biological Chemistry. - 0021-9258. ; 294:23, s. 9100-9117
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Journal article (peer-reviewed)abstract
- The galactomannan utilization locus (BoManPUL) of the human gut bacterium Bacteroides ovatus encodes BoMan26B, a cell-surface– exposed endomannanase whose functional and structural features have been unclear. Our study now places BoMan26B in context with related enzymes and reveals the structural basis for its specificity. BoMan26B prefers longer substrates and is less restricted by galactose side-groups than the mannanase BoMan26A of the same locus. Using galactomannan, BoMan26B generated a mixture of (galactosyl) manno-oligosaccharides shorter than mannohexaose. Three defined manno-oligosaccharides had affinity for the SusD-like surface–exposed glycan-binding protein, predicted to be implicated in saccharide transport. Co-incubation of BoMan26B and the periplasmic -galactosidase BoGal36A increased the rate of galactose release by about 10-fold compared with the rate without BoMan26B. The results suggested that BoMan26B performs the initial attack on galactomannan, generating oligosaccharides that after transport to the periplasm are processed by BoGal36A. A crystal structure of BoMan26B with galactosyl-mannotetraose bound in subsites 5 to 2 revealed an open and long active-site cleft with Trp-112 in subsite 5 concluded to be involved in mannosyl interaction. Moreover, Lys-149 in the 4 subsite interacted with the galactosyl side-group of the ligand. A phylogenetic tree consisting of GH26 enzymes revealed four strictly conserved GH26 residues and disclosed that BoMan26A and BoMan26B reside on two distinct phylogenetic branches (A and B). The three other branches contain lichenases, xylanases, or enzymes with unknown activities. Lys-149 is conserved in a narrow part of branch B, and Trp-112 is conserved in a wider group within branch B.
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