| 1. |
- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Noguchi, S, et al.
(författare)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Tidskriftsartikel (refereegranskat)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 3. |
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| 4. |
- Ramilowski, JA, et al.
(författare)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Tidskriftsartikel (refereegranskat)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 5. |
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| 6. |
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| 7. |
- Melas, P. A., et al.
(författare)
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Allele-specific programming of Npy and epigenetic effects of physical activity in a genetic model of depression
- 2013
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Ingår i: Translational Psychiatry. - : Springer Science and Business Media LLC. - 2158-3188. ; 3, s. e255-
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Tidskriftsartikel (refereegranskat)abstract
- Neuropeptide Y (NPY) has been implicated in depression, emotional processing and stress response. Part of this evidence originates from human single-nucleotide polymorphism (SNP) studies. In the present study, we report that a SNP in the rat Npy promoter (C/T; rs105431668) affects in vitro transcription and DNA-protein interactions. Genotyping studies showed that the C-allele of rs105431668 is present in a genetic rat model of depression (Flinders sensitive line; FSL), while the SNP's T-allele is present in its controls (Flinders resistant line; FRL). In vivo experiments revealed binding of a transcription factor (CREB2) and a histone acetyltransferase (Ep300) only at the SNP locus of the FRL. Accordingly, the FRL had increased hippocampal levels of Npy mRNA and H3K18 acetylation; a gene-activating histone modification maintained by Ep300. Next, based on previous studies showing antidepressant-like effects of physical activity in the FSL, we hypothesized that physical activity may affect Npy's epigenetic status. In line with this assumption, physical activity was associated with increased levels of Npy mRNA and H3K18 acetylation. Physical activity was also associated with reduced mRNA levels of a histone deacetylase (Hdac5). Conclusively, the rat rs105431668 appears to be a functional Npy SNP that may underlie depression-like characteristics. In addition, the achieved epigenetic reprogramming of Npy provides molecular support for the putative effectiveness of physical activity as a non-pharmacological antidepressant.
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| 11. |
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| 14. |
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| 16. |
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| 17. |
- Brodin, N., et al.
(författare)
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Coaching patients with early rheumatoid arthritis to healthy physical activity : A multicenter, randomized, controlled study
- 2008
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Ingår i: Arthritis and Rheumatism. - Hoboken, NJ : Wiley. - 0004-3591 .- 1529-0131. ; 59:3, s. 325-331
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Tidskriftsartikel (refereegranskat)abstract
- Objective. To investigate the effect of a 1-year coaching program for healthy physical activity on perceived health status, body function, and activity limitation in patients with early rheumatoid arthritis. Methods. A total of 228 patients (169 women, 59 men, mean age 55 years, mean time since diagnosis 21 months) were randomized to 2 groups after assessments with the EuroQol visual analog scale (VAS), Grippit, Timed-Stands Test, Escola Paulista de Medicina Range of Motion scale, walking in a figure-of-8, a visual analog scale for pain, the Health Assessment Questionnaire disability index, a self-reported physical activity questionnaire, and the Disease Activity Score in 28 joints. All patients were regularly seen by rheumatologists and underwent rehabilitation as prescribed. Those in the intervention group were further individually coached by a physical therapist to reach or maintain healthy physical activity (=30 minutes, moderately intensive activity, most days of the week). Results. The retention rates after 1 year were 82% in the intervention group and 85% in the control group. The percentages of individuals in the intervention and control groups fulfilling the requirements for healthy physical activity were similar before (47% versus 51%, P > 0.05) and after (54% versus 44%, P > 0.05) the intervention. Analyses of outcome variables indicated improvements in the intervention group over the control group in the EuroQol VAS (P = 0.025) and muscle strength (Timed-Stands Test, P = 0.000) (Grippit, P = 0.003), but not in any other variables assessed. Conclusion. A 1-year coaching program for healthy physical activity resulted in improved perceived health status and muscle strength, but the mechanisms remain unclear, as self-reported physical activity at healthy level did not change. © 2008, American College of Rheumatology.
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| 18. |
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| 20. |
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| 21. |
- Lennartsson, T, et al.
(författare)
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'The Meadow is the Mother of the Field.' Comparing Transformations in Hay Production in Three European Agroecosystems
- 2016
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Ingår i: Martor. - 1224-6271. ; 21, s. 103-126
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Tidskriftsartikel (refereegranskat)abstract
- This research compares the production of hay in three historical European agroecological systems: in northern Romania, central Sweden and eastern central France. We analyse hay production in relation to the entire production system, the local natural conditions, and the variety of ways by which hay production was transformed over time. We found broad commonalities, but also discovered significant differences in each of three historical trajectories. Introduction of fodder crops, crop rotations and mechanization are important drivers of changes in all three areas, although the timing, sequence and causation vary from place to place. There are signifcant differences in the organization of farm labour, in the role of beef and dairy production, the role of political reforms and the climatic constraints of outdoor grazing which affected the transformation of fodder production. This paper highlights the potential of an integrated, interdisciplinary approach for better understanding the complex interaction of people, their social and economic contexts, and their environment.
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| 22. |
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| 23. |
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| 24. |
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| 25. |
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| 26. |
- Theorell, Töres, et al.
(författare)
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Predictors of continued playing or singing - from childhood and adolescence to adult years
- 2015
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Ingår i: Acta Paediatrica. - : Wiley. - 0803-5253 .- 1651-2227. ; 104:3, s. 274-284
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Tidskriftsartikel (refereegranskat)abstract
- Aim: Many individuals play an instrument or sing during childhood, but they often stop later in life. This study surveyed adults representative of the Swedish population about musical activities during childhood.Methods: We asked 3820 adults (65% women) aged from 27 to 54 from the Swedish Twin Registry, who took extra music lessons to those provided at school, to fill in a web-based questionnaire. Factors analysed were the age they started studying music, the instrument they played, kind of teaching, institution and educational content, number of lessons and perceived characteristics of the lessons, the music environment during their childhood years and their preferred music genre. All variables were dichotomised.Results: Factors strongly associated with continued playing or singing were male sex, young starting age, cultural family background, self-selected instrument, attending music classes and more than once a week, church-related or private education, pop, rock or classical music, playing by ear and improvisation.Conclusion: Several significant predictors determined whether a child continued to sing or play an instrument as an adult and many could be externally influenced, such as starting at a young age, taking music classes more than once a week, improvisation and the type of music they played.
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| 27. |
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| 28. |
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| 29. |
- Ullen, A., et al.
(författare)
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Prostate cancer cell lines lack amplification: overexpression of HER2
- 2005
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Ingår i: Acta Oncol. - : Informa UK Limited. - 0284-186X .- 1651-226X. ; 44:5, s. 490-5
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Tidskriftsartikel (refereegranskat)abstract
- The potential overexpression of HER2 in prostate cancer cells has attended significant interest during the past few years, both as potential target for HER2 pathway focused therapy and as a mechanism involved in the progression to androgen independence. Conflicting results have been reported concerning HER2 status on clinical material, differences which generally have been attributed to methodological differences. Nevertheless, HER2 has been utilized for targeted therapy of prostate cancer in a number of preclinical studies and is still regarded as an exciting target molecule. In this study, the HER2 status of three widely used prostate cancer cell lines and corresponding xenografts has been analysed. By use of validated and FDA approved analytical staining techniques none of these cell lines or xenografts were shown to overexpress/amplify HER2, as demonstrated by immunohistochemistry and fluorescence in situ hybridization. These findings are important for the interpretation and understanding of the therapeutic effects when developing drugs targeting HER2 in prostate cancer cell lines and also emphasize the importance of using broad and validated analytical techniques.
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| 30. |
- Varnoosfaderani, FS, et al.
(författare)
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A regulatory role for CHD2 in myelopoiesis
- 2020
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Ingår i: Epigenetics. - : Informa UK Limited. - 1559-2308 .- 1559-2294. ; 15:6-7, s. 702-714
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Tidskriftsartikel (refereegranskat)
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| 31. |
- Agahi, Neda, et al.
(författare)
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Trajectories of social activities from middle age to old age and late-life disability: a 36-year follow-up
- 2013
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Ingår i: Age and Ageing. - : Oxford University Press (OUP). - 0002-0729 .- 1468-2834. ; 42:6, s. 790-793
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: to examine the association between 34-year trajectories of social activity, from middle age to old age and late-life disability.METHODS: data from the Swedish Level of Living Survey (LNU) and the Swedish Panel Study of the Oldest Old (SWEOLD) were used. LNU data from 1968, 1981, 1991 and 2000 were merged with SWEOLD data from 1992, 2002 and 2004 to create a longitudinal data set with five observation periods. Trajectories of social activities covered 1968-2002, and late-life disability was measured in 2004. The sample consisted of 729 individuals aged 33-61 at baseline (1968), who participated in at least four observation periods and who were free from mobility limitations at baseline. Four trajectories of social activity were identified and used as predictors of late-life disability.RESULTS: reporting low/medium levels of social activity from mid-life to old age was the most common trajectory group. Persons reporting continuously low/medium or decreasing levels of social activity had higher odds ratios for late-life disability (OR = 2.33 and OR = 2.15, respectively) compared with those having continuously high levels of activity, even when adjusting for age, sex and mobility limitations, and excluding persons with baseline mobility limitations.CONCLUSIONS: results suggest that the disability risk associated with social activities is related to recent levels of activity, but also that risk may accumulate over time, as indicated by the higher disability risk associated with the continuously low/medium level social activity trajectory.
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| 32. |
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| 33. |
- Bátori, Veronika, et al.
(författare)
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Ethanol and Protein from Ethanol Plant By-Products Using Edible Fungi Neurospora intermedia and Aspergillus oryzae
- 2015
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Ingår i: BioMed Research International. - : Hindawi Limited. - 2314-6133 .- 2314-6141. ; 2015:nov23
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Tidskriftsartikel (refereegranskat)abstract
- Feasible biorefineries for production of second-generation ethanol are difficult to establish due to the process complexity. An alternative is to partially include the process in the first-generation plants. Whole stillage, a by-product from dry-mill ethanol processes from grains, is mostly composed of undegraded bran and lignocelluloses can be used as a potential substrate for production of ethanol and feed proteins. Ethanol production and the proteins from the stillage were investigated using the edible fungi Neurospora intermedia and Aspergillus oryzae, respectively. N. intermedia produced 4.7 g/L ethanol from the stillage and increased to 8.7 g/L by adding 1 FPU of cellulase/g suspended solids. Saccharomyces cerevisiae produced 0.4 and 5.1 g/L ethanol, respectively. Under a two-stage cultivation with both fungi, up to 7.6 g/L of ethanol and 5.8 g/L of biomass containing 42% (w/w) crude protein were obtained. Both fungi degraded complex substrates including arabinan, glucan, mannan, and xylan where reductions of 91, 73, 38, and 89% (w/v) were achieved, respectively. The inclusion of the current process can lead to the production of 44,000 m(3) of ethanol (22% improvement), around 12,000 tons of protein-rich biomass for animal feed, and energy savings considering a typical facility producing 200,000 m(3) ethanol/year.
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| 34. |
- Baumann, I., et al.
(författare)
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Do cognitively stimulating activities affect the association between retirement timing and cognitive functioning in old age?
- 2022
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Ingår i: Ageing & Society. - : Cambridge University Press. - 0144-686X .- 1469-1779. ; 42:2, s. 306-330
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Tidskriftsartikel (refereegranskat)abstract
- In response to the rising financial pressure on old-age pension systems in industrialised economies, many European countries plan to increase the eligibility age for retirement pensions. We used data from Sweden to examine whether (and if so, how) retirement after age 65 - the eligibility age for basic pension - compared to retiring earlier affects older adults' (between ages 70 and 85) cognitive functioning. Using a propensity score matching (PSM) approach, we addressed the selection bias potentially introduced by non-random selection into either early or late retirement. We also examined average and heterogeneous treatment effects (HTEs). HTEs were evaluated for different levels of cognitive stimulation from occupational activities before retirement and from leisure activities after retirement. We drew from a rich longitudinal data-set linking two nationally representative Swedish surveys with a register data-set and found that, on average, individuals who retire after age 65 do not have a higher level of cognitive functioning than those who retire earlier. Similarly, we did not observe HTEs from occupational activities. With respect to leisure activities, we found no systematic effects on cognitive functioning among those working beyond age 65. We conclude that, in general, retirement age does not seem to affect cognitive functioning in old age. Yet, the rising retirement age may put substantial pressure on individuals who suffer from poor health at the end of their occupational career, potentially exacerbating social- and health-related inequalities among older people.
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| 35. |
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| 36. |
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| 37. |
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| 38. |
- Celeste, R. K., et al.
(författare)
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Social Mobility and Tooth Loss : A Systematic Review and Meta-analysis
- 2022
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Ingår i: Journal of Dental Research. - : SAGE Publications. - 0022-0345 .- 1544-0591. ; 101:2, s. 143-150
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Forskningsöversikt (refereegranskat)abstract
- This study systematically reviews the evidence of the association between life course social mobility and tooth loss among middle-aged and older people. PubMed, Scopus, Embase, and Web of Science were systematically searched in addition to gray literature and contact with the authors. Data on tooth loss were collated for a 4-category social mobility variable (persistently high, upward or downward mobility, and persistently low) for studies with data on socioeconomic status (SES) before age 12 y and after age 30 y. Several study characteristics were extracted to investigate heterogeneity in a random effect meta-analysis. A total of 1,384 studies were identified and assessed for eligibility by reading titles and abstracts; 21 original articles were included, of which 18 provided sufficient data for a meta-analysis with 40 analytical data sets from 26 countries. In comparison with individuals with persistently high social mobility, the pooled odds ratios (ORs) for the other categories were as follows: upwardly mobile, OR = 1.73 (95% CI, 1.53 to 1.95); downwardly mobile, OR = 2.52 (95% CI, 2.19 to 2.90); and persistently low, OR = 3.96 (95% CI, 3.13 to 5.03). A high degree of heterogeneity was found(I2 > 78%), and subgroup analysis was performed with 17 study-level characteristics; however, none could explain heterogeneity consistently in these 3 social mobility categories. SES in childhood and adulthood is associated with tooth loss, but the high degree of heterogeneity prevented us from forming a robust conclusion on whether upwardly or downwardly mobile SES may be more detrimental. The large variability in effect size among the studies suggests that contextual factors may play an important role in explaining the difference in the effects of low SES in different life stages (PROSPERO CRD42018092427).
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| 39. |
- Claesson, A., et al.
(författare)
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Unmanned aerial vehicles (drones) in out-of-hospital-cardiac-arrest
- 2016
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Ingår i: Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine. - : BioMed Central (BMC). - 1757-7241. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The use of an automated external defibrillator (AED) prior to EMS arrival can increase 30-day survival in out-of-hospital cardiac arrest (OHCA) significantly. Drones or unmanned aerial vehicles (UAV) can fly with high velocity and potentially transport devices such as AEDs to the site of OHCAs. The aim of this explorative study was to investigate the feasibility of a drone system in decreasing response time and delivering an AED. Methods: Data of Global Positioning System (GPS) coordinates from historical OHCA in Stockholm County was used in a model using a Geographic Information System (GIS) to find suitable placements and visualize response times for the use of an AED equipped drone. Two different geographical models, urban and rural, were calculated using a multi-criteria evaluation (MCE) model. Test-flights with an AED were performed on these locations in rural areas. Results: In total, based on 3,165 retrospective OHCAs in Stockholm County between 2006-2013, twenty locations were identified for the potential placement of a drone. In a GIS-simulated model of urban OHCA, the drone arrived before EMS in 32 % of cases, and the mean amount of time saved was 1.5 min. In rural OHCA the drone arrived before EMS in 93 % of cases with a mean amount of time saved of 19 min. In these rural locations during (n = 13) test flights, latch-release of the AED from low altitude (3-4 m) or landing the drone on flat ground were the safest ways to deliver an AED to the bystander and were superior to parachute release. Discussion: The difference in response time for EMS between urban and rural areas is substantial, as is the possible amount of time saved using this UAV-system. However, yet another technical device needs to fit into the chain of survival. We know nothing of how productive or even counterproductive this system might be in clinical reality. Conclusions: To use drones in rural areas to deliver an AED in OHCA may be safe and feasible. Suitable placement of drone systems can be designed by using GIS models. The use of an AED equipped drone may have the potential to reduce time to defibrillation in OHCA.
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| 40. |
- Classen, Jean-Francois, et al.
(författare)
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Lack of evidence of stimulatory autoantibodies to platelet-derived growth factor receptor in patients with systemic sclerosis
- 2009
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Ingår i: Arthritis and Rheumatism. - : Wiley. - 0004-3591 .- 1529-0131. ; 60:4, s. 1137-1144
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Systemic sclerosis (SSc) is a severe connective tissue disease of unknown etiology, characterized by fibrosis of the skin and multiple internal organs. Recent findings suggested that the disease is driven by stimulatory autoantibodies to platelet-derived growth factor receptor (PDGFR), which stimulate the production of reactive oxygen species (ROS) and collagen by fibroblasts. These results opened novel avenues of research into the diagnosis and treatment of SSc. The present study was undertaken to confirm the presence of anti-PDGFR antibodies in patients with SSc. METHODS: Immunoglobulins from 37 patients with SSc were purified by protein A/G chromatography. PDGFR activation was tested using 4 different sensitive bioassays, i.e., cell proliferation, ROS production, signal transduction, and receptor phosphorylation; the latter was also tested in a separate population of 7 patients with SSc from a different research center. RESULTS: Purified IgG samples from patients with SSc were positive when tested for antinuclear autoantibodies, but did not specifically activate PDGFRalpha or PDGFRbeta in any of the tests. Cell stimulation with PDGF itself consistently produced a strong signal. CONCLUSION: The present results raise questions regarding the existence of agonistic autoantibodies to PDGFR in SSc.
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| 41. |
- Clayton, Zoe E., et al.
(författare)
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Induced pluripotent stem cell-derived endothelial cells promote angiogenesis and accelerate wound closure in a murine excisional wound healing mode
- 2018
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Ingår i: Bioscience Reports. - : PORTLAND PRESS LTD. - 0144-8463 .- 1573-4935. ; 38
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Tidskriftsartikel (refereegranskat)abstract
- Chronic wounds are a major complication in patients with cardiovascular diseases. Cell therapies have shown potential to stimulate wound healing, but clinical trials using adult stem cells have been tempered by limited numbers of cells and invasive procurement procedures. Induced pluripotent stem cells (iPSCs) have several advantages of other cell types, for example they can be generated in abundance from patients somatic cells (autologous) or those from a matched donor. iPSCs can be efficiently differentiated to functional endothelial cells (iPSC-ECs). Here, we used a murine excisional wound model to test the pro-angiogenic properties of iPSC-ECs in wound healing. Two full-thickness wounds were made on the dorsum of NOD-SCID mice and splinted. iPSC-ECs (5 x 10(5)) were topically applied to one wound, with the other serving as a control. Treatment with iPSC-ECs significantly increased wound perfusion and accelerated wound closure. Expression of endothelial cell (EC) surface marker, platelet endothelial cell adhesion molecule (PECAM-1) (CD31), and pro-angiogenic EC receptor, Tie1, mRNA was up-regulated in iPSC-EC treated wounds at 7 days post-wounding. Histological analysis of wound sections showed increased capillary density in iPSC-EC wounds at days 7 and 14 post-wounding, and increased collagen content at day 14. Anti-GFP fluorescence confirmed presence of iPSC-ECs in the wounds. Bioluminescent imaging (BLI) showed progressive decline of iPSC-ECs over time, suggesting that iPSC-ECs are acting primarily through short-term paracrine effects. These results highlight the pro-regenerative effects of iPSC-ECs and demonstrate that they are a promising potential therapy for intractable wounds.
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| 42. |
- Dong, WB, et al.
(författare)
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Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin
- 2020
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 6055-
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Tidskriftsartikel (refereegranskat)abstract
- Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.
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| 43. |
- Dong, WB, et al.
(författare)
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The Role of Non-Catalytic Domains of Hrp3 in Nucleosome Remodeling
- 2021
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Ingår i: International journal of molecular sciences. - : MDPI AG. - 1422-0067. ; 22:4
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Tidskriftsartikel (refereegranskat)abstract
- The Helicase-related protein 3 (Hrp3), an ATP-dependent chromatin remodeling enzyme from the CHD family, is crucial for maintaining global nucleosome occupancy in Schizosaccharomyces pombe (S. pombe). Although the ATPase domain of Hrp3 is essential for chromatin remodeling, the contribution of non-ATPase domains of Hrp3 is still unclear. Here, we investigated the role of non-ATPase domains using in vitro methods. In our study, we expressed and purified recombinant S. pombe histone proteins, reconstituted them into histone octamers, and assembled nucleosome core particles. Using reconstituted nucleosomes and affinity-purified wild type and mutant Hrp3 from S. pombe we created a homogeneous in vitro system to evaluate the ATP hydrolyzing capacity of truncated Hrp3 proteins. We found that all non-ATPase domain deletions (∆chromo, ∆SANT, ∆SLIDE, and ∆coupling region) lead to reduced ATP hydrolyzing activities in vitro with DNA or nucleosome substrates. Only the coupling region deletion showed moderate stimulation of ATPase activity with the nucleosome. Interestingly, affinity-purified Hrp3 showed co-purification with all core histones suggesting a strong association with the nucleosomes in vivo. However, affinity-purified Hrp3 mutant with SANT and coupling regions deletion showed complete loss of interactions with the nucleosomes, while SLIDE and chromodomain deletions reduced Hrp3 interactions with the nucleosomes. Taken together, nucleosome association and ATPase stimulation by DNA or nucleosomes substrate suggest that the enzymatic activity of Hrp3 is fine-tuned by unique contributions of all four non-catalytic domains.
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| 44. |
- Fazelinejad, Somayeh, et al.
(författare)
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Fungal biomass and ethanol from lignocelluloses using Rhizopus pellets under simultaneous saccharification, filtration, and fermentation (SSFF)
- 2016
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Ingår i: Biofuel Research Journal. - 2292-8782. ; 9, s. 372-378
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Tidskriftsartikel (refereegranskat)abstract
- The economic viability of the 2nd generation bioethanol production process cannot rely on a single product but on a biorefinery built around it. In this work, ethanol and fungal biomass (animal feed) were produced from acid-pretreated wheat straw slurry under an innovative simultaneous saccharification, fermentation, and filtration (SSFF) strategy. A membrane unit separated the solids from the liquid and the latter was converted to biomass or to both biomassand ethanol in the fermentation reactor containing Rhizopus sp. pellets. Biomass yields of up to 0.34 g/g based on the consumed monomeric sugars and acetic acid were achieved. A surplus of glucose in the feed resulted in ethanol production and reduced the biomass yield, whereas limiting glucose concentrations resulted in higher consumption of xylose and acetic acid. The specific growth rate, in the range of 0.013-0.015/h, did not appear to be influenced by the composition of the carbon source. Under anaerobic conditions, an ethanol yield of 0.40 g/g was obtained. The present strategy benefits fromthe easier separation of the biomass from the medium and the fungus ability to assimilate carbon residuals in comparison with when yeast is used. More specifically, it allows in-situ separation of insoluble solids leading to the production of pure fungal biomass as a value-added product. (C) 2016 BRTeam. All rights reserved.
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| 45. |
- Ferreira, Jorge A., et al.
(författare)
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Airlift bioreactors for fish feed fungal biomass production using edible filamentous fungi
- 2017
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Konferensbidrag (refereegranskat)abstract
- Airlift bioreactors are generally considered to be better alternatives for cultivation of filamentous fungi in comparison to stirred-tank bioreactors or bubble columns bioreactors. The reason for the former includes fungal growth around all internal parts including impellers, baffles or pH, temperature and oxygen probes limiting mass transfer, whereas the latter is limited by air flow rates that can be applied before the system provides deficient mixing and so mass transfer rates. Spent sulphite liquor, a by-product from the paper pulp industry, was used for cultivation of edible Rhizopus sp., a strain isolated from Indonesian tempeh used as human food, using a 26 L airlift bioreactor. Increasing the aeration rate from 0.15 to 1 vvm led to increased biomass production (1 vs 7 g/L). The aeration rate was also found to influence fungal morphology and metabolite production during batch cultivation. Rhizopus sp. shifted from mycelial suspensions at 0.15 and 0.5 vvm to small compact pellets of regular size at 1 vvm. The production of ethanol and lactic acid, a proof of sub-optimal aeration conditions, was also reduced when increasing the aeration rate from 0.15 to 1 vvm. The produced biomass was found to be composed, on a dry weight basis, of 30-50% protein, 2-7% lipids, and 3-9% glucosamine. Considering the edible character of the fungus used as well as its biomass nutritional characteristics, there is a potential for its use as fishmeal replacement within the increasing aquaculture sector.
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| 46. |
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| 47. |
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| 48. |
- Ferreira, Jorge A, et al.
(författare)
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Production of ethanol and biomass from thin stillage by Neurospora intermedia : A pilot study for process diversification
- 2015
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Ingår i: Engineering in Life Sciences. - : Wiley-VCH Verlagsgesellschaft. - 1618-0240 .- 1618-2863. ; 15:8, s. 751-759
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Tidskriftsartikel (refereegranskat)abstract
- Dry mill ethanol processes produce ethanol and animal feed from whole grains,where the wastewater after the distillation and separation of solid materials is called“thin stillage.” In this work, similar production of ethanol (3.5 g/L) and biomass(5 g/L) from thin stillage was obtained during batch cultivation of the edible fungusNeurospora intermedia in a 2-m high airlift reactor and bubble column. The fungalbiomass, containing 50% w/w protein and 12% w/w lipids, was rich in essentialamino acids and omega-3 and -6 fatty acids. In a continuousmode of fermentation,dilution rates of up to 0.2 h−1 could be applied without cell washout in the bubblecolumn at 0.5 vvm. At 0.1 h−1, around 5 g/L of ethanol and 4 g/L of biomasscontaining ca. 50% w/w protein were produced. The fungus was able to assimilatesaccharides in the liquid fraction as well as sugar backbones such as xylan andarabinan in the solid fraction. The inclusion of the current process could potentiallylead to the production of 11 000 m3 of ethanol (5.5% improvement vs. normalindustrial process) and around 6300 tons of high-quality biomass for animal feed ata typical facility producing 200 000 m3 ethanol per year.
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| 49. |
- Ferreira, Jorge A., et al.
(författare)
-
Production of Ethanol and Biomass from Thin Stillage Using Food-Grade Zygomycetes and Ascomycetes Filamentous Fungi
- 2014
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Ingår i: Energies. - : MDPI. - 1996-1073. ; 7:6, s. 3872-3885
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Tidskriftsartikel (refereegranskat)abstract
- A starch-based ethanol facility producing 200,000 m3 ethanol/year also produces ca. 2 million m3 thin stillage, which can be used to improve the entire process. In this work, five food-grade filamentous fungi, including a Zygomycete and four Ascomycetes were successfully grown in thin stillage containing 9% solids. Cultivation with Neurospora intermedia led to the production of ca. 16 g·L−1 biomass containing 56% (w/w) crude protein, a reduction of 34% of the total solids, and 5 g·L−1 additional ethanol. In an industrial ethanol production process (200,000 m3 ethanol/year), this can potentially lead to the production of 11,000 m3 extra ethanol per year. Cultivation with Aspergillus oryzae resulted in 19 g·L−1 biomass containing 48% (w/w) crude protein and the highest reduction of the thin stillage glycerol (54%) among the Ascomycetes. Cultivation with Rhizopus sp. produced up to 15 g·L−1 biomass containing 55% (w/w) crude protein. The spent thin stillage had been reduced up to 85%, 68% and 21% regarding lactic acid, glycerol and total solids, respectively. Therefore, N. intermedia, in particular, has a high potential to improve the ethanol process via production of additional ethanol and high-quality biomass, which can be considered for animal feed applications such as for fish feed.
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| 50. |
- Ferreira, Jorge A., et al.
(författare)
-
Spent sulphite liquor for cultivation of an edible Rhizopus sp.
- 2012
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Ingår i: BioResources. - : North Carolina State University: College of Natural Resources. - 1930-2126. ; 7:1, s. 173-188
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Tidskriftsartikel (refereegranskat)abstract
- Spent sulphite liquor, the major byproduct from the sulphite pulp production process, was diluted to 50% and used for production of an edible zygomycete Rhizopus sp. The focus was on production, yield, and composition of the fungal biomass composition. The fungus grew well at 20 to 40°C, but 32°C was found to be preferable compared to 20 and 40°C in terms of biomass production and yield (maximum of 0.16 g/g sugars), protein content (0.50-0.60 g/g), alkali-insoluble material (AIM) (ca 0.15 g/g), and glucosamine content (up to 0.30 g/g of AIM). During cultivation in a pilot airlift bioreactor, the yield increased as aeration was raised from 0.15 to 1.0 vvm, indicating a high demand for oxygen. After cultivation at 1.0 vvm for 84 h, high yield and production of biomass (up to 0.34 g/g sugars), protein (0.30-0.50 g/g), lipids (0.02-0.07 g/g), AIM (0.16-0.28 g/g), and glucosamine (0.22-0.32 g/g AIM) were obtained. The fungal biomass produced from spent sulphite liquor is presently being tested as a replacement for fishmeal in feed for fish aquaculture and seems to be a potential source of nutrients and for production of glucosamine.
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