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Challenging the Hypothesis of de novo Biosynthesis of Bile Acids by Marine Bacteria
Tueros Felipe Gonzalo,Ellabaan Mostafa M. Hashim,Henricsson Marcus,Vazquez-Uribe Ruben,Bäckhed Fredrik,Sommer Morten Otto Alexander 한국미생물·생명공학회 2022 한국미생물·생명공학회지 Vol.50 No.1
Bile acids are essential molecules produced by vertebrates that are involved in several physiological roles, including the uptake of nutrients. Bacterial isolates capable of producing bile acids de novo have been identified and characterized. Such isolates may provide access to novel biochemical pathways suitable for the design of microbial cell factories. Here, we further characterized the ability of Maribacter dokdonensis, Dokdonia donghaensis, and Myroides pelagicus to produce bile acids. Contrary to previous reports, we did not observe de novo production of bile acids by these isolates. Instead, we found that these isolates deconjugated the amino acid moiety of bile acids present in the growth medium used in previous reports. Through genomic analysis, we identified putative bile salt hydrolases, which could be responsible for the different bile acid modifications observed. Our results challenge the hypothesis of de novo microbial bile acid production, while further demonstrating the diverse capacity of bacteria to modify bile acids.
Validation and Recommendation of Methods to Measure Biogas Production Potential of Animal Manure
Pham, C.H.,Triolo, J.M.,Cu, T.T.T.,Pedersen, L.,Sommer, S.G. Asian Australasian Association of Animal Productio 2013 Animal Bioscience Vol.26 No.6
In developing countries, biogas energy production is seen as a technology that can provide clean energy in poor regions and reduce pollution caused by animal manure. Laboratories in these countries have little access to advanced gas measuring equipment, which may limit research aimed at improving local adapted biogas production. They may also be unable to produce valid estimates of an international standard that can be used for articles published in international peer-reviewed science journals. This study tested and validated methods for measuring total biogas and methane ($CH_4$) production using batch fermentation and for characterizing the biomass. The biochemical methane potential (BMP) ($CH_4$ NL $kg^{-1}$ VS) of pig manure, cow manure and cellulose determined with the Moller and VDI methods was not significantly different in this test (p>0.05). The biodegradability using a ratio of BMP and theoretical BMP (TBMP) was slightly higher using the Hansen method, but differences were not significant. Degradation rate assessed by methane formation rate showed wide variation within the batch method tested. The first-order kinetics constant k for the cumulative methane production curve was highest when two animal manures were fermented using the VDI 4630 method, indicating that this method was able to reach steady conditions in a shorter time, reducing fermentation duration. In precision tests, the repeatability of the relative standard deviation (RSDr) for all batch methods was very low (4.8 to 8.1%), while the reproducibility of the relative standard deviation (RSDR) varied widely, from 7.3 to 19.8%. In determination of biomethane concentration, the values obtained using the liquid replacement method (LRM) were comparable to those obtained using gas chromatography (GC). This indicates that the LRM method could be used to determine biomethane concentration in biogas in laboratories with limited access to GC.
Alexander Kretschmer,Alexander Buchner,Benedikt Leitl,Markus Grabbert,Anne Sommer,Wael Khoder,Christian Gozzi,Christian G. Stief,Ricarda M. Bauer 대한배뇨장애요실금학회 2016 International Neurourology Journal Vol.20 No.4
Purpose: To evaluate long-term outcomes of AdVance and AdVanceXP male slings in patients with persistent stress urinary incontinence (SUI) after transurethral resection of the prostate (TURP). Methods: A total of 18 consecutive patients received AdVance (n=14) or AdVanceXP (n=4) male sling implantation between 2007 and 2013. Continence was determined by pad use, 24-hour pad testing and validated questionnaires (International Consultation on Incontinence Questionnaire Short Form, ICIQ-SF). Quality of life was evaluated by International Quality of Life (IQoL) score. Patient satisfaction was measured with patient’s global impression of improvement score. Cure was defined as 0–5 g in the 24-hour pad test. Statistical analysis included Fisher exact and Wilcoxon test (P<0.05). Results: Follow-up was available for 15 patients who underwent further analysis. After a median follow-up of 70 months (range, 18–83 months), mean daily pad usage was 1.8±2.1 pads (P=0.015 vs. baseline level). Mean IQoL score was 66.4±31.6 (P=0.050 vs. baseline level), and mean ICIQ-SF score was 9.5±6.6 (P=0.077 vs. baseline level). Based on 24-hour pad testing, mean daily urine loss was 31.2±64.5 g (median, 0 g; range, 0–209 g). Cure rate was 46.7%, and cure-and-improved rate was 60.0%. Assessing predictive features for success, better results were found in patients who needed up to 4 pads preoperatively (P=0.041) as well as for patients ≤71 years at the time of implantation (P=0.041). Conclusions: The findings indicate that AdVance and AdVanceXP implantation can be performed effectively and safely in men suffering from SUI after TURP. However, long-term success rates seem to be lower compared to SUI after radical prostatectomy and patients should be counseled accordingly.
T.T.T. Cu,T.X. Nguyen,J.M. Triolo,L. Pedersen,V.D. Le,P.D. Le,S.G. Sommer 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.2
Anaerobic digestion is an efficient and renewable energy technology that can produce biogas from a variety of biomasses such as animal manure, food waste and plant residues. In developing countries this technology is widely used for the production of biogas using local biomasses, but there is little information about the value of these biomasses for energy production. This study was therefore carried out with the objective of estimating the biogas production potential of typical Vietnamese biomasses such as animal manure, slaughterhouse waste and plant residues, and developing a model that relates methane (CH4) production to the chemical characteristics of the biomass. The biochemical methane potential (BMP) and biomass characteristics were measured. Results showed that piglet manure produced the highest CH4 yield of 443 normal litter (NL) CH4 kg–1 volatile solids (VS) compared to 222 from cows, 177 from sows, 172 from rabbits, 169 from goats and 153 from buffaloes. Methane production from duckweed (Spirodela polyrrhiza) was higher than from lawn grass and water spinach at 340, 220, and 110.6 NL CH4 kg–1 VS, respectively. The BMP experiment also demonstrated that the CH4 production was inhibited with chicken manure, slaughterhouse waste, cassava residue and shoe-making waste. Statistical analysis showed that lipid and lignin are the most significant predictors of BMP. The model was developed from knowledge that the BMP was related to biomass content of lipid, lignin and protein from manure and plant residues as a percentage of VS with coefficient of determination (R-square) at 0.95.This model was applied to calculate the CH4 yield for a household with 17 fattening pigs in the highlands and lowlands of northern Vietnam.
Cu, T.T.T.,Nguyen, T.X.,Triolo, J.M.,Pedersen, L.,Le, V.D.,Le, P.D.,Sommer, S.G. Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.2
Anaerobic digestion is an efficient and renewable energy technology that can produce biogas from a variety of biomasses such as animal manure, food waste and plant residues. In developing countries this technology is widely used for the production of biogas using local biomasses, but there is little information about the value of these biomasses for energy production. This study was therefore carried out with the objective of estimating the biogas production potential of typical Vietnamese biomasses such as animal manure, slaughterhouse waste and plant residues, and developing a model that relates methane ($CH_4$) production to the chemical characteristics of the biomass. The biochemical methane potential (BMP) and biomass characteristics were measured. Results showed that piglet manure produced the highest $CH_4$ yield of 443 normal litter (NL) $CH_4kg^{-1}$ volatile solids (VS) compared to 222 from cows, 177 from sows, 172 from rabbits, 169 from goats and 153 from buffaloes. Methane production from duckweed (Spirodela polyrrhiza) was higher than from lawn grass and water spinach at 340, 220, and 110.6 NL $CH_4kg^{-1}$ VS, respectively. The BMP experiment also demonstrated that the $CH_4$ production was inhibited with chicken manure, slaughterhouse waste, cassava residue and shoe-making waste. Statistical analysis showed that lipid and lignin are the most significant predictors of BMP. The model was developed from knowledge that the BMP was related to biomass content of lipid, lignin and protein from manure and plant residues as a percentage of VS with coefficient of determination (R-square) at 0.95.This model was applied to calculate the $CH_4$ yield for a household with 17 fattening pigs in the highlands and lowlands of northern Vietnam.
Integral Neutronics Experiment with a Mock-up of the European HCLL-TBM for ITER
A. Klix,U. Fischer,D. Lebrun-Grandie,P. Batistoni,S. Villari,R. Bottger,K. Fleischer,J. Henniger,D. Gehre,M. Sommer 한국물리학회 2011 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.59 No.23
An ITER TBM mock-up made of lithium-lead and sheets of EUROFER was irradiated with short pulses of DT neutrons from the neutron generator at TU Dresden, and time-of-arrival spectra of the slow neutron flux were measured by means of a ^3He counter in two regions inside the mock-up. Fast neutron spectra were obtained by continuous irradiation of the mock-up with DT neutrons and application of a NE-213 spectrometer. The same mock-up was also irradiated at the Frascati Neutron Generator and tritium production rates were measured by means of Li_2CO_3 pellet detectors and LiF thermoluminescense detectors (TLD) inserted into the mock-up. In case of the first type of detectors, the accumulated tritium activity was measured while with the LiF TLD the tritium production rate was obtained from the dose deposited in the detector by the tritium-producing reactions. The Calculation/Experiment ratio for the TPR measurement was nearly 1.0 with an uncertainty of approximately 7.4%. Preliminary results from calculations with FENDL-2.1 and JEFF-3.1.1 suggest a good agreement between experiment and calculation.
KPC1-Mediated Ubiquitination and Proteasomal Processing of NF-κB1 p105 to p50 Restricts Tumor Growth
Kravtsova-Ivantsiv, Y.,Shomer, I.,Cohen-Kaplan, V.,Snijder, B.,Superti-Furga, G.,Gonen, H.,Sommer, T.,Ziv, T.,Admon, A.,Naroditsky, I.,Jbara, M.,Brik, A.,Pikarsky, E.,Kwon, Y.,Doweck, I.,Ciechanover, Cell Press ; MIT Press 2015 Cell Vol.161 No.2
NF-κB is a key transcriptional regulator involved in inflammation and cell proliferation, survival, and transformation. Several key steps in its activation are mediated by the ubiquitin (Ub) system. One uncharacterized step is limited proteasomal processing of the NF-κB1 precursor p105 to the p50 active subunit. Here, we identify KPC1 as the Ub ligase (E3) that binds to the ankyrin repeats domain of p105, ubiquitinates it, and mediates its processing both under basal conditions and following signaling. Overexpression of KPC1 inhibits tumor growth likely mediated via excessive generation of p50. Also, overabundance of p50 downregulates p65, suggesting that a p50-p50 homodimer may modulate transcription in place of the tumorigenic p50-p65. Transcript analysis reveals increased expression of genes associated with tumor-suppressive signals. Overall, KPC1 regulation of NF-κB1 processing appears to constitute an important balancing step among the stimulatory and inhibitory activities of the transcription factor in cell growth control.
Braten, Ori,Livneh, Ido,Ziv, Tamar,Admon, Arie,Kehat, Izhak,Caspi, Lilac H.,Gonen, Hedva,Bercovich, Beatrice,Godzik, Adam,Jahandideh, Samad,Jaroszewski, Lukasz,Sommer, Thomas,Kwon, Yong Tae,Guharoy, M National Academy of Sciences 2016 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.113 No.32
<P>The 'canonical' proteasomal degradation signal is a substrate-anchored polyubiquitin chain. However, a handful of proteins were shown to be targeted following monoubiquitination. In this study, we established-in both human and yeast cells-a systematic approach for the identification of monoubiquitination-dependent proteasomal substrates. The cellular wild-type polymerizable ubiquitin was replaced with ubiquitin that cannot form chains. Using proteomic analysis, we screened for substrates that are nevertheless degraded under these conditions compared with those that are stabilized, and therefore require polyubiquitination for their degradation. For randomly sampled representative substrates, we confirmed that their cellular stability is in agreement with our screening prediction. Importantly, the two groups display unique features: monoubiquitinated substrates are smaller than the polyubiquitinated ones, are enriched in specific pathways, and, in humans, are structurally less disordered. We suggest that monoubiquitination-dependent degradation is more widespread than assumed previously, and plays key roles in various cellular processes.</P>