23 research outputs found
Comparative whole genome transcriptional responses of Ruminococcus albus strain 7 and 8: a case for specialization and niche differentiation
No full textRuminococcus albus strains are one of dominant fibrolytic bacteria in the rumen that contribute to plant biomass as well as vitamin utilization in host nutrition. To better understanding of host-microbe interactions, it is relevant to establish the model for fiber degradation and vitamin metabolism of the dominant fibrolytic bacteria and investigate their roles in the gut ecosystem. However, the fibrolytic mechanism and vitamin metabolism of Ruminococcus albus remain largely unknown. In the current study, comparative genomic and transcriptomic analyses of two different strains 7 and 8 of R. albus for plant fiber and folate utilization were used to investigate the conserved and differential mechanism between the two R. albus strains.
Through comparative transcriptomic analyses of both strains grown on alkaline peroxide hydrogen treated corn stalk (AHPCS), phosphoric acid swollen cellulose (PASC) and wheat arabinoxylan (WAX), this research demonstrated that the top 5 highly expressed glycoside hydrolase (GH) families, including the versatile GH5, GH9 (Cel9B), GH10, GH11, and GH48 (Cel48A), are the primary GH enzymes employed by both strains of R. albus for the hydrolysis of plant cell wall. In addition, the co-expression of these endoglucanases and endoxylanases in response to cellulose and hemicellulose was observed. The previously known adhering mechanism of R. albus were transcriptionally analyzed and verified in this research. The genes encoding Pil-like protein or a family 37 carbohydrate binding module (CBM37) domain were highly expressed in both strains during growth on different polysaccharides. Especially, the significant role of CBM37 in the fiber utilization of R. albus was highlighted based on the prevalence of CBM37 domain on the highly expressed GH genes as well as hypothetical genes.
It is notable that distinct strategies between two strains for plant cell wall utilization were proposed in this research. Based on phenotypic, genomic, and transcriptomic evidence, wild type of R. albus 8 in rumen appears to preferentially utilize hemicellulose rather than cellulose embedded in the plant cell wall, while R. albus 7 prefers to utilize cellulose over hemicellulose. To support this conclusion, R. albus 8 utilized more hemicellosic sugars derived from the hydrolysis of AHPCS than R. albus 7. More CAZyme genes of R. albus 8 responded to WAX than PASC, while those genes of R. albus 7 responded to more PASC than WAX. When hemicellulose in AHPCS started to decrease in the culture, R. albus 8 down-regulated the expression of genes for sugar transporters and intracellular GH. In contrast, R. albus 7 exhibited a sequential expression of sugar transporters and intracellular GH genes, as preferred cellulosic sugars were released from AHPCS after removal of hemicellulose. Notably, we found the putative genes belonging to c-di-GMP regulatory and the accessory gene regulator quorum sensing (Agr QS) systems in R. albus 7 and 8. The transcriptional pattern of these genes were in accordance with differential transcriptional pattern of GH genes between both strains and the preferred planktonic growth of strain 8 on AHPCS as opposed to the substrate adherent growth of R. albus 7. These results suggest that c-di-GMP and Agr QS systems are implicated not only in biofilm formation of pathogenic bacteria, but also in the fibrolytic systems of commensal bacteria. Supported by the fermentation profile and the growth rate on beechwood xylan together with genomic and transcriptomic evidence, R. albus 8 was found to possess a predicted unique phosphoketolase (PK) pathway, which likely enables R. albus 8 to catabolize pentose rapidly as well as conserve energy and costs for enzyme synthesis required for the lower glycolytic sequence. With our proposal for the differential strategies between strains, the co-culture experiment demonstrated that despite a similar fibrolytic mechanism, R. albus 7 and 8 could co-exist on complex substrate containing cellulose and hemicellulose.
This research on folate metabolism in R. albus 7 and 8 provided genomic evidence for three folate utilization pathways (either de novo synthesis, salvage, or both pathways) conserved in the Firmicutes including R. albus strains. Through the growth experiments in the presence or absence of folate and para-aminobenzoate (pABA), it was shown that R. albus strains 7 and 8 rely on different folate metabolic pathways, de novo synthesis or salvage pathway, respectively. In addition, the results of transcriptomic analysis suggest that the folate autotrophic strain, R. albus 7, also has an alternative pathway for pABA synthesis and likewise other Ruminococcus species lacking the canonical pABA synthetic pathway are likely autotrophs and not auxotrophs.
Notably, the potential long non-coding RNA (lncRNA) loci was identified in the genomes of R. albus strains. The putative lncRNA loci consisted of four sequence components; lncRNA, DUF1292 gene, putative 6S RNA, and alcohol dehydrogenase. Based on their transcriptional profiles assessed by RNA-seq and northern blot analyses, it seems likely that the lncRNA loci are involved in the regulatory system related to the stationary phase of cells.
This study provides molecular insight in conserved and differentiated fibrolytic system and folate metabolism between R. albus 7 and 8. In addition, the presence of novel lncRNA loci was identified, providing more information on the regulatory mechanism in Gram-positive Firmicutes.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2018-05-01The student, Inhyuk Kwon, accepted the attached license on 2016-03-23 at 18:58.The student, Inhyuk Kwon, submitted this Dissertation for approval on 2016-03-23 at 19:08.This Dissertation was approved for publication on 2016-03-28 at 11:20.DSpace SAF Submission Ingestion Package generated from Vireo submission #9116 on 2016-07-07 at 13:48:38Made available in DSpace on 2016-07-07T20:27:00Z (GMT). No. of bitstreams: 3
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Previous issue date: 2016-03-28Embargo set by: Seth Robbins for item 93083
Lift date: 2018-07-07T20:28:14Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 93083
Lift date: 2018-07-07T20:35:34Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Only Restriction Lifted for Item 93083 on 2018-07-08T09:15:09Z
Continuous Patterning of Copper Nanowire-Based Transparent Conducting Electrodes for Use in Flexible Electronic Applications
No full textSimple,
low-cost and scalable patterning methods for Cu nanowire
(NW)-based flexible transparent conducting electrodes (FTCEs) are
essential for the widespread use of Cu NW FTCEs in numerous flexible
optoelectronic devices, wearable devices, and electronic skins. In
this paper, continuous patterning for Cu NW FTCEs via a combination of selective intense pulsed light (IPL) and roll-to-roll
(R2R) wiping process was explored. The development of continuous R2R
patterning could be achieved because there was significant difference
in adhesion properties between NWs and substrates depending on whether
Cu NW coated area was irradiated by IPL or not. Using a custom-built,
R2R-based wiping apparatus, it was confirmed that nonirradiated NWs
could be clearly removed out without any damage on irradiated NWs
strongly adhered to the substrate, resulting in continuous production
of low-cost Cu NW FTCE patterns. In addition, the variations in microscale
pattern size by varying IPL process parameters/the mask aperture sizes
were investigated, and possible factors affecting on developed pattern
size were meticulously examined. Finally, the successful implementation
of the patterned Cu NW FTCEs into a phosphorescent organic light-emitting
diode (PhOLED) and a flexible transparent conductive heater (TCH)
were demonstrated, verifying the applicability of the patterned FTCEs.
It is believed that our study is the key step toward realizing the
practical use of NW FTCEs in various flexible electronic devices
Soft X-ray harmonic lasing self-seeded free electron laser at Pohang Accelerator Laboratory X-ray free electron laser
No full textThe demonstration of a harmonic lasing self-seeded free-electron laser (HLSS FEL) scheme in the soft X-ray range at the Pohang Accelerator Laboratory X-ray Free Electron Laser is presented. We report the experimental results of HLSS FEL radiation with the shortest wavelength of 1nm by using the optimized phase shift of 2/3 pi. The key feature of the HLSS scheme is that the mode number is decreased (the longitudinal coherence length is enhanced) which is directly observed using a single-shot spectrometer. The spectral brightness is enhanced by a factor of 1.7 compared to the self-amplified spontaneous emission FEL because of the narrowed bandwidth. Our results show a good agreement with the theoretical expectation and simulations. The HLSS mode is a promising standard operation mode to generate a stable and high-brightness X-ray FEL that will provide more benefits to users for various applications. Published by AIP Publishing.11sciescopu
A photonic sintering derived Ag flake/nanoparticle-based highly sensitive stretchable strain sensor for human motion monitoring
No full textA highly stretchable sensor with excellent sensitivity was obtained using an Ag flake/Ag NC hybrid by an intense pulsed light sintering process.</p
High-brightness self-seeded X-ray free-electron laser covering the 3.5 keV to 14.6 keV range
No full textA self-seeded X-ray free-electron laser (XFEL) is a promising approach to realize bright, fully coherent free-electron laser (FEL) sources in the hard X-ray domain that have been a long-standing issue with longitudinal coherence remaining challenging. At the Pohang Accelerator Laboratory XFEL, we have demonstrated a hard X-ray self-seeded XFEL with a peak brightness of 3.2 �� 1035 photons s?1 mm?2 mrad?2 0.1% bandwidth (BW)?1 at 9.7 keV. The bandwidth (0.19 eV) is about 1/70 times as wide (close to the Fourier transform limit) and the peak spectral brightness is 40 times higher than in self-amplified spontaneous emission (SASE), with substantial improvements in the stability of self-seeding and noticeably suppressed pedestal effects. We could reach an excellent self-seeding performance at a photon energy of 3.5 keV (lowest) and 14.6 keV (highest) with the same stability as the 9.7 keV self-seeding. The bandwidth of the 14.6 keV seeded FEL was 0.32 eV, and the peak brightness was 1.3 �� 1035 photons s?1 mm?1 mrad?1 0.1%BW?1. We show that the use of seeded FEL pulses with higher reproducibility and a cleaner spectrum results in serial femtosecond crystallography data of superior quality compared with data collected using SASE mode. ? 2021, The Author(s), under exclusive licence to Springer Nature Limited part of Springer Nature.11Nsciescopu
Characterization of Endolysin LyJH307 with Antimicrobial Activity against Streptococcus bovis
No full textStreptococcus bovis (S. bovis) is one of the critical initiators of acute acidosis in ruminants. Therefore, we aimed to develop and characterize the endolysin LyJH307, which can lyse ruminal S. bovis. We tested the bactericidal activity of recombinant LyJH307 against S. bovis JB1 under a range of pH, temperature, NaCl, and metal ion concentrations. In silico analyses showed that LyJH307 has a modular design with a distinct, enzymatically active domain of the NLPC/P60 superfamily at the N-terminal and a cell wall binding domain of the Zoocin A target recognition domain (Zoocin A_TRD) superfamily at the C-terminal. The lytic activity of LyJH307 against S. bovis JB1 was the highest at pH 5.5, and relatively higher under acidic, than under alkaline conditions. LyJH307 activity was also the highest at 39 °C, but was maintained between 25°C and 55°C. LyJH307 bactericidal action was retained under 0-500 mM NaCl. While the activity of LyJH307 significantly decreased on treatment with ethylenediaminetetraacetic acid (EDTA), it was only restored with supplementation of 10 mM Ca2+. Analyses of antimicrobial spectra showed that LyJH307 lysed Lancefield groups D (S. bovis group and Enterococcus faecalis) and H (S. sanguinis) bacteria. Thus, LyJH307 might help to prevent acute ruminal acidosis
One-Body Capillary Plasma Source for Plasma Accelerator Research at e-LABs
No full textWe report on the development of a compact, gas-filled capillary plasma source for plasma accelerator applications. The one-body sapphire capillary was created through a diamond machining technique, which enabled a straightforward and efficient manufacturing process. The effectiveness of the capillary as a plasma acceleration source was investigated through laser wakefield acceleration experiments with a helium-filled gas cell, resulting in the production of stable electron beams of 200 MeV. Discharge capillary plasma was generated using a pulsed, high-voltage system for potential use as an active plasma lens. A peak current of 140 A, corresponding to a focusing gradient of 97 T/m, was observed at a voltage of 10 kV. These results demonstrate the potential utility of the developed capillary plasma source in plasma accelerator research using electron beams from a photocathode gun
In vitro evaluation of Aloe saponaria as a potential feed additive to modulate ruminal fermentation and microbial diversity
No full textSaponin possessed antiprotozoal activity; therefore, it is generally used to mitigate enteric methane (CH4) emission in ruminant nutrition. The objective of this study was to evaluate the effects of Aloe saponaria (AS) supplementation on rumen fermentation, CH4, and microbial diversity in an in vitro experiment over 48 h incubation. Five treatments were used: (1) no additives (CON), 1% and 2% dosage of heat-dried AS (HAS), and freeze-dried AS (FAS), and the experiments were performed three times. After the incubation, volatile fatty acids (VFAs), CH4 proportion in total gas, and microbial diversity were evaluated. Gas production was assessed at 3, 6, 9, 12, 24, 36, and 48 h incubation. FAS addition significantly increased gas production compared to CON except for 6 and 48 h, whereas HAS addition did not significantly affect the gas production at all observed time points. AS addition significantly increased total VFA and the absolute abundances of fungi and Ruminococcus albus regardless of drying method. There was no significant change in the CH4 proportion at 48 h, although the reduction in ciliate protozoa was detected in FAS-treated groups. In conclusion, FAS may be an effective feed additive to improve ruminal fermentation via enhancing feed utilization by rumen microbes
A Study on the Applicability and Development Utilization of Assessment System of Urban Fire Risk for Disaster Prevention City
No full text
