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Academic Journal

AMP 0 : Species-Specific Prediction of Anti-microbial Peptides Using Zero and Few Shot Learning

  • Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics ; volume 19, issue 1, page 275-283 ; ISSN 1545-5963 1557-9964 2374-0043

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Academic Journal

Ag(0) nanocatalyst stabilized with networks of p(SPA-co-AMPS) for the hydrogen generation process from ethylenediamine bisborane hydrolysis

  • Source: International Journal of Hydrogen Energy ; volume 45, issue 35, page 17649-17661 ; ISSN 0360-3199

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Figure 6. Acetyl phosphate-mediated acetylation of MsNrtR. ; (A) Genetic context of the two types of acetylation pathways in M. smegmatis. The two genes pat (MSMEG_5458) and cobB (MSMEG_5175) are responsible for the reversible enzymatic route of acetylation. The two loci ackA (MSMEG_0784) and pta (MSMEG_0783) participate in the non-enzymatic AcP pathway. Of note, ackA and pta are two overlapping loci that appear as an operon. (B) The acetylation levels of USP are dependent on the Pat/CobB-requiring enzymatic route in M. smegmatis. USP denotes the universal stress protein (MSMEG_4207). Using the recombinant plasmid pMV261-usp, the 6 × His tagged USP protein was expressed in wild-type M. smegmatis and its derivatives (ΔcobB and Δpat). As a result, the acetylation levels of the purified USP proteins were detected with the pan anti-acetyl lysine antibody (α-Acetyl) and an anti-6 ×his antibody was used as a loading control. A representative result for three independent experiments displayed. (C) The acetylation levels of NrtR are not distinguishable in the three strains of M. smegmatis (wild-type, ΔcobB and Δpat). 6 × His tagged MsNrtR was expressed in the three strains described for panel (B) using pMV261-nrtR. The acetylation levels of the purified MsNrtR proteins were determined using the α-Acetyl antibody, and anti-NrtR antiserum (α-NrtR) acted as a loading control. Western blots were conducted in triplicates. (D) Western-blot-based detection of the in vitro non-enzymatic acetylation of MsNrtR using AcP as the phosphate donor. Acetylation of MsNrtR by AcP (10 mM) was measured by incubating MsNrtR and AcP for 0, 0.5, 1, 2 and 4 hr at 37°C. The concentration of NrtR was determined by Western blot with anti-NrtR serum as a primary antibody (lower panel). (E) Acetylation of MsNrtR is AcP dose-dependent. MsNrtR was incubated with different levels of AcP (0, 2, 5 and 10 mM) for 2 hr at 37°C. (F) Altered acetylation of MsNrtR as incubation progresses over time with constant AcP. Acetylation was quantified using Image J software and normalized to the signal at 0 hr. (G) MsNrtR acetylation at various levels of AcP. Data were measured with Image J software and normalized to the signal at 0 mM AcP. Data are shown as mean ± standard deviation (SD). (H) In vivo evidence that the AcP pathway is associated with NrtR acetylation. In addition to the parental strain, a single mutant (ΔackA) and double mutant (ΔackA+Δpta) were used to prepare the recombinant MsNrtR proteins with varied levels of acetylation. Of note, the bacterial growth conditions were supplemented with an inducer of 0.2% glucose or 1.0% acetate recommended by Weinert et al. (2013). The Western blot was performed as described for panels (B) and (C). Representative results of three or more independent experiments are shown. (I) Contribution of the AckA and Pta-requiring AcP pathway to NrtR acetylation. The acetylation signal was quantified using Image J software, and the density in the WT was normalized as 1. Each dot denotes a Western blot experiment. (J) Working model for non-enzymatic acetylation of MsNrtR in a metabolic context, and the working model for the enzymatic acetylation of USP. Abbreviations: MsNrtR, M. smegmatis NrtR; AcP, Acetyl-phosphate; AcAMP, Acetyl-AMP; Ac-CoA, acetyl-CoA; USP (MSMEG_4207), universal stress protein (130aa); Pta (MSMEG_0783), phosphate acetyltransferase (692aa); and AckA (MSMEG_0784), acetate kinase (376aa).

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Figure 1—source data 1. Amputee demographic and clinical details. ; To measure phantom sensations, as well as other demographic and clinical details of potential relevance to the studied missing hand representation, amputees completed a range of questionnaires (e.g. amputation details, prosthesis usage etc.). Amputees rated intensities of phantom/stump pain and non-painful phantom sensations (vividness), using a 0 – 100 scale, as follows: (i) intensity of worst pain/vivid sensation experienced during the last week (or in a typical week involving such sensations); (ii) intensity of phantom pain on average over the last week (or in a typical week if last week was atypical); and (iii) current intensity/vividness of phantom pain and sensations, during the scanning day. Phantom limb pain magnitude was calculated by dividing worst pain intensity by pain frequency (1- all the time; 2- daily; 3- weekly). An analogous measure was obtained for vividness of non-painful phantom sensations. This approach represented the chronic aspect of the phantom pain/sensation as it combines frequency and intensity (Makin et al., 2013a). We also asked the amputees whether they experienced telescoping, a common phenomenon where the perceived length of the phantom limb is changed (Flor and Nikolajsen, 2006). Amp. = amputation; Amp. level = amputation level measured in percentages: (residual arm length/intact arm length) x 100. Intact arm length is measured from shoulder to fingertips, where 41% is equivalent to the level of the elbow and 75% is equivalent to the level of the wrist; PLS = phantom limb sensations; mag. = magnitude; scan = score of sensation phantom limb vividness/pain intensity on scanning day (scale 0 – 100); PLP = phantom limb pain; ave. = score of average phantom limb pain in a typical week (scale 0 – 100); prosthetics usage = prosthetic limb usage (frequency): 0- never, 1- rarely, 2- occasionally, 3- daily, 4- more than 4 hours a day, 5- more than 8 hours a day; Y. = yes; N. = no.

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