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Aminoglycosides (AGs) are a class of antibiotics with a broad spectrum of activity. However, their use is limited by safety concerns associated with nephrotoxicity and ototoxicity, as well as drug resistance. To address these issues, semi-synthetic approaches for modifying natural AGs have generated new generations of AGs, however, with limited types of modification due to significant challenges in synthesis. This study explores a novel approach that harness the bacterial biosynthetic machinery of gentamicins and kanamycins to create hybrid AGs. This was achieved by glycodiversification of gentamicins via swapping the glycosyltransferase (GT) in their producer with the GT from kanamycins biosynthetic pathway and resulted in the creation of a series of novel AGs, therefore referred to as genkamicins (GKs). The manipulation of the hybrid biosynthetic pathway enabled the targeted accumulation of different GK species and the isolation and characterization of six GK components. These compounds display retained antimicrobial activity against a panel of World Health Organization (WHO) critical priority pathogens, and GK-C2a, in particular, demonstrates low ototoxicity compared to clinical drugs in zebrafish embryos. This study provides a new strategy for diversifying the structure of AGs and a potential avenue for developing less toxic AG drugs to combat infectious diseases.

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In this study, we isolated a highly cadmium (Cd)-resistant bacterium, Pseudomonas sp. B7, which immobilized 100% Cd(II) from medium. Culturing strain B7 with Cd(II) led to the change of functional groups, mediating extracellular Cd(II) adsorption. Proteomics showed that a carbonic anhydrase, CadW, was upregulated with Cd(II). CadW expression in Escherichia coli conferred resistance to Cd(II) and increased intracellular Cd(II) accumulation. Fluorescence assays demonstrated that CadW binds Cd(II) and the His123 residue affected Cd(II) binding activity, indicating that CadW participates in intracellular Cd(II) sequestration. Chinese cabbage pot experiments were performed using strain B7 and silicate [Si(IV)]. Compared with the control, Cd content in aboveground parts significantly decreased by 21.3%, 29.4% and 32.9%, and nonbioavailable Cd in soil significantly increased by 129.4%, 45.0% and 148.7% in B7, Si(IV) and B7 +Si(IV) treatments, respectively. The application of Si(IV) alone reduced chlorophyll content by 20.8% and arylsulfatase activity in soil by 33.9%, and increased malonaldehyde activity by 15.0%. The application of strain B7 alleviated the negative effect of Si(IV) on plant and soil enzymes. Overall, application of Si(IV) is most conducive to the decreased Cd accumulation in plant, and strain B7 is beneficial to maintaining soil and plant health.

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A Gram-stain-negative, facultative anaerobic strain, designated WSJ-3T, was isolated from soil. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WSJ-3T belongs to genus Sediminibacterium and exhibits the highest sequence similarities to Sediminibacterium roseum SYL130T (97.0%), Sediminibacterium goheungense DSM 28323T (96.9%), Sediminibacterium aquarii AA5T (96.7%), and Sediminibacterium salmoneum NBRC 103935T (95.2%). The average nucleotide identity values of strain WSJ-3T/S. roseum SYL130T and strain WSJ-3T/S. goheungense DSM 28323T are 72.2% and 70.4%, respectively, and digital DNA-DNA hybridization values for these are 19.2% and 19.1%, respectively. Strain WSJ-3T has a genome size of 3.88 Mb, with a DNA G + C content of 50.1 mol% and comprises of 3263 predicted genes. A phylogenetic tree constructed using the genomic core protein coding sequences revealed that strain WSJ-3T clusters with S. roseum SYL130T. Strain WSJ-3T has menaquinone-7 as the only respiratory quinone and phosphatidylethanolamine, three unidentified phospholipids, four unidentified aminophospholipids, two unidentified aminolipids, and three unidentified lipids as the polar lipids. The major fatty acids of strain WSJ-3T are iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. On the basis of the polyphasic results, the isolate represents a novel species of the genus Sediminibacterium, for which the name Sediminibacterium soli sp. nov. is proposed. The type strain is WSJ-3T (= KCTC 72839T = CCTCC AB 2019408T).

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The heavy metals cadmium (Cd) and chromium (Cr) are extensively used in industry and result in water and soil contamination. The highly toxic Cd(II) and Cr(VI) are the most common soluble forms of Cd and Cr, respectively. They enter the human body through the food chain and drinking water and then cause serious illnesses. Microorganisms can adsorb metals or transform Cd(II) and Cr(VI) into insoluble or less bioavailable forms, and such strategies are applicable in Cd and Cr bioremediation. This review focuses on the highlighting of novel achievements on microbial Cd(II) and Cr(VI) resistance mechanisms and their bioremediation applications. In addition, the knowledge gaps and research perspectives are also discussed in order to build a bridge between the theoretical breakthrough and the resolution of Cd(II) and Cr(VI) contamination problems.

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Strain ZZJ9T is a Gram-stain-negative, rod-shaped, aerobic bacterium isolated from manganese mine soil. Strain ZZJ9T showed the highest 16S rRNA gene sequence similarities with Larkinella rosea 15J16-1T3AT (97.1%), Larkinella terrae 15J8-8T (97.0%), Larkinella knui 15J6-3T6T (96.8%), and Larkinella ripae 15J11-1T (95.3%). The genome size of strain ZZJ9T was 8.01 Mb and the DNA G+C content was 51.8 mol%. ANI values among strain ZZJ9T and Larkinella rosea 52004 T, Larkinella knui KCTC 42998T, and Larkinella terrae 52001T were 80.5%, 82.7%, and 80.5%, respectively. dDDH values among strain ZZJ9T and Larkinella rosea 52004T, Larkinella knui KCTC 42998T, and Larkinella terrae 52001T were 23.5%, 26.0%, and 23.6%, respectively. Furthermore, the genome of strain ZZJ9T contained 6302 predicted protein-coding genes and 3114 (49%) of them had classificatory functions. The major quinone of strain ZZJ9T was menaquinone-7 and the main cellular fatty acids were C16:1ω5c (39.5%), iso-C15:0 (25.6%), and iso-C17:0 3OH (11.5%). The polar lipids of strain ZZJ9T were phosphatidylethanolamine, unidentified lipid, and two unidentified aminolipids. Based on the results of phylogenetic, genome, phenotypic, and chemotaxonomic analytical, strain ZZJ9T represents a novel species of the genus Larkinella, for which the name Larkinella punicea sp. Nov. is proposed. The type strain is ZZJ9T (= KCTC 62876T = CCTCC AB 2018215T).

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Strain ZH6T is a Gram-stain-negative, rod-shaped, aerobic bacterium isolated from manganese mine soil. Strain ZH6T had highest 16S rRNA gene sequence similarities to Mucilaginibacter yixingensis YX-36T (96.9 %) and Mucilaginibacter psychrotolerans NH7-4T (96.8 %). The genome size of strain ZH6T was 4.61 Mb with a DNA G+C content of 44.0 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain ZH6T and M. yixingensis DSM 26809T were 70.6 and 19.2 %, respectively. Strain ZH6T had menaquinone-7 as a major quinone and main cellular fatty acids of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids of strain ZH6T were a phosphatidylethanolamine, an unidentified glycolipid, an unidentified phospholipid, three unidentified aminophospholipids and four unidentified lipids. Based on the phenotypic, chemotaxonomic and phylogenetic results, strain ZH6T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacterterrenus sp. nov., is proposed. The type strain is ZH6T (=CCTCC AB 2018373T=KCTC 72075T).

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Alishewanella sp. WH16-1 is a heavy metal-resistant bacterium. Previously, a putative YebC family regulator gene, designated ruvR, was associated with Cr(VI) resistance. In this study, comprehensive analyses were performed to study the role of ruvR and its adjunct putative DNA repairing genes, ruvCAB, in the heavy metal resistance of Alishewanella sp. WH16-1. RT-PCR analysis showed that ruvR is cotranscribed with ruvCAB. Gene mutation and complementation experiments indicated that ruvRCAB contributes to Cr(VI), As(III), Sb(III), and Cd(II) resistance in vivo. Random amplification of polymorphic DNA-PCR revealed that ruvCAB is associated with DNA repair mediated by these metals, and the presence of the metals in the cells was confirmed by elemental mapping and energy-dispersive X-ray spectrograph analysis. In addition, qRT-PCR, reporter gene assay, and in vivo and in vitro protein-DNA interaction experiments indicated that RuvR positively regulates the transcription of ruvCAB and is induced by Cr(VI). Finally, site-directed mutagenesis demonstrated that Asp103 is essential for the DNA binding ability of RuvR. The above results suggest that RuvR is involved in Cr(VI) resistance and resistance to other metals and that RuvR positively regulates the expression of ruvCAB. Based on our study and literatures, a model of RuvRCAB detailing bacterial heavy metal resistance is proposed. The RuvRCAB system plays an important role in the ability of Alishewanella sp. WH16-1 to survive in environments with heavy metals.

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Pseudomonas stutzeri TS44 was able to aerobically reduce Se(IV) into SeNPs and transform Se(IV)/Cd(II) mixture into CdSe-QDs. The SeNPs and CdSe-QDs were systematically characterized by surface feature analyses, and the molecular mechanisms of SeNPs and CdSe-QD formation in P. stutzeri TS44 were characterized in detail. In vivo, under 2.5 mmol/L Se(IV) exposure, GorA was essential for catalyzing of Se(IV) reduction rate decreased by 67% when the glutathione reductase gene gorA was disrupted, but it was not decreased in the glutathione synthesis rate-limiting gene gshA mutated strain compared to the wild type. The complemented strains restored the phenotypes. While under low amount of Se(IV) (0.5 mmol/L), GSH played an important role for Se(IV) reduction. In vitro, GorA catalyzed Se(IV) reduction with NADPH as the electron donor (Vmax of 3.947 ± 0.1061 µmol/min/mg protein under pH 7.0 and 28℃). In addition, CdSe-QDs were successfully synthesized by a one-step method in which Se(IV) and Cd(II) were added to bacterial culture simultaneously. GSH rather than GorA is necessary for CdSe-QD formation in vivo and in vitro. In conclusion, the results provide new findings showing that GorA functions as a selenite reductase under high amount Se(IV) and GSH is essential for bacterial CdSe-QD synthesis.

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A novel bacterial strain, designated WSJ-1T, was isolated from geopark soil in Gansu province, PR China. The highest 16S rRNA gene sequence similarities were to those of Nocardioides sediminis MSL-01T (97.10 %), Nocardioides aquiterrae GW-9T (97.08 %) and Nocardioides terrigena DS-17T (96.94 %). Strain WSJ-1T grouped with N. terrigena DS-17T and N. sediminis MSL-01T in 16S rRNA gene-based phylogenetic trees. The DNA-DNA relatedness of WSJ-1T/N. sediminis JCM19559T and WSJ-1T/N. aquiterrae JCM11813T were 44.8 and 29.2 %, respectively. Average nucleotide identity values of whole genome sequences of WSJ-1T/N. terrigena KCTC19217T and WSJ-1T/N. sediminis KCTC19271T were 78.83 and 78.83 %, respectively. Its genome size was 4.76 Mb, comprising 4517 predicted genes with a DNA G+C content of 70.9 %. Strain WSJ-1T contained menaquinone-8(H4) as the major respiratory quinone and ll-2,6-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. The major cellular fatty acids were iso-C16 : 0, C18 : 1ω9c and C17 : 1ω8c. Based on the polyphasic analyses, the isolate is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioidesgansuensis sp. nov. is proposed. The type strain is WSJ-1T (=KCTC 49117T=CCTCC AB 2018027T).

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Sulfate-reducing bacteria are a group of microorganisms that use sulfate as an electron acceptor. These bacteria are useful in the bioremediation of heavy metal pollution since they can reduce/precipitate metals. Previously, we identified the Alishewanella strain WH16-1 from soil of a copper and iron mine and determined that it can reduce sulfate and chromate and that it was tolerant to many heavy metals. In this study, we investigated the chromate reduction mechanism of strain WH16-1 through Tn5 transposon mutagenesis. A cytochrome bd (cytbd) Tn5 mutant was generated (Δcytbd), and a detail analysis showed that the following: (1) gene cydE (coding for a GbsR-type regulator) was co-transcribed with the two subunits coding genes of the Cytochrome bd complex (Cytbd), namely, cydA and cydB, based on RT-PCR analysis, and similar gene arrangements were also found in other Alteromonadaceae family strains; (2) the chromate resistance level was dramatically decreased and chromate reduction efficiency also decreased in strain Δcytbd compared to the wild-type and a complemented strain (Δcytbd-C); (3) Cytbd could catalyze the decomposition of H2O2 according to the analyses of H2O2 decomposition ability, cellular H2O2 contents, H2O2 inhibition zone, and H2O2 sensitivity tests; (4) surprisingly, chromate was not an inducer of the expression of Cytbd, but sulfate induced expression of Cytbd, and sulfate/sulfide resistance levels were also decreased in the Δcytbd strain; (5) the addition of sulfate enhanced the chromate resistance level and reduction efficiency; (6) Cytbd expression was repressed by CydE and derepressed by sulfate based on an in vivo bacterial one hybrid system and in vitro EMSA tests; and (7) DNA footprinting and short-fragment EMSA tests revealed two binding sites of CydE in its promoter region. All these results showed that Cytbd is negatively regulated by CydE and derepressed by sulfate. In addition, Cytbd contributes to the resistance of sulfate and sulfide, and sulfide could be used as a reductant to reduce chromate. Moreover, Cytbd is essential to decompose H2O2 to decrease cellular oxidative stress. Thus, the regulation and function of Cytbd may explain why sulfate could enhance chromate reduction.

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Selenite reductase CsrF overexpressed Escherichia coli was used as a microbial factory to produce Se(0) nanoparticles (Bio-SeNPs). The Bio-SeNPs were characterized by transmission electronic microscopy, element mapping, scanning electron microscopy, energy-dispersive X-ray spectrographs, Zeta-potential, dynamic light scattering, Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy analyses. The results indicated that Bio-SeNPs are irregular spheres with diameters from 60 to105 nm and mainly consist of Se(0), proteins and lipids. Furthermore, it exhibited maximum adsorption capacity for anionic dye (congo red) at acidic pH and cationic dyes (safranine T and methylene blue) at alkaline pH. To gain more insight, adsorption kinetics, adsorption isotherms and adsorption thermodynamics studies were carried out. These results showed that the adsorption capacities of congo red, safranine T and methylene blue were 1577.7, 1911.0 and 1792.2 mg/g, respectively. These adsorption processes were spontaneous and primarily physical reactions. In addition, Bio-SeNPs can be effectively reused by 200 mmol/L NaCl. To the best of our knowledge, this is the first report of adsorption removal dyes by Bio-SeNPs. The adsorption capacities of Bio-SeNPs for congo red, safranine T and methylene blue were 6.8%, 25.2% and 49.0% higher than that for traditional bio-based materials, respectively.

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Alishewanella sp. WH16-1 is a facultative anaerobic bacterium isolated from mining soil. Under aerobic conditions, this bacterium efficiently reduces selenite and chromate. A flavoprotein showing 37% amino acid identity to E. coli chromate reductase ChrR was identified from the genome (named CsrF). Gene mutation and complementation along with heterologous expression revealed the ability of CsrF to reduce selenite and chromate in vivo. The purified CsrF was yellow and showed an absorption spectra similar to that of FMN. The molecular weight of CsrF was 23,906 for the monomer and 47,960 for the dimer. In vitro, CsrF catalyzes the reduction of Se(IV) and Cr(VI) using NAD(P)H as cofactors with optimal condition of pH 7.0 and temperature of 30-37°C. This enzyme also catalyze the reduction of sulfate and ferric iron but not arsenate and nitrate. Using NADPH as its electron donor, the Km for the reduction of Se(IV) and Cr(VI) was 204.1±27.91 and 250.6±23.46µmol/L, respectively. Site-directed mutagenesis showed that Arg13 and Gly113 were essential for the reduction of Se(IV) and Cr(VI). The products of the reduction of Se(IV) and Cr(VI) were Se(0)- and Cr(III)-nanoparticles, respectively. To our knowledge, CsrF is a novel and well-characterized bacterial aerobic selenite reductase.

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Leakage of underwater crude oil pipes causes severe pollution to soil and water, and results in great economic loss. To predict the diffusion area of spilled oil before it reaches the water's surface and to reduce the time required for emergency response, numerical simulations were conducted on underwater spilled oil diffusion of bare crude oil pipes using FLUENT software. The influences of water-surface wind speed, leakage hole diameter, water velocity, and initial leakage velocity on oil diffusion were analyzed. The results revealed the following: (1) with wind blowing on the surface of the water, the vertical displacement of spilled oil jet-flow was affected by the combined action of water flow and wind, making it difficult for a high-speed jet-flow to form. A horizontal oil flow mostly moved in the direction of the bottom water, and frontier oil droplets dispersed quickly; (2) during the diffusion of spilled oil in water, the maximum horizontal displacement mostly increased linearly, while the maximum vertical displacement initially increased quickly and then slowed; (3) the greater the initial velocity and leakage hole diameter, the higher the oil jet-flow and the wider the diffusion area; the higher the water flow rate and water-surface wind speed, the smaller the vertical displacement of spilled oil. The existence of water-surface wind had no obvious influence on the horizontal displacement of underwater spilled oil.

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A Gram-staining-negative, rod-shaped, motile by gliding and facultative anaerobic bacterial strain, YS-25T, was isolated from a sludge of a manganese mine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YS-25T formed a single branch within the strains of the family Sphingobacteriaceae and showed low similarities to Pedobacter arcticus CCTCC AB 2010223T (91.7 %), 'Pedobacter zeaxanthinifaciens' TDMA-5 (91.5 %), Pedobacter terricola DS-45T (90.9 %), Pedobacter ureilyticus THG-T11T (90.9 %), Pseudopedobacter beijingensis MCCC 1A01299T (90.8 %) and Pedobacter heparinus CCTCC AB 209030T (88.5 %). Strain YS-25T had some unique physiological and biochemical characteristics: facultative anaerobic, able to hydrolyse Tween 40, positive for cystine arylamidase and negative for mannose assimilation and ß-galactosidase. The polar lipids of strain YS-25T were phosphatidylethanolamine, aminolipid, two unknown lipids and two glycolipids. The presence of glycolipids and absence of sphingolipid were different from the Pedobacter and Pseudopedobacter strains. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), unknown ECL 13.565, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and anteiso-C15 : 0. The genomic DNA G+C content was 42.0 mol%, and the only respiratory quinone was menaquinone 7. On the basis of polyphasic taxonomic analyses, strain YS-25T is considered to represent a novel genus and species, for which the name Pelobium manganitolerans gen. nov., sp. nov. is proposed. The type strain is YS-25T (=KCTC 52203T=CCTCC AB 2016051T).

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Geological conditions along long distance pipelines are complex. In consideration of differences in elevation and terrain obstacles, long distance pipelines are commonly laid through tunnels. Oil and gas pipelines are often laid side by side to reduce construction costs and minimize geological impact. The layout and construction of parallel oil and gas pipelines are more complex than those of single pipelines. In order to reduce safety hazards, it is necessary to carry out stress analysis of the oil and gas pipelines that run through tunnels. In this study, a stress analysis model of pipelines running through a tunnel was developed. On the basis of the finite element method, CAESAR II software was used to analyze the stress and displacement of a section of parallel oil and gas pipelines that run through tunnels and stress and displacement distribution laws were drawn from the analyses. A study of the factors influencing stress recommended that: (1) The buttress interval of the parallel oil and gas pipelines in a tunnel should be 12 m; (2) The angle of inclined pipelines should be no greater than 25°; (3) The stress of oil pipelines enhances more obviously than that of gas pipelines under earthquake action; (4) The average stress can be reduced by adopting "ladder" laying; and (5) Guide bend can be set at the tunnel entrance and exit in order to reduce the stress.

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Improving the separation efficiency of the inclined oil/water separator, a new type of gravity separation equipment, is of great importance. In order to obtain a comprehensive understanding of the internal flow field of the separation process of oil and water within this separator, a numerical simulation based on Euler multiphase flow analysis and the realizable k-ε two equation turbulence model was executed using Fluent software. The optimal value ranges of the separator's various structural parameters used in the numerical simulation were selected through orthogonal array experiments. A field experiment on the separator was conducted with optimized structural parameters in order to validate the reliability of the numerical simulation results. The research results indicated that the horizontal position of the dispenser, the hole number, and the diameter had significant effects on the oil/water separation efficiency, and that the longitudinal position of the dispenser and the position of the weir plate had insignificant effects on the oil/water separation efficiency. The optimal structural parameters obtained through the orthogonal array experiments resulted in an oil/water separation efficiency of up to 95%, which was 4.996% greater than that realized by the original structural parameters.

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When a long distance oil pipeline crosses an earthquake disaster area, inertial force and strong ground motion can cause the pipeline stress to exceed the failure limit, resulting in bending and deformation failure. To date, researchers have performed limited safety analyses of oil pipelines in earthquake disaster areas that include stress analysis. Therefore, using the spectrum method and theory of one-dimensional beam units, CAESAR II is used to perform a dynamic earthquake analysis for an oil pipeline in the XX earthquake disaster area. This software is used to determine if the displacement and stress of the pipeline meet the standards when subjected to a strong earthquake. After performing the numerical analysis, the primary seismic action axial, longitudinal and horizontal displacement directions and the critical section of the pipeline can be located. Feasible project enhancement suggestions based on the analysis results are proposed. The designer is able to utilize this stress analysis method to perform an ultimate design for an oil pipeline in earthquake disaster areas; therefore, improving the safe operation of the pipeline.

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Phenylethanolamine N-methyltransferase (PNMT), the terminal enzyme of the catecholamine biosynthesis pathway, catalyzes the conversion of norepinephrine (NE) to epinephrine (EPI). PNMT is a candidate gene for multiple sclerosis (MS) for two reasons. PNMT is known to map to a region identified in two genome screens for MS and it directly regulates the amounts of NE and EPI, both of which play a significant role in the modulation of the innate immune response. The frequencies of two promoter polymorphisms of the PNMT gene showed genetic association in a case-control study of 108 patients with MS and 774 ethnically and age-matched control subjects. In subjects with MS, significant differences in the frequency of the GG genotype at the G-387A marker and the AA genotype at the G-182A marker were observed. Additionally, when both markers were combined and evaluated, highly significant differences between the polymorphism distributions in patients with MS and control subjects were detected. The data suggest that these promoter polymorphisms of the PNMT gene, both independently and cumulatively, show association with MS.

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