Antigenic analysis of the HIV-1 envelope trimer implies small differences between structural states 1 and 2.

The conformationally dynamic HIV-1 envelope trimer (Env) is the target of broadly neutralizing antibodies (bnAbs) that block viral entry. Single-molecule Förster resonance energy transfer (smFRET) has revealed that HIV-1 Env exists in at least three conformational states on the virion. Prior to complete host-receptor engagement (State 3), Env resides most prevalently in the smFRET-defined State 1, which is preferentially recognized by most bnAbs that are elicited by natural infection. smFRET has also revealed that soluble trimers containing prefusion-stabilizing disulfide and isoleucine-to-proline substitutions reside primarily in State 2, which is a required intermediate between States 1 and 3. While high-resolution Env structures have been determined for States 2 and 3, the structure of these trimers in State 1 is unknown. To provide insight into the State 1 structure, here we characterized antigenic differences between smFRET-defined states and then correlated these differences with known structural differences between States 2 and 3. We found that cell surface-expressed Env was enriched in each state using state-enriching antibody fragments or small-molecule virus entry inhibitors and then assessed binding to HIV-1 bnAbs preferentially binding different states. We observed small but consistent differences in binding between Env enriched in States 1 and 2, and a more than 10-fold difference in binding to Env enriched in these states versus Env enriched in State 3. We conclude that structural differences between HIV-1 Env States 1 and 3 are likely more than 10-fold greater than those between States 1 and 2, providing important insight into State 1.

GLYCO: a tool to quantify glycan shielding of glycosylated proteins.

MOTIVATION: Glycans play important roles in protein folding and cell-cell interactions-and, furthermore, glycosylation of protein antigens can dramatically impact immune responses. While there have been attempts to quantify the glycan shielding or coverage of a protein surface, none of the publicly available tools analyzes glycan shielding computationally at an atomistic level. RESULTS: Here, we developed an in silico approach, GLYCO (GLYcan COverage), to quantify the glycan shielding of a protein surface. The software provides insights into glycan-dense/sparse regions of the entire protein surface or a subset of the protein surface. GLYCO calculates glycan shielding from a single coordinate file or from multiple coordinate files, for instance, as obtained from molecular dynamics simulations or by nuclear magnetic resonance spectroscopy structure determination, enabling analysis of glycan dynamics. Overall, GLYCO provides fundamental insights into the glycan shielding of glycosylated proteins. AVAILABILITY AND IMPLEMENTATION: GLYCO is freely available at GitHub (https://github.com/myungjinlee/GLYCO). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Analysis of Weather Factors on Aircraft Cancellation using a Multilayer Complex Network.

Airlines provide one of the most popular and important transportation services for passengers. While the importance of the airline industry is rising, flight cancellations are also increasing due to abnormal weather factors, such as rainfall and wind speed. Although previous studies on cancellations due to weather factors considered both aircraft and weather factors concurrently, the complex network studies only treated the aircraft factor with a single-layer network. Therefore, the aim of this study was to apply a multilayer complex network (MCN) method that incorporated three different factors, namely, aircraft, rainfall, and wind speed, to investigate aircraft cancellations at 14 airports in the Republic of Korea. The results showed that rainfall had a greater impact on aircraft cancellations compared with wind speed. To find out the most important node in the cancellation, we applied centrality analysis based on information entropy. According to the centrality analysis, Jeju Airport was identified as the most influential node since it has a high demand for aircraft. Also, we showed that characteristics and factors of aircraft cancellation should be appropriately defined by links in the MCN. Furthermore, we verified the applicability of the MCN method in the fields of aviation and meteorology. It is expected that the suggested methodology in this study can help to understand aircraft cancellation due to weather factors.

RING-Type E3 Ubiquitin Ligases AtRDUF1 and AtRDUF2 Positively Regulate the Expression of PR1 Gene and Pattern-Triggered Immunity.

The importance of E3 ubiquitin ligases from different families for plant immune signaling has been confirmed. Plant RING-type E3 ubiquitin ligases are members of the E3 ligase superfamily and have been shown to play positive or negative roles during the regulation of various steps of plant immunity. Here, we present Arabidopsis RING-type E3 ubiquitin ligases AtRDUF1 and AtRDUF2 which act as positive regulators of flg22- and SA-mediated defense signaling. Expression of AtRDUF1 and AtRDUF2 is induced by pathogen-associated molecular patterns (PAMPs) and pathogens. The atrduf1 and atrduf2 mutants displayed weakened responses when triggered by PAMPs. Immune responses, including oxidative burst, mitogen-activated protein kinase (MAPK) activity, and transcriptional activation of marker genes, were attenuated in the atrduf1 and atrduf2 mutants. The suppressed activation of PTI responses also resulted in enhanced susceptibility to bacterial pathogens. Interestingly, atrduf1 and atrduf2 mutants showed defects in SA-mediated or pathogen-mediated PR1 expression; however, avirulent Pseudomonas syringae pv. tomato DC3000-induced cell death was unaffected. Our findings suggest that AtRDUF1 and AtRDUF2 are not just PTI-positive regulators but are also involved in SA-mediated PR1 gene expression, which is important for resistance to P. syringae.

On the control of the proton current in the voltage-gated proton channel Hv1.

The nature of the action of voltage-activated proton transport proteins is a conundrum of great current interest. Here we approach this issue by exploring the action of Hv1, a voltage-gated proton channel found in different cells in humans and other organisms. Our study focuses on evaluating the free energy of transporting a proton through the channel, as well as the effect of the proton transfer through D112, in both the closed and open channel conformations. It is found that D112 allows a transported proton to bypass the electrostatic barrier of the open channel, while not being able to help in passing the barrier in the closed form. This reflects the change in position of the gating arginine residues relative to D112, upon voltage activation. Significantly, the effect of D112 accounts for the observed trend in selectivity by overcoming the electrostatic barrier at its highest point. Thus, the calculations provide a structure/function correlation for the Hv1 system. The present work also clarifies that the action of Hv1 is not controlled by a Grotthuss mechanism but, as is always the case, by the protein electrostatic potential at the rate-limiting barriers.

Durable Oral Biofilm Resistance of 3D-Printed Dental Base Polymers Containing Zwitterionic Materials.

Poly(methyl methacralyate) (PMMA) has long been used in dentistry as a base polymer for dentures, and it is recently being used for the 3D printing of dental materials. Despite its many advantages, its susceptibility to microbial colonization remains to be overcome. In this study, the interface between 3D-printed PMMA specimens and oral salivary biofilm was studied following the addition of zwitterionic materials, 2-methacryloyloxyethyl phosphorylcholine (MPC) or sulfobetaine methacrylate (SB). A significant reduction in bacterial and biofilm adhesions was observed following the addition of MPC or SB, owing to their protein-repellent properties, and there were no significant differences between the two test materials. Although the mechanical properties of the tested materials were degraded, the statistical value of the reduction was minimal and all the properties fulfilled the requirements set by the International Standard, ISO 20795-2. Additionally, both the test materials maintained their resistance to biofilm when subjected to hydrothermal fatigue, with no further deterioration of the mechanical properties. Thus, novel 3D-printable PMMA incorporated with MPC or SB shows durable oral salivary biofilm resistance with maintenance of the physical and mechanical properties.

Comparative Transcriptome-Based Mining of Senescence-Related MADS, NAC, and WRKY Transcription Factors in the Rapid-Senescence Line DLS-91 of Brassica rapa.

Leaf senescence is a developmental process induced by various molecular and environmental stimuli that may affect crop yield. The dark-induced leaf senescence-91 (DLS-91) plants displayed rapid leaf senescence, dramatically decreased chlorophyll contents, low photochemical efficiencies, and upregulation of the senescence-associated marker gene BrSAG12-1. To understand DLS molecular mechanism, we examined transcriptomic changes in DLS-91 and control line DLS-42 following 0, 1, and 4 days of dark treatment (DDT) stages. We identified 501, 446, and 456 DEGs, of which 16.7%, 17.2%, and 14.4% encoded TFs, in samples from the three stages. qRT-PCR validation of 16 genes, namely, 7 MADS, 6 NAC, and 3 WRKY, suggested that BrAGL8-1, BrAGL15-1, and BrWRKY70-1 contribute to the rapid leaf senescence of DLS-91 before (0 DDT) and after (1 and 4 DDT) dark treatment, whereas BrNAC046-2, BrNAC029-2/BrNAP, and BrNAC092-1/ORE1 TFs may regulate this process at a later stage (4 DDT). In-silico analysis of cis-acting regulatory elements of BrAGL8-1, BrAGL42-1, BrNAC029-2, BrNAC092-1, and BrWRKY70-3 of B. rapa provides insight into the regulation of these genes. Our study has uncovered several AGL-MADS, WRKY, and NAC TFs potentially worthy of further study to understand the underlying mechanism of rapid DLS in DLS-91.

Role of Zinc-Doped Bioactive Glass Encapsulated with Microspherical Gelatin in Localized Supplementation for Tissue Regeneration: A Contemporary Review.

Gelatin, a natural polymer, provides excellent tissue compatibility for use in tissue rehabilitation. Bioactive glasses (BAG) offer superior capacity in stimulating a bioactive response but show high variability in uptake and solubility. To tackle these drawbacks, a combination of gelatin with BAG is proposed to form composites, which then offer a synergistic response. The cross-linked gelatin structure's mechanical properties are enhanced by the incorporation of the inorganic BAG, and the rate of BAG ionic supplementation responsible for bioactivity and regenerative potential is better controlled by a protective gelatin layer. Several studies have demonstrated the cellular benefits of these composites in different forms of functional modification such as doping with zinc or incorporation of zinc such as ions directly into the BAG matrix. This review presents a comprehensive perspective on the individual characteristics of BAG and gelatin, including the synthesis and mechanism of action. Further, adaptation of the composite into various applications for bone tissue engineering is discussed and future challenges are highlighted.

Surface Characterization, Biocompatibility and Antifungal Efficacy of a Denture-Lining Material Containing Cnidium officinale Extracts.

Herein, we investigated the surface characterization and biocompatibility of a denture-lining material containing Cnidium officinale extracts and its antifungal efficacy against Candida albicans. To achieve this, a denture-lining material containing various concentrations of C. officinale extract and a control group without C. officinale extract were prepared. The surface characterization and biocompatibility of the samples were investigated. In addition, the antifungal efficacy of the samples on C. albicans was investigated using spectrophotometric growth and a LIVE/DEAD assay. The results revealed that there was no significant difference between the biocompatibility of the experimental and control groups (p > 0.05). However, there was a significant difference between the antifungal efficiency of the denture material on C. albicans and that of the control group (p < 0.05), which was confirmed by the LIVE/DEAD assay. These results indicate the promising potential of the C. officinale extract-containing denture-lining material as an antifungal dental material.

Stormwater runoff treatment filtration system and backwashing system.

This study has been carried out to evaluate the applicability of the pilot scale hybrid type of stormwater runoff treatment system for treatment of combined sewer overflow. Also, to determine the optimum operation parameter such as coagulation dosage concentration, effectiveness of coagulant usage, surface loading rate and backwashing conditions. The pilot scale stormwater filtration system (SFS) was installed at the municipal wastewater plant serving the city of Cheongju (CWTP), Korea. CWTP has a capacity of 280,000 m3/day. The SFS consists of a hydrocyclone coagulation/flocculation with polyaluminium chloride silicate (PACS) and an upflow filter to treat combined sewer overflows. There are two modes (without PACS use and with PACS use) of operation for the SFS. In case of no coagulant use, the range of suspended solids (SS) and turbidity removal efficiency were 72.0-86.6% (mean 80.0%) and 30.9-71.1% (mean 49.3%), respectively. And, the recovery rate of filter was 79.2-83.6% (mean 81.2%); the rate of remaining solid loading in filter media was 16.4-20.8% (mean 18.8%) after backwashing. The influent turbidity, SS concentrations were 59.0-90.7 NTU (mean 72.0 NTU), 194.0-320.0 mg/L (mean 246.7 mg/L), respectively. The range of PACS dosage concentration was 6.0-7.1 mg/L (mean 6.7 mg/L). The range of SS and turbidity removal efficiency was 84.9-98.2 (mean 91.4%) and 70.7-96.3 (mean 84.0%), respectively. It was found that removal efficiency was enhanced with PACS dosage. The recovery rate of filter was 92.0-92.5% (mean 92.3%) the rate of remaining solid loading in filter media was 6.1-8.2% (mean 7.2%) after backwashing. In the case of coagulant use, the particle size of the effluent is bigger than influent particle size. The results showed that SFS with PACS use more effective than without PACS use in SS and turbidity removal efficiency and recovery rate of filter.

Purple Brassica oleracea var. capitata F. rubra is due to the loss of BoMYBL2-1 expression.

BACKGROUND: Water-soluble anthocyanin pigments are important ingredients in health-improving supplements and valuable for the food industry. Although great attention has been paid to the breeding and production of crops containing high levels of anthocyanin, genetic variation in red or purple cabbages (Brassica oleracea var. capitata F. rubra) has not yet been characterized at the molecular level. In this study, we identified the mechanism responsible for the establishment of purple color in cabbages. RESULTS: BoMYBL2-1 is one of the regulatory genes in the anthocyanin biosynthesis pathway in cabbages. It is a repressor whose expression is inversely correlated to anthocyanin synthesis and is not detectable in purple cabbages. Sequence analysis of purple cabbages revealed that most lacked BoMYBL2-1 coding sequences, although a few had a substitution in the region of the promoter 347 bp upstream of the gene that was associated with an absence of BoMYBL2-1 expression. Lack of transcriptional activity of the substitution-containing promoter was confirmed using transgenic Arabidopsis plants transformed with promoter::GUS fusion constructs. The finding that the defect in BoMYBL2-1 expression was solely responsible for purple coloration in cabbages was further demonstrated using genomic PCR and RT-PCR analyses of many other structural and regulatory genes in anthocyanin biosynthesis. Molecular markers for purple cabbages were developed and validated using 69 cabbage lines. CONCLUSION: Expression of BoMYBL2-1 was inversely correlated to anthocyanin content, and purple color in cabbages resulted from a loss of BoMYBL2-1 expression, caused by either the promoter substitution or deletion of the gene. This is the first report of molecular markers that distinguish purple cabbages. Such markers will be useful for the production of intraspecific and interspecific hybrids for functional foods, and for industrial purposes requiring high anthocyanin content.

Detection of waterborne norovirus genogroup I strains using an improved real time RT-PCR assay.

Noroviruses (NoVs) are the major global source of acute gastroenteritis (AGE) outbreaks. To detect NoVs, real-time reverse transcription-quantitative PCR (RT-qPCR) assays have been widely employed since the first decade of the 21st century. We developed a redesigned probe, JJV1PM, for RT-qPCR assay detection of NoV genogroup (G) I strains. The new RT-qPCR assay using the JJV1PM-probe showed broader strain reactivity for 10 NoV GI genotypes, while the old method, using the JJV1PT-probe assay, detected only 7 NoV GI genotypes in a validation panel using human fecal specimens. The improved RT-qPCR assay was also successfully applied to water samples. The JJV1PM-probe assay identified 7 NoV GI genotypes, whereas the JJV1PT-probe assay detected only 2 NoV GI genotypes from water samples. Notably, groundwater-borne NoV GI strains detected by the improved JJV1PM-probe assay were associated with groundwater-borne AGE outbreaks in South Korea. The results of this study underscore the importance of the evaluation of RT-qPCR assays using recently circulating NoV strains prior to field application.

Migration of alloplastic bone graft material in infected conditions: a case study and animal experiment.

PURPOSE: Distant migration associated with sinus lifting procedures has not been investigated. In the present study, a case of distant migration of graft material was observed, and the potential mechanisms of migration were analyzed using material analysis and in vivo experiments. MATERIALS AND METHODS: The migrated graft material was biphasic calcium phosphate-based alloplastic material (BCP), and its physical properties were compared with those of xenogenic material (Bio-Oss). The comparisons of the physical properties were performed using scanning electronic microscopic, x-ray diffraction, and Fourier-transform infrared absorbance spectra analysis. The comparative graft migration study was performed using the subcutaneous pocket model in rats (n = 10). The clinical case was analyzed by histologic section and energy dispersive x-ray (EDX) microanalysis. RESULTS: The observed diffraction patterns from the Bio-Oss revealed characteristic diffractions for the hydroxyapatite phase, and those from the BCP revealed additional diffractions that could be assigned to the tricalcium phosphate phase. In the animal model, the graft migration distances observed in the BCP group were significantly greater than those observed in the Bio-Oss group (P = .012). In the clinical case, the lymphatic vessels of the submandibular gland contained foreign materials that were morphologically similar to those of the maxillary sinus. EDX microanalysis revealed that the particles in the lymphatic vessels exhibited calcium concentrations that were approximately 200 times greater than those in the adjacent glandular tissue. CONCLUSIONS: In the present study, BCP-based sinus grafts had migrated into the submandibular glandular area by way of the lymphatic chain in the presented clinical case.

Hydroxyapatite and collagen combination-coated dental implants display better bone formation in the peri-implant area than the same combination plus bone morphogenetic protein-2-coated implants, hydroxyapatite only coated implants, and uncoated implants.

PURPOSE: The objective of this study was to compare peri-implant bone formation among uncoated (UC), hydroxyapatite (HA), collagen plus HA (CH), and collagen, HA, plus bone morphogenetic protein-2 (BMP-2) implant groups. MATERIALS AND METHODS: Implants in the UC group had acid-etched surfaces. The surface coating was applied using the aerosol deposition method. The coated surfaces were examined by scanning electron microscopy, x-ray diffraction (XRD), and Fourier-transformed infrared absorption analysis. Subsequently, 6 implants from each group (total, 24 implants) were installed in the tibias of rabbits. The animals were sacrificed at 6 weeks after implant installation. Peri-implant bone formation and bone-to-implant contact (BIC) were measured in histologic sections. Significant differences among groups were evaluated using analysis of variance. RESULTS: Based on the measured XRD patterns, there was a characteristic HA phase (International Centre for Diffraction Data [ICDD], 086-0740) coated on the titanium (ICDD, 089-3725). Subsequent coating processes for collagen and BMP-2 did not display additional diffraction peaks, but maintained the diffraction patterns of the HA-coated titanium. The presence of collagen was verified by infrared absorption analysis. When comparing these modifications with UC surfaces, only the CH coating displayed significantly greater peri-implant bone formation and BIC (P = .003 and P < .001, respectively). Adding BMP-2 to the implant surface did not produce any advantage compared with the CH coating. CONCLUSIONS: In this study, the CH group displayed significantly greater new bone formation and BIC than the other groups. There was no significant difference among the other groups.

The ICL1 and MLS1 Genes, Integral to the Glyoxylate Cycle, are Essential and Specific for Caloric Restriction-Mediated Extension of Lifespan in Budding Yeast.

The regulation of complex energy metabolism is intricately linked to cellular energy demands. Caloric restriction (CR) plays a pivotal role in modulating the expression of genes associated with key metabolic pathways, including glycolysis, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle. In this study, the chronological lifespan (CLS) of 35 viable single-gene deletion mutants under both non-restricted and CR conditions, focusing on genes related to these metabolic pathways is evaluated. CR is found to increase CLS predominantly in mutants associated with the glycolysis and TCA cycle. However, this beneficial effect of CR is not observed in mutants of the glyoxylate cycle, particularly those lacking genes for critical enzymes like isocitrate lyase 1 (icl1Δ) and malate synthase 1 (mls1Δ). This analysis revealed an increase in isocitrate lyase activity, a key enzyme of the glyoxylate cycle, under CR, unlike the activity of isocitrate dehydrogenase, which remains unchanged and is specific to the TCA cycle. Interestingly, rapamycin, a compound known for extending lifespan, does not increase the activity of the glyoxylate cycle enzyme. This suggests that CR affects lifespan through a distinct metabolic mechanism.

Near-strain-free anode architecture enabled by interfacial diffusion creep for initial-anode-free quasi-solid-state batteries.

Anode-free (or lithium-metal-free) batteries with garnet-type solid-state electrolytes are considered a promising path in the development of safe and high-energy-density batteries. However, their practical implementation has been hindered by the internal strain that arises from the repeated plating and stripping of lithium metal at the interlayer between the solid electrolyte and negative electrode. Herein, we utilize the titanium nitrate nanotube architecture and a silver-carbon interlayer to mitigate the anisotropic stress caused by the recurring formation of lithium deposition layers during the cycling process. The mixed ionic-electronic conducting nature of the titanium nitrate nanotubes effectively accommodates the entry of reduced Li into its free volume space via interfacial diffusion creep, achieving near-strain-free operation with nearly tenfold volume suppressing capability compared to a conventional Cu anode counterpart during the lithiation process. Notably, the fabricated Li6.4La3Zr1.7Ta0.3O12 (LLZTO)-based initial-anode-free quasi-solid-state battery full cell, coupled with an ionic liquid catholyte infused high voltage LiNi0.33Co0.33Mn0.33O2-based cathode with an areal capacity of 3.2 mA cm-2, exhibits remarkable room temperature (25 °C) cyclability of over 600 cycles at 1 mA cm-2 with an average coulombic efficiency of 99.8%.

Adsorption sequence of multifunctional groups: a study on the reaction pathway and the adsorption structure of homocysteine on the Ge(100) surface.

We investigated the adsorption mechanism of homocysteine (HS-CH2-CH2-CH(NH2)-COOH) on the Ge(100) surface along with its electronic structures and adsorption geometries to determine the sequence of adsorption of this amino acid's functional groups using core-level photoemission spectroscopy (CLPES) in conjunction with density functional theory (DFT) calculations. We found that the "SH-dissociated OH-dissociated N-dative-bonded structure" and the "SH-dissociated OH-dissociation-bonded structure" were preferred at a monolayer (ML) coverage of 0.30 (lower coverage) and 0.60 (higher coverage), respectively. The "SH-dissociated OH-dissociated N-dative-bonded structure" was the most stable structure. Moreover, we systematically confirmed the sequence of adsorption of the functional groups of the homocysteine molecule on the Ge(100) surface, which is thiol group (-SH), carboxyl group (-COOH), and amine group (-NH2).

Paracoccus limosus sp. nov., isolated from activated sludge in a sewage treatment plant.

Two strains of gram-negative, catalase- and oxidase-positive, coccus-shaped bacteria, designated NB88(T) and LNB004, were isolated from activated sludge in the Mae-san sewage treatment plant in South Korea. They were characterized in a polyphasic taxonomic study based on phenotypic, phylogenetic and genotypic approaches. Comparative 16S rRNA gene sequence analysis indicated that strains NB88(T) and LNB004 represented a novel subline within the genus Paracoccus in the family Rhodobacteraceae. According to 16S rRNA gene sequence comparisons, strains NB88(T) and LNB004 were indistinguishable and showed 94.5-97.6 % similarity to the type strains of other Paracoccus species. Strain NB88(T) exhibited relatively high levels of DNA hybridization (84±3.5 %) with LNB004 and low hybridization values (<40 %) with type strains of other Paracoccus species. Both strains showed chemotaxonomic characteristics typical of the genus Paracoccus, with Q-10 as the predominant respiratory quinone and C18 : 1ω7c as the major fatty acid, and both strains accumulated poly-ß-hydroxybutyrate granules. The DNA G+C contents of strains NB88(T) and LNB004 were 66.4 and 65.1 mol%, respectively. The polar lipid profiles of strains NB88(T) and LNB004 included major amounts of phosphatidylglycerol, phosphatidylcholine and an unknown aminolipid. The taxonomic position of strains NB88(T) and LNB004 was clarified by the low level of DNA-DNA hybridization with closely related strains and the strains could be distinguished from other recognized species by using biochemical tests and molecular genetic analysis. On the basis of their phenotypic and genotypic properties and their phylogenetic distinctiveness, strains NB88(T) and LNB004 should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus limosus sp. nov. is proposed. The type strain is NB88(T) ( = KEMC 5401-184(T)  = JCM 17370(T)); strain LNB004 ( = KEMC 5401-001) is a reference strain.

Brevibacterium daeguense sp. nov., a nitrate-reducing bacterium isolated from a 4-chlorophenol enrichment culture.

A Gram-reaction-positive, non-spore-forming, aerobic actinobacterial strain (2C6-41(T)) was isolated from the activated sludge from an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, closest phylogenetic relatives to strain 2C6-41(T) were Brevibacterium pityocampae DSM 21720(T) (97.2 %), Brevibacterium salitolerans KCTC 19616(T) (96.7 %), Brevibacterium album KCTC 19173(T) (96.2 %) and Brevibacterium samyangense KCCM 42316(T) (96.2 %). The DNA G+C content of strain 2C6-41(T) was 66.4 mol%. Chemotaxonomic data, which included MK-8(H(2)) as the major menaquinone; meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; ribose, mannose and glucose as major cell-wall sugars; and anteiso-C(15 : 0), anteiso-C(17 : 0), C(16 : 0) and iso-C(15 : 0) as major fatty acids, supported the affiliation of strain 2C6-41(T) to the genus Brevibacterium. The aromatic ring cleavage enzyme catechol 1,2-dioxygenase was not detected in strain 2C6-41(T), but catechol 2,3-dioxygenase was detected. The results of physiological and biochemical tests, and the low level of DNA-DNA relatedness to the closest phylogenetic relative enabled strain 2C6-41(T) to be differentiated genotypically and phenotypically from recognized species of the genus Brevibacterium. The isolate is therefore considered to represent a novel species in the genus Brevibacterium, for which the name Brevibacterium daeguense sp. nov. is proposed. The type strain is 2C6-41(T) (=KCTC 19800(T) = JCM 17458(T)).

Nocardioides daeguensis sp. nov., a nitrate-reducing bacterium isolated from activated sludge of an industrial wastewater treatment plant.

A Gram-reaction-positive, rod-shaped, non-spore-forming bacterium (strain 2C1-5(T)) was isolated from activated sludge of an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, the closest phylogenetic relatives were the type strains of Nocardioides nitrophenolicus (98.6 % similarity), N. kongjuensis (98.5 %), N. caeni (98.4 %), N. simplex (98.3 %), N. aromaticivorans (98.1 %) and N. ginsengisoli (97.5 %); the phylogenetic distance from other species with validly published names within the genus Nocardioides was greater than 3 %. Strain 2C1-5(T) was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C16 : 0 and C17 : 1ω6c as the major fatty acids. The G+C content of the genomic DNA was 74.9 mol%. These chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain 2C1-5(T) to the genus Nocardioides. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 2C1-5(T) from existing species with validly published names. Therefore, strain 2C1-5(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides daeguensis sp. nov. is proposed, with the type strain 2C1-5(T) ( = JCM 17460(T) = KCTC 19799(T)).