Multilocus sequence typing and antibiotic resistance of Aeromonas isolated from freshwater fish in Hebei Province.

Aeromonas spp. are the opportunistic pathogens that infect both aquatic and terrestrial homeotherms. They were commonly present in aquatic environments, including effluent, tap water, marine, river, and lake, where they are often isolated from aquatic animals, including fish, molluscs, and crustaceans. The Aeromonas infections can cause sepsis, ulcer, and other symptoms, resulting in the death of massive aquatic animals. Therefore, the prevention and control of Aeromonas is of great significance for the healthy development of aquaculture. In this study, we used modern molecular methods to enhance disease control of Aeromonas isolates from freshwater fish in Hebei Province. A total of 130 Aeromonas spp. isolates were isolated from freshwater fish farms in Hengshui, Handan, and Shijiazhuang and all 130 Aeromonas spp. isolates were sequenced for species identification. Of the 130 Aeromonas spp. isolates, 104 isolates were successfully sequenced, and BLAST analysis showed that Aeromonas veronii was predominant in freshwater fish farms in Hebei Province. In addition, 26 antibiotic resistance profiles were obtained from 102 fully cultured isolates among the 104 Aeromonas spp. isolates whose species was primarily identified, and 44 multidrug-resistant bacteria among the 102 isolates were identified using an antibiotic susceptibility test. Using the Multilocus Sequence Typing (MLST) method, 33 out of 44 multidrug-resistant isolates with 14 non-Aeromonas reference strains were selected for phylogenetic and MLST analysis, and all 33 multidrug-resistant isolates were A. veronii. A total of 30 new Sequence Types (STs) were obtained by comparing concatenated sequences (gyrB-groL-gltA-metG-ppsA-recA) on PubMLST website. Furthermore, recombination event analysis detected using RDP5 and ClonalFrameML software 42 and 49 recombination events, respectively, and 22 recombination events were validated by four or more algorithms. Since mutation and recombination events increase clonal diversity and single housekeeping gene sequence alignments are limited for identifying species, we propose the use of multiple concatenated sequence loci to increase discriminatory power. In addition, we propose that the MLST method is an appropriate technique to study and develop the resistance mechanisms of multidrug-resistant Aeromonas and to identify Aeromonas systematically in complex samples obtained from the environment.

Object-stable unsupervised dual contrastive learning image-to-image translation with query-selected attention and convolutional block attention module.

Recently, contrastive learning has gained popularity in the field of unsupervised image-to-image (I2I) translation. In a previous study, a query-selected attention (QS-Attn) module, which employed an attention matrix with a probability distribution, was used to maximize the mutual information between the source and translated images. This module selected significant queries using an entropy metric computed from the attention matrix. However, it often selected many queries with equal significance measures, leading to an excessive focus on the background. In this study, we proposed a dual-learning framework with QS-Attn and convolutional block attention module (CBAM) called object-stable dual contrastive learning generative adversarial network (OS-DCLGAN). In this paper, we utilize a CBAM, which learns what and where to emphasize or suppress, thereby refining intermediate features effectively. This CBAM was integrated before the QS-Attn module to capture significant domain information for I2I translation tasks. The proposed framework outperformed recently introduced approaches in various I2I translation tasks, showing its effectiveness and versatility. The code is available at https://github.com/RedPotatoChip/OSUDL.

Dermatobacter hominis gen. nov., sp. nov., a new member of the family Iamiaceae, revealed the potential utilisation of skin-derived metabolites.

A non-motile, novel actinobacterial strain, Kera-3T, which is a gram-positive, aerobic, rod-shaped bacterium, was isolated from human keratinocytes on 1/10 diluted R2A agar. Whole-cell hydrolysis of amino acids revealed the presence of meso-DAP, alanine, and glutamic acid. The predominant menaquinone was MK-9 (H8), whereas the primary fatty acids were C16:0 and C18:1 ω9c. The major phospholipids included diphosphatidylglycerol and aminophospholipids, along with an unidentified phosphoglycolipid and an aminophosphoglycolipid. The G+C content of the genomic DNA was 73.2%, based on the complete genome sequence. Phylogenetic analyses of the 16S rRNA gene sequence and phylogenomic analysis of 91 core genes showed that strain Kera-3T formed a new lineage in the family Iamiaceae, with the closest neighbour Rhabdothermincola sediminis SYSU G02662T having 91.19% 16S rRNA gene sequence identity. A comparative genomic study of the predicted general metabolism and carbohydrate-active enzymes supported the phylogenetic and phylogenomic data. Based on the analysis of physiological, biochemical, and genomic characteristics, strain Kera-3T can be distinguished from known genera in the family Iamiaceae and represents a novel genus and species. Therefore, the name Dermatobacter hominis gen. nov., sp. nov. was proposed, with the type strain Kera-3T (= KACC 22415T = LMG 32493T).

Genome-Wide Pathway Exploration of the Epidermidibacterium keratini EPI-7T.

Functional cosmetics industries using skin microbiome screening and beneficial materials isolated from key microorganisms are receiving increasing attention. Since Epidermidibacterium keratini EPI-7T was first discovered in human skin, previous studies have confirmed that it can produce a new pyrimidine compound, 1,1'-biuracil, having anti-aging effects on human skin. Therefore, we conducted genomic analyses to judge the use value of E. keratini EPI-7T and provide up-to-date information. Whole-genome sequencing analysis of E. keratini EPI-7T was performed to generate new complete genome and annotation information. E. keratini EPI-7T genome was subjected to comparative genomic analysis with a group of closely-related strains and skin flora strains through bioinformatic analysis. Furthermore, based on annotation information, we explored metabolic pathways for valuable substances that can be used in functional cosmetics. In this study, the whole-genome sequencing (WGS) and annotation results of E. keratini EPI-7T were improved, and through comparative analysis, it was confirmed that the E. keratini EPI-7T has more metabolite-related genes than comparison strains. In addition, we annotated the vital genes for biosynthesis of 20 amino acids, orotic acid, riboflavin (B2) and chorismate. In particular, we were able to prospect that orotic acid could accumulate inside E. keratini EPI-7T under uracil-enriched conditions. Therefore, through a genomics approach, this study aims to provide genetic information for the hidden potential of E. keratini EPI-7T and the strain development and biotechnology utilization to be conducted in further studies.

A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data.

Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries.

Effective microbial molecular diagnosis of periodontitis-related pathogen Porphyromonas gingivalis from salivary samples using rgpA gene.

Importance of accurate molecular diagnosis and quantification of particular disease-related pathogenic microorganisms is highlighted as an introductory step to prevent and care for diseases. In this study, we designed a primer/probe set for quantitative real-time polymerase chain reaction (qRT-PCR) targeting rgpA gene, known as the specific virulence factor of periodontitis-related pathogenic bacteria 'Porphyromonas gingivalis', and evaluated its diagnostic efficiency by detecting and quantifying relative bacterial load of P. gingivalis within saliva samples collected from clinical subjects. As a result of qRT-PCR, we confirmed that relative bacterial load of P. gingivalis was detected and quantified within all samples of positive control and periodontitis groups. On the contrary, negative results were confirmed in both negative control and healthy groups. Additionally, as a result of comparison with next-generation sequencing (NGS)-based 16S metagenome profiling data, we confirmed relative bacterial load of P. gingivalis, which was not identified on bacterial classification table created through 16S microbiome analysis, in qRT-PCR results. It showed that an approach to quantifying specific microorganisms by applying qRT-PCR method could solve microbial misclassification issues at species level of an NGS-based 16S microbiome study. In this respect, we suggest that P. gingivalis-specific primer/probe set introduced in present study has efficient applicability in various oral healthcare industries, including periodontitis-related microbial molecular diagnosis field.

Comparative analysis of human facial skin microbiome between topical sites compared to entire face.

BACKGROUND: Skin is an essential outer barrier and supports the growth of commensal microorganisms that protects a host from the offense of foreign toxic organisms. With the rapid development of next-generation sequencing (NGS)-based applications, skin microbiome research for facial health care has reached industry growth, such as therapy and cosmetic product development. Despite the acceleration of skin microbiome research, experimental standardization protocol has not yet been established in the facial site and method of sampling. OBJECTIVE: Thus, we aimed to investigate the differences in microbial composition at each facial site (cheek, mouth, forehead, and entire face) using comprehensive microbiome analysis. METHODS: Twelve specimens from three men (four specimens per one person) were collected. The hypervariable regions (V3-V4) of the bacterial 16S rRNA gene were targeted for 16S amplicon library construction and classification of bacterial taxonomy. Skin microbial composition for all specimens was investigated, and the differences site-by-site in skin microbial composition were analyzed and evaluated by the various statistical tests. RESULTS: We were able to validate the independent correlation between the skin microbiome composition and the facial sites. The cheek site showed the highest alpha-diversity in richness and evenness scores compared to the forehead and mouth. The cheek and mouth sites showed a positive correlation (R2 value > 0.93) with the entire face, while the forehead sites were negatively correlated (R2 value < 0.2). Given the relative abundance based on statistical correlation analysis, we estimated that the cheek site could be considered an optimal topical site to replace the entire face. CONCLUSION: Our study suggests that skin microbiome profiling of four facial sites confirms that the cheek shows the most similar skin flora with the entire face. This study would be informative for preventing bias caused by sampling methods before researching and understanding skin cosmetics development or skin diseases.

Expanding therapeutic utility of carfilzomib for breast cancer therapy by novel albumin-coated nanocrystal formulation.

Carfilzomib (CFZ) is the second-in-class proteasome inhibitor with much improved efficacy and safety profiles over bortezomib in multiple myeloma patients. In expanding the utility of CFZ to solid cancer therapy, the poor aqueous solubility and in vivo instability of CFZ are considered major drawbacks. We investigated whether a nanocrystal (NC) formulation can address these issues and enhance anticancer efficacy of CFZ against breast cancer. The surface of NC was coated with albumin in order to enhance the formulation stability and drug delivery to tumors via interactions with albumin-binding proteins located in and near cancer cells. The novel albumin-coated NC formulation of CFZ (CFZ-alb NC) displayed improved metabolic stability and enhanced cellular interactions, uptake and cytotoxic effects in breast cancer cells in vitro. Consistently, CFZ-alb NC showed greater anticancer efficacy in a murine 4T1 orthotopic breast cancer model than the currently used cyclodextrin-based formulation. Overall, our results demonstrate the potential of CFZ-alb NC as a viable formulation for breast cancer therapy.

Suppression of Canine ATP Binding Cassette ABCB1 in Madin-Darby Canine Kidney Type II Cells Unmasks Human ABCG2-Mediated Efflux of Olaparib.

Endogenous canine ATP binding cassette B1 (cABCB1) is expressed abundantly in Madin-Darby canine kidney type II (MDCKII) cells, and its presence often complicates phenotyping of the transport process. Errors in estimating the corrected efflux ratio (cER), as a result of the variable expression of cABCB1, were examined for the dual substrates of ABCB1 and ABCG2 in MDCKII cells expressing human ABCG2 (hABCG2). cABCB1 mRNA and protein expression was 60% and 55% lower, respectively, in MDCKII cells expressing hABCG2 compared with the wild type, suggesting that the expression of endogenous cABCB1 became variable after the expression of hABCG2. To minimize the contribution of endogenous efflux, cABCB1 was suppressed kinetically (using verapamil as a selective inhibitor) or biochemically (transfecting short-hairpin RNA against cABCB1). Under these suppression conditions, cER values for irinotecan and topotecan (dual substrates of ABCB1 and ABCG2) were elevated by more than 4-fold and 2-fold, respectively, compared with cER values without the suppression. The cER of olaparib was similarly increased to 3- and 5-fold in MDCKII cells under the kinetic and biochemical suppression of cABCB1, respectively, suggesting that hABCG2-mediated efflux cannot be ruled out for olaparib. Since the substrate selectivity for ABCB1 and ABCG2 overlapped considerably, the possibility of an inaccurate estimation of cER must be considered for dual substrates in the case of the variable expression of cABCB1 in MDCKII cells.

Inhibition of Organic Anion Transporting Polypeptide 1B1 and 1B3 by Betulinic Acid: Effects of Preincubation and Albumin in the Media.

Betulinic acid (BA), a plant-derived pentacyclic triterpenoid, may interact with the members of the organic anion transporting polypeptide 1B subfamily. Here, we investigated the interactions of BA and its analogs with OATP1B1/3 and rat Oatp1b2 in vitro and in vivo. BA inhibited the activity of OATP1B1/3 and rat Oatp1b2 in vitro. Systemic exposure of atorvastatin was substantially altered with the intravenous co-administration of BA (20 mg/kg). Preincubation (incubation with inhibitors, followed by washout) with BA led to a sustained inhibition of OATP1B3, which recovered rapidly in the media containing 10% fetal bovine serum. The addition of albumin to the media decreased intracellular concentrations of BA and expedited the recovery of OATP1B3 activity following preincubation. For asunaprevir and cyclosporin A (previously known to inhibit OATP1B3 upon preincubation), the addition of albumin to the media shortened recovery time with asunaprevir, but not with cyclosporin A. Overall, our results showed that BA inhibits OATP1B transporters in vitro and may incur hepatic transporter-mediated drug interactions in vivo. Our results identify BA as another OATP1B3 inhibitor with preincubation effect and suggest that the preincubation effect and its duration is impacted by altered equilibrium of inhibitors between intracellular and extracellular space (e.g., albumin in the media).

Polymer micelle formulation for the proteasome inhibitor drug carfilzomib: Anticancer efficacy and pharmacokinetic studies in mice.

Carfilzomib (CFZ) is a peptide epoxyketone proteasome inhibitor approved for the treatment of multiple myeloma (MM). Despite the remarkable efficacy of CFZ against MM, the clinical trials in patients with solid cancers yielded rather disappointing results with minimal clinical benefits. Rapid degradation of CFZ in vivo and its poor penetration to tumor sites are considered to be major factors limiting its efficacy against solid cancers. We previously reported that polymer micelles (PMs) composed of biodegradable block copolymers poly(ethylene glycol) (PEG) and poly(caprolactone) (PCL) can improve the metabolic stability of CFZ in vitro. Here, we prepared the CFZ-loaded PM, PEG-PCL-deoxycholic acid (CFZ-PM) and assessed its in vivo anticancer efficacy and pharmacokinetic profiles. Despite in vitro metabolic protection of CFZ, CFZ-PM did not display in vivo anticancer efficacy in mice bearing human lung cancer xenograft (H460) superior to that of the clinically used cyclodextrin-based CFZ (CFZ-CD) formulation. The plasma pharmacokinetic profiles of CFZ-PM were also comparable to those of CFZ-CD and the residual tumors that persisted in xenograft mice receiving CFZ-PM displayed an incomplete proteasome inhibition. In summary, our results showed that despite its favorable in vitro performances, the current CFZ-PM formulation did not improve in vivo anticancer efficacy and accessibility of active CFZ to solid cancer tissues over CFZ-CD. Careful consideration of the current results and potential confounding factors may provide valuable insights into the future efforts to validate the potential of CFZ-based therapy for solid cancer and to develop effective CFZ delivery strategies that can be used to treat solid cancers.

The N-terminal region of organic anion transporting polypeptide 1B3 (OATP1B3) plays an essential role in regulating its plasma membrane trafficking.

Organic anion transporting polypeptide 1B3 (OATP1B3) is a major influx transporter mediating the hepatic uptake of various endogenous substrates as well as clinically important drugs such as statins and anticancer drugs. However, molecular mechanisms controlling the membrane trafficking of OATP1B3 have been largely unknown. Several reports recently indicated the presence of a distinct, cancer-type OATP1B3 variant lacking the N-terminal 28 amino acids compared to OATP1B3 expressed in non-malignant hepatocytes. Interestingly, the cancer-type OATP1B3 variant is located predominantly in the cytoplasm, implicating the involvement of the N-terminal region of OATP1B3 in its membrane trafficking. In the current study, we set out to experimentally validate the importance of the N-terminal region of OATP1B3 and to identify responsible sequence motif(s) in that region. A number of truncation or point mutants of OATP1B3 were transiently expressed in HEK293T, HCT-8 or MDCK II cells and their expression in cytoplasmic and surface membrane fractions were analyzed by immunoblotting. Our results indicated that the N-terminal sequence of OATP1B3, in particular, at the amino acid positions between 12 and 28, may be indispensable in its membrane trafficking. Moreover, our results using a fusion construct indicated that the first 50 amino acids of OATP1B3 are sufficient for its membrane localization. The importance of the N-terminal region in membranous localization was shared among the other OATP1B subfamily members, OATP1B1 and rat Oatp1b2. Our efforts to identify the responsible amino acid(s) or structure motif(s) in the N-terminal region did not pinpoint individual amino acids or motifs with putative secondary structures. Our current findings however demonstrate that the N-terminal region is important for the membrane localization of the OATP1B subfamily members and should facilitate future investigations of the mechanisms involved in the regulation and membrane trafficking of these important transporter proteins.